Transcription Factor CHOP
Structural Homology, Protein
Amino Acid Sequence
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Sequence Homology, Amino Acid
Sequence Homology, Nucleic Acid
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Protein Structure, Secondary
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
src Homology Domains
Regions of AMINO ACID SEQUENCE similarity in the SRC-FAMILY TYROSINE KINASES that fold into specific functional tertiary structures. The SH1 domain is a CATALYTIC DOMAIN. SH2 and SH3 domains are protein interaction domains. SH2 usually binds PHOSPHOTYROSINE-containing proteins and SH3 interacts with CYTOSKELETAL PROTEINS.
Electrophoresis, Polyacrylamide Gel
A rod-shaped bacterium surrounded by a sheath-like structure which protrudes balloon-like beyond the ends of the cell. It is thermophilic, with growth occurring at temperatures as high as 90 degrees C. It is isolated from geothermally heated marine sediments or hot springs. (From Bergey's Manual of Determinative Bacteriology, 9th ed)
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Nucleic Acid Conformation
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Nuclear Magnetic Resonance, Biomolecular
Hidden Markov models-based system (HMMSPECTR) for detecting structural homologies on the basis of sequential information. (1/1667)HMMSPECTR is a tool for finding putative structural homologs for proteins with known primary sequences. HMMSPECTR contains four major components: a data warehouse with the hidden Markov models (HMM) and alignment libraries; a search program which compares the initial protein sequences with the libraries of HMMs; a secondary structure prediction and comparison program; and a dominant protein selection program that prepares the set of 10-15 "best" proteins from the chosen HMMs. The data warehouse contains four libraries of HMMs. The first two libraries were constructed using different HHM preparation options of the HAMMER program. The third library contains parts ("partial HMM") of initial alignments. The fourth library contains trained HMMs. We tested our program against all of the protein targets proposed in the CASP4 competition. The data warehouse included libraries of structural alignments and HMMs constructed on the basis of proteins publicly available in the Protein Data Bank before the CASP4 meeting. The newest fully automated versions of HMMSPECTR 1.02 and 1.02ss produced better results than the best result reported at CASP4 either by r.m.s.d. or by length (or both) in 64% (HMMSPECTR 1.02) and 79% (HMMSPECTR 1.02ss) of the cases. The improvement is most notable for the targets with complexity 4 (difficult fold recognition cases). (+info)
Modelling the structure of the fusion protein from human respiratory syncytial virus. (2/1667)The fusion protein of respiratory syncytial virus (RSV-F) is responsible for fusion of virion with host cells and infection of neighbouring cells through the formation of syncytia. A three-dimensional model structure of RSV-F was derived by homology modelling from the structure of the equivalent protein in Newcastle disease virus (NDV). Despite very low sequence homology between the two structures, most features of the model appear to have high credibility, although a few small regions in RSV-F whose secondary structure is predicted to be different to that in NDV are likely to be poorly modelled. The organization of individual residues identified in escape mutants against monoclonal antibodies correlates well with known antigenic sites. The location of residues involved in point mutations in several drug-resistant variants is also examined. (+info)
Novel carbohydrate specificity of the 16-kDa galectin from Caenorhabditis elegans: binding to blood group precursor oligosaccharides (type 1, type 2, Talpha, and Tbeta) and gangliosides. (3/1667)Galectins, a family of soluble beta-galactosyl-binding lectins, are believed to mediate cell-cell and cell-extracellular matrix interactions during development, inflammation, apoptosis, and tumor metastasis. However, neither the detailed mechanisms of their function(s) nor the identities of their natural ligands have been unequivocally elucidated. Of the several galectins present in the nematode Caenorhabditis elegans, the 16-kDa "proto" type and the 32-kDa "tandem-repeat" type are the best characterized so far, but their carbohydrate specificities have not been examined in detail. Here, we report the carbohydrate-binding specificity of the recombinant C. elegans 16-kDa galectin and the structural analysis of its binding site by homology modeling. Our results indicate that unlike the galectins characterized so far, the C. elegans 16-kDa galectin interacts with most blood group precursor oligosaccharides (type 1, Galbeta1,3GlcNAc, and type 2, Galbeta1,4GlcNAc; Talpha, Galbeta1,3GalNAcalpha; Tbeta, Galbeta1,3GalNAcbeta) and gangliosides containing the Tbeta structure. Homology modeling of the C. elegans 16-kDa galectin CRD revealed that a shorter loop containing residues 66-69, which enables interactions of Glu(67) with both axial and equatorial -OH at C-3 of GlcNAc (in Galbeta1,4GlcNAc) or at C-4 of GalNAc (in Galbeta1,3GalNAc), provides the structural basis for this novel carbohydrate specificity. (+info)
A comprehensive analysis of 40 blind protein structure predictions. (4/1667)BACKGROUND: We thoroughly analyse the results of 40 blind predictions for which an experimental answer was made available at the fourth meeting on the critical assessment of protein structure methods (CASP4). Using our comparative modelling and fold recognition methodologies, we made 29 predictions for targets that had sequence identities ranging from 50% to 10% to the nearest related protein with known structure. Using our ab initio methodologies, we made eleven predictions for targets that had no detectable sequence relationships. RESULTS: For 23 of these proteins, we produced models ranging from 1.0 to 6.0 A root mean square deviation (RMSD) for the Calpha atoms between the model and the corresponding experimental structure for all or large parts of the protein, with model accuracies scaling fairly linearly with respect to sequence identity (i.e., the higher the sequence identity, the better the prediction). We produced nine models with accuracies ranging from 4.0 to 6.0 A Calpha RMSD for 60-100 residue proteins (or large fragments of a protein), with a prediction accuracy of 4.0 A Calpha RMSD for residues 1-80 for T110/rbfa. CONCLUSIONS: The areas of protein structure prediction that work well, and areas that need improvement, are discernable by examining how our methods have performed over the past four CASP experiments. These results have implications for modelling the structure of all tractable proteins encoded by the genome of an organism. (+info)
The SBP2 and 15.5 kD/Snu13p proteins share the same RNA binding domain: identification of SBP2 amino acids important to SECIS RNA binding. (5/1667)Selenoprotein synthesis in eukaryotes requires the selenocysteine insertion sequence (SECIS) RNA, a hairpin in the 3' untranslated region of selenoprotein mRNAs. The SECIS RNA is recognized by the SECIS-binding protein 2 (SBP2), which is a key player in this specialized translation machinery. The objective of this work was to obtain structural insight into the SBP2-SECIS RNA complex. Multiple sequence alignment revealed that SBP2 and the U4 snRNA-binding protein 15.5 kD/Snu13p share the same RNA binding domain of the L7A/L30 family, also found in the box H/ACA snoRNP protein Nhp2p and several ribosomal proteins. In corollary, we have detected a similar secondary structure motif in the SECIS and U4 RNAs. Combining the data of the crystal structure of the 15.5 kD-U4 snRNA complex, and the SBP2/15.5 kD sequence similarities, we designed a structure-guided strategy predicting 12 SBP2 amino acids that should be critical for SECIS RNA binding. Alanine substitution of these amino acids followed by gel shift assays of the SBP2 mutant proteins identified four residues whose mutation severely diminished or abolished SECIS RNA binding, the other eight provoking intermediate down effects. In addition to identifying key amino acids for SECIS recognition by SBP2, our findings led to the proposal that some of the recognition principles governing the 15.5 kD-U4 snRNA interaction must be similar in the SBP2-SECIS RNA complex. (+info)
Group D prothrombin activators from snake venom are structural homologues of mammalian blood coagulation factor Xa. (6/1667)Procoagulant venoms of several Australian elapids contain proteinases that specifically activate prothrombin; among these, Group D activators are functionally similar to coagulation factor Xa (FXa). Structural information on this class of prothrombin activators will contribute significantly towards understanding the mechanism of FXa-mediated prothrombin activation. Here we present the purification of Group D prothrombin activators from three Australian snake venoms (Hoplocephalus stephensi, Notechis scutatus scutatus and Notechis ater niger) using a single-step method, and their N-terminal sequences. The N-terminal sequence of the heavy chain of hopsarin D (H. stephensi) revealed that a fully conserved Cys-7 was substituted with a Ser residue. We therefore determined the complete amino acid sequence of hopsarin D. Hopsarin D shows approximately 70% similarity with FXa and approximately 98% similarity with trocarin D, a Group D prothrombin activator from Tropidechis carinatus. It possesses the characteristic Gla domain, two epidermal growth factor-like domains and a serine proteinase domain. All residues important for catalysis are conserved, as are most regions involved in interactions with factor Va and prothrombin. However, there are some structural differences. Unlike FXa, hopsarin D is glycosylated in both its chains: in light-chain residue 52 and heavy-chain residue 45. The glycosylation on the heavy chain is a large carbohydrate moiety adjacent to the active-site pocket. Overall, hopsarin D is structurally and functionally similar to mammalian coagulation FXa. (+info)
Structural aspects of oligomerization taking place between the transmembrane alpha-helices of bitopic membrane proteins. (7/1667)Recent advances in biophysical methods have been able to shed more light on the structures of helical bundles formed by the transmembrane segments of bitopic membrane proteins. In this manuscript, I attempt to review the biological importance and diversity of these interactions, the energetics of bundle formation, motifs capable of inducing oligomerization and methods capable of detecting, solving and predicting the structures of these oligomeric bundles. Finally, the structures of the best characterized instances of transmembrane alpha-helical bundles formed by bitopic membrane proteins are described in detail. (+info)
Interaction of three Caenorhabditis elegans isoforms of translation initiation factor eIF4E with mono- and trimethylated mRNA 5' cap analogues. (8/1667)Translation initiation factor eIF4E binds the m(7)G cap of eukaryotic mRNAs and mediates recruitment of mRNA to the ribosome during cap-dependent translation initiation. This event is the rate-limiting step of translation and a major target for translational control. In the nematode Caenorhabditis elegans, about 70% of genes express mRNAs with an unusual cap structure containing m(3)(2,2,7)G, which is poorly recognized by mammalian eIF4E. C. elegans expresses five isoforms of eIF4E (IFE-1, IFE-2, etc.). Three of these (IFE-3, IFE-4 and IFE-5) were investigated by means of spectroscopy and structural modelling based on mouse eIF4E bound to m(7)GDP. Intrinsic fluorescence quenching of Trp residues in the IFEs by iodide ions indicated structural differences between the apo and m(7)G cap bound proteins. Fluorescence quenching by selected cap analogues showed that only IFE-5 forms specific complexes with both m(7)G- and m(3)(2,2,7)G-containing caps (K(as) 2 x 10(6) M(-1) to 7 x 10(6) M(-1)) whereas IFE-3 and IFE-4 discriminated strongly in favor of m(7)G-containing caps. These spectroscopic results quantitatively confirm earlier qualitative data derived from affinity chromatography. The dependence of K(as) on pH indicated optimal cap binding of IFE-3, IFE-4 and IFE-5 at pH 7.2, lower by 0.4 pH units than that of eIF4E from human erythrocytes. These results provide insight into the molecular mechanism of recognition of structurally different caps by the highly homologous IFEs. (+info)
MODBASE, a Database of Annotated Comparative Protein Structure Models
MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAS …
SWISS-MODEL | Mus musculus
The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline
dali sp - Script for DaliLite to perform Serial Structure Comparison
dali_sp :: DESCRIPTION dali_sp is a wrapper script for DaliLite to perform serial structure comparison and to merge output pairwise alignments into single multiple alignment. ::DEVELOPER Laboratory of Bioinform
SWISS-MODEL | References
SWISS-MODEL is a fully automated protein structure homology-modelling server. The purpose of this server is to make protein modelling accessible to all life science researchers worldwide.
Protein Structure Initiative - Wikipedia
The Protein Structure Initiative (PSI) was a USA based project that aimed at accelerating discovery in structural genomics and contribute to understanding biological function. Funded by the U.S. National Institute of General Medical Sciences (NIGMS) between 2000 and 2015, its aim was to reduce the cost and time required to determine three-dimensional protein structures and to develop techniques for solving challenging problems in structural biology, including membrane proteins. Over a dozen research centers have been supported by the PSI for work in building and maintaining high-throughput structural genomics pipelines, developing computational protein structure prediction methods, organizing and disseminating information generated by the PSI, and applying high-throughput structure determination to study a broad range of important biological and biomedical problems. The project has been organized into three separate phases. The first phase of the Protein Structure Initiative (PSI-1) spanned from ...
NIGMS to Transition Protein Structure Initiatives Format after 2015 | Genomeweb
NEW YORK (GenomeWeb News) - The National Institute of General Medical Sciences said yesterday that it does not plan to renew the Protein Structure Initiative in its present form, as a large-scale initiative with a distinct set-aside budget, after the program completes its current five-year phase
Comparative Analysis of Protein Structure Alignments | BMC Structural Biology | Full Text
Several methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of structurally/evolutionary related proteins, but so far there has been less focus on the objective comparison between the alignments produced by different methods. We analysed and compared the structural alignments obtained by different methods using three sets of pairs of structurally related proteins. The first set corresponds to 355 pairs of remote homologous proteins according to the SCOP database (ASTRAL40 set). The second set was derived from the SISYPHUS database and includes 69 protein pairs (SISY set). The third set consists of 40 pairs that are challenging to align (RIPC set). The alignment of pairs of this set requires indels of considerable number and size and some of the proteins are related by circular permutations, show extensive conformational variability or include repetitions. Two standard methods (CE and DALI) were applied
BiO BB] TopMatch protein structure alignment and superposition web service
Ive used the Protein3dfit link from here , http://biotool.uni-koeln.de but it seems to be down right now. One suggestion I would make, however, is to offer an API and not just a web interface. I have a script to use the above link so I can submit files from a command line ( and integrate into automated stuff) and I imagine your form could be reverse engineered too. Trying to reverse engineer html is always annoying and it would probably be easier for you to write your web pages on top of a documented stable API. Whlie the interactive java viwer may not make much sense in this usage situation, your do offer pdf and pdb downloads that could be automated- if there is really something in the pdf that is not in the pdb, text format may be easier although certainly the pdb file is quite usable for automated analysis. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C),- leave message 989-348-4796 (P),- emergency only marchywka at hotmail.com Note: If I am asking for free ...
DeepAlign 1.13 - Pairwise Protein Structure Alignment
DeepAlign 1.13 :: DESCRIPTION Different from many other tools, DeepAlign aligns two protein structures using evolutionary information and beta strand orientation in addition to geometric similarity. Therefore, DeepAl
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Article | Netherlands Cancer Institute
Comparison of homologous structure models is a key step in analyzing protein structure. With a wealth of homologous structures, comparison becomes a tedious process, and often only a small (user-biased) selection of data is used. A multitude of structural superposition algorithms are then typically used to visualize the structures together in 3D and to compare them. Here, the Local Annotation of Homology-Matched Amino acids (LAHMA) website (https://lahma.pdb-redo.eu) is presented, which compares any structure model with all of its close homologs from the PDB-REDO databank. LAHMA displays structural features in sequence space, allowing users to uncover differences between homologous structure models that can be analyzed for their relevance to chemistry or biology. LAHMA visualizes numerous structural features, also allowing one-click comparison of structure-quality plots (for example the Ramachandran plot) and `in-browser structural visualization of 3D models.. ...
Generation, Validation, and Application of a P450 Homology Model<...
TY - JOUR. T1 - Generation, Validation, and Application of a P450 Homology Model. AU - Lewis, Benjamin. AU - Miners, John. PY - 2013. Y1 - 2013. N2 - In vitro validation of a protein homology model is critical for determining the predictivity of a computationally generated structure. Here we discuss the generation, validation, and application of a homology model for CYP1A1. Validation of the CYP1A1 homology model, generated using the highly homologous crystal template of human CYP1A2 (pdb 2HI4), was achieved using the prototypic substrate 7-ethoxyresorufin (Eres). The model was subsequently applied to generate CYP1A1 mutants with increased catalytic efficiency (Vmax/Km) towards the anticancer prodrug dacarbazine (DTIC). Thirty-three directed CYP1A1 mutants were generated and expressed in E. coli; six of these were generated to rationalise docking data obtained from in silico experiments using Eres. DTIC N-demethylation by the CYP1A1 E161K, E256K, and I458V mutants exhibited Michaelis-Menten ...
Sequence & Structure Alignment BioCode | BioCodeKB - Learn Bioinformatics
Learn Bioinformatics Online Sequence alignment is a method of arranging protein or DNA sequences to identify regions of similarity that may be a result of functional, structural, evolutionary relationships between the sequences.
Center for Structural Genomics of Infectious Diseases - Pages
Title: Crystal structure of Zika virus NS2B-NS3 protease in apo-form.. Authors: S.Nocadello,S.H.Light,G.Minasov,L.Shuvalova,A.A.Cardona-Correa,I.Ojeda,J.Vargas,M.E.Johnson,H.Lee,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases,Center For Structural Genomics Of Infectious Diseases (Csgid) ...
Protein Model Portal - PSI SBKB
The Protein Model Portal was developed as a module of the Protein Structure Initiative Knowledgebase (PSI KB). The goal of the Models Module was to develop a portal that gave access to the various models that can be leveraged from PSI targets and other experimental protein structures. The Protein Structure Initiative has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Experimental structural biology and homology modeling thereby complement each other in the exploration of the protein structure space.. Reference: Haas J., Roth S., Arnold, K., Kiefer, F., Schmidt T., Bordoli, L. and Schwede, T. (2013). The Protein Model Portal - a comprehensive resource for protein structure and model ...
Protein Model Portal - PSI SBKB
The Protein Model Portal was developed as a module of the Protein Structure Initiative Knowledgebase (PSI KB). The goal of the Models Module was to develop a portal that gave access to the various models that can be leveraged from PSI targets and other experimental protein structures. The Protein Structure Initiative has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Experimental structural biology and homology modeling thereby complement each other in the exploration of the protein structure space.. Reference: Haas J., Roth S., Arnold, K., Kiefer, F., Schmidt T., Bordoli, L. and Schwede, T. (2013). The Protein Model Portal - a comprehensive resource for protein structure and model ...
Members of this protein family represent a subset of those belonging to Pfam family PF00188 (SCP-like extracellular protein). Based on currently cuttoffs for this model, all member proteins are found in Bacteria capable of endospore formation. Members include a named but uncharacterized protein, YkwD of Bacillus subtilis. Only the C-terminal region is well-conserved and is included in the seed alignment for this model. Three members of this family have an N-terminal domain homologous to the spore coat assembly protein SafA ...
Biology - BioTech Mag
CircMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. Topology-independent and global protein structure alignment through an FFT-based algorithm. Context awareness and embedding for biomedical event extraction. MOOMIN...
Structural genomics target selection for the New York consortium on membrane protein structure<...
TY - JOUR. T1 - Structural genomics target selection for the New York consortium on membrane protein structure. AU - Punta, Marco. AU - Love, James. AU - Handelman, Samuel. AU - Hunt, John F.. AU - Shapiro, Lawrence. AU - Hendrickson, Wayne A.. AU - Rost, Burkhard. PY - 2009/12. Y1 - 2009/12. N2 - The New York Consortium on Membrane Protein Structure (NYCOMPS), a part of the Protein Structure Initiative (PSI) in the USA, has as its mission to establish a high-throughput pipeline for determination of novel integral membrane protein structures. Here we describe our current target selection protocol, which applies structural genomics approaches informed by the collective experience of our team of investigators. We first extract all annotated proteins from our reagent genomes, i.e. the 96 fully sequenced prokaryotic genomes from which we clone DNA. We filter this initial pool of sequences and obtain a list of valid targets. NYCOMPS defines valid targets as those that, among other features, have at ...
Identification and characterization of human polyserase-3, a novel protein with tandem serine-protease domains in the same...
In this work, we have performed an exhaustive bioinformatic analysis of the human genome to try to identify new serine proteases that could contain different catalytic domains within the same polypeptide chain. These bioinformatic searches led us to find a region in chromosome 16p11.2 putatively encoding a new polyprotease. After completing the cloning process using liver cDNA as template, we confirmed that the identified sequence was a new polyserine proteinase that we called polyserase-3 to underline its structural relationship with the previously described polyserases-1 and -2 [3, 9]. However, the polyserase-3 architecture is less complex than the exhibited by the two other human polyproteases. Thus, this new polyserase is composed of two serine protease domains preceded by a signal peptide, whereas both polyserase-1 and polyserase-2 contain three catalytic domains in a single polypeptide chain.. A comparative structural analysis also revealed that polyserase-3 is more closely related to ...
HEADER LIGASE 27-JAN-06 1VS0 TITLE CRYSTAL STRUCTURE OF THE LIGASE DOMAIN FROM M. TUBERCULOSIS LIGD AT TITLE 2 2.4A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE DNA LIGASE-LIKE PROTEIN RV0938/MT0965; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LIGD LIGASE DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ADENYLATED FORM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV0938, MT0965; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PAEB1120; SOURCE 11 OTHER_DETAILS: TEV CLEAVABLE HIS TAG KEYWDS LIGASE; OB FOLD; NUCLEOTIDYL TRANSFERASE, STRUCTURAL GENOMICS, PSI, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, TB STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 3 TBSGC, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR ...
putaive YfrE protein, Vibrio parahaemolyticus, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TPR repeat, UNKNOWN ...
PDB Structure Aligner | Geneious
Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).. Once installed, run the plugin by selecting two protein structures and clicking on Align/Assemble - Protein Structure Alignment in the toolbar. ...
Print - Biology-Online
In this work, we have performed an exhaustive bioinformatic analysis of the human genome to try to identify new serine proteases that could contain different catalytic domains within the same polypeptide chain. These bioinformatic searches led us to find a region in chromosome 16p11.2 putatively encoding a new polyprotease. After completing the cloning process using liver cDNA as template, we confirmed that the identified sequence was a new polyserine proteinase that we called polyserase-3 to underline its structural relationship with the previously described polyserases-1 and -2 [3,9]. However, the polyserase-3 architecture is less complex than the exhibited by the two other human polyproteases. Thus, this new polyserase is composed of two serine protease domains preceded by a signal peptide, whereas both polyserase-1 and polyserase-2 contain three catalytic domains in a single polypeptide chain.. A comparative structural analysis also revealed that polyserase-3 is more closely related to ...
PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach | BMC Bioinformatics | Full Text
Accurate and efficient structural alignment of non-coding RNAs (ncRNAs) has grasped more and more attentions as recent studies unveiled the significance of ncRNAs in living organisms. While the Sankoff style structural alignment algorithms cannot efficiently serve for multiple sequences, mostly progressive schemes are used to reduce the complexity. However, this idea tends to propagate the early stage errors throughout the entire process, thereby degrading the quality of the final alignment. For multiple protein sequence alignment, we have recently proposed PicXAA which constructs an accurate alignment in a non-progressive fashion. Here, we propose PicXAA-R as an extension to PicXAA for greedy structural alignment of ncRNAs. PicXAA-R efficiently grasps both folding information within each sequence and local similarities between sequences. It uses a set of probabilistic consistency transformations to improve the posterior base-pairing and base alignment probabilities using the information of all
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework | BMC...
Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or
ASU Scholarship Showcase | ASU Digital Repository
The mission of the DNASU Plasmid Repository is to accelerate research by providing high-quality, annotated plasmid samples and online plasmid resources to the research community through the curated DNASU database, website and repository (http://dnasu.asu.edu or http://dnasu.org). The collection includes plasmids from grant-funded, high-throughput cloning projects performed in our laboratory, plasmids from external researchers, and large collections from consortia such as the ORFeome Collaboration and the NIGMS-funded Protein Structure Initiative: Biology (PSI:Biology). Through DNASU, researchers can search for and access detailed information about each plasmid such as the full length gene insert sequence, vector information, associated publications, and links to external .... ...
PDB-Ligand | Small molecules : Chemoinformatics databases - OMICtools
A three-dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). PDB-Ligand is also a database tool that allows one to browse, classify, superimpose and visualize these structures. PDB-Ligand serves as an interactive structural analysis and clustering tool for all the ligand-binding structures in the PDB. PDB-Ligand also provides an easier way to obtain a number of different structure alignments of many related ligand-binding structures based on a simple and flexible ligand clustering method.
Improving protein structure similarity searches using domain boundaries based on conserved sequence information | BMC...
As the amount of diverse biological data continues to grow, it is important for new methods of analysis to be devised and current methods to be improved. The ability to detect that two proteins have diverged from a common ancestor allows one to infer functional similarity between the two. A common method for identifying similarity between proteins is the use of sequence alignment tools such as FASTA  and BLAST , which provide an alignment of two sequences and a score indicating whether the alignment is significant or could be attributed to chance. The comparison of protein structures allows one to peer back farther into evolutionary time, based on the concept that a form or structure remains similar long after sequence similarity has become undetectable [3-6]. There are many methods [7-15] and databases [16-19] currently available for protein structure comparisons. While the performance of the methods and databases available are for the most part satisfactory, it is not unusual for such ...
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
A novel method, Multiple Mapping Method with Multiple Templates (M4T) is introduced that implements an algorithm to automatically select and combine Multiple Template structures (MT) and an alignment optimization protocol (Multiple Mapping Method, MMM). The MT module of M4T selects and combines mult …
Rowland, R.S. and Taylor, R. (1996) Intermolecular Nonbonded Contact Distances in Organic Crystal Structures Comparison with...
Rowland, R.S. and Taylor, R. (1996) Intermolecular Nonbonded Contact Distances in Organic Crystal Structures Comparison with Distances Expected from van der Waals Radii. Journal of Physical Chemistry, 100, 7384-7391.
CIS 555: Advanced Bioinformatics
Advanced coverage of computational approaches used in bioinformatics. The course focuses on algorithmic challenges in analyzing molecular sequences, structures, and functions. It covers the following topics: Sequence comparison, assembly and annotation. Phylogenetic analysis. RNA secondary structure. Protein structure comparison, prediction, and docking. Microarrays, clustering, and classification. Genome, Hapmap, SNPs, and phenotypes. Proteomics and protein identification. Determining protein function and metabolic pathways.
Structural alignment software - Wikipedia
This list of structural comparison and alignment software is a compilation of software tools and web portals used in pairwise or multiple structural comparison and structural alignment. Key map: Class: Cα -- Backbone Atom (Cα) Alignment; AllA -- All Atoms Alignment; SSE -- Secondary Structure Elements Alignment; Seq -- Sequence-based alignment Pair -- Pairwise Alignment (2 structures *only*); Multi -- Multiple Structure Alignment (MStA); C-Map -- Contact Map Surf -- Connolly Molecular Surface Alignment SASA -- Solvent Accessible Surface Area Dihed -- Dihedral Backbone Angles PB -- Protein Blocks Flexible: No -- Only rigid-body transformations are considered between the structures being compared. Yes -- The method allows for some flexibility within the structures being compared, such as movements around hinge regions. Aung, Zeyar; Kian-Lee Tan (Dec 2006). MatAlign: Precise protein structure comparison by matrix alignment. Journal of Bioinformatics and Computational Biology. 4 (6): 1197-216. ...
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy...
Motivation: Template-based prediction of DNA binding proteins requires not only structural similarity between target and template structures but also prediction of binding affinity between the target and DNA to ensure binding. Here, we propose to predict protein- DNA binding affinity by introducing a new volume-fraction correction to a statistical energy function based on a distance-scaled, finite, ideal-gas reference (DFIRE) state. Results: We showed that this energy function together with the structural alignment program TM-align achieves the Matthews correlation coefficient (MCC) of 0.76 with an accuracy of 98%, a precision of 93% and a sensitivity of 64%, for predicting DNA binding proteins in a benchmark of 179 DNA binding proteins and 3797 nonbinding proteins. The MCC value is substantially higher than the best MCC value of 0.69 given by previous methods. Application of this method to 2235 structural genomics targets uncovered 37 as DNA binding proteins, 27 (73%) of which are putatively ...
Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs ...
We introduce a new type of knowledge-based potentials for protein structure prediction, called evolutionary potentials, which are derived using a single experimental protein structure and all three-dimensional models of its homologous sequences. The new potentials have been benchmarked against other knowledge-based potentials, resulting in a significant increase in accuracy for model assessment. In contrast to standard knowledge-based potentials, we propose that evolutionary potentials capture key determinants of thermodynamic stability and specific sequence constraints required for fast folding.
Our final step is to align all of these structures using Chimeras Sequence/Structure tools6. Some important notes about this procedure. First, this is a pairwise alignment method, so were going to align each structure to 1EZ2. As a result, care must be taken when interpreting the results, just as when viewing the results from pairwise blast values. Second, the alignment reports three values: RMSD, Aligned Pairs, and Score. The alignment score provides a rough indication of similarity in sequence and secondary structure. Unfortunately, there is currently no agreed-upon metric for structural alignment beyond RMSD, which might be misleading when differing numbers of residues are used for the alignment.. To align the structures, we will use the Chimera menu of the Molecular Structure Navigator: Chimera→Align structures→by model. This will bring up the Cytoscape/Chimera Structure Alignment Dialog. Because we are doing pairwise alignments, we need to select a reference structure, then select all ...
Safety and Immunogenicity of a Human Hookworm Candidate Vaccine With Different Doses of a Novel Adjuvant - Full Text View -...
Biological: 10 μg Na-GST-1/Alhydrogel Biological: 30 μg Na-GST-1/Alhydrogel Biological: 100 μg Na-GST-1/Alhydrogel Biological: 10 μg Na-GST-1/Alhydrogel/GLA-AF (1 μg) Biological: 30 μg Na-GST-1/Alhydrogel/GLA-AF (1 μg) Biological: 30 μg Na-GST-1/Alhydrogel/GLA-AF (5 μg) Biological: 100 μg Na-GST-1/Alhydrogel/GLA-AF (5 μg) ...
Safety and Immunogenicity of a Human Hookworm Candidate Vaccine With Different Doses of a Novel Adjuvant - Full Text View -...
Biological: 10 μg Na-GST-1/Alhydrogel Biological: 30 μg Na-GST-1/Alhydrogel Biological: 100 μg Na-GST-1/Alhydrogel Biological: 10 μg Na-GST-1/Alhydrogel/GLA-AF (1 μg) Biological: 30 μg Na-GST-1/Alhydrogel/GLA-AF (1 μg) Biological: 30 μg Na-GST-1/Alhydrogel/GLA-AF (5 μg) Biological: 100 μg Na-GST-1/Alhydrogel/GLA-AF (5 μg) ...
Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods
Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome Conformation Capture technologies, especially the Hi-C assays, provide us an opportunity to study how the 3D structures of the chromatin are organized. Based on the data from Hi-C experiments, many chromatin 3D structure modeling methods have been proposed. However, there is limited ground truth to validate these methods and no robust chromatin structure alignment algorithms to evaluate the performance of these methods. In our work, we first made a thorough literature review of 25 publicly available population Hi-C-based chromatin 3D structure modeling methods. Furthermore, to evaluate and to compare the performance of these methods, we proposed a novel data simulation method, which combined the population Hi-C data and single-cell Hi-C data without ad ...
RCSB PDB - 2GUP: Structural Genomics, the crystal structure of a ROK family protein from Streptococcus pneumoniae TIGR4 in...
2GUP: Structural Genomics, the crystal structure of a ROK family protein from Streptococcus pneumoniae TIGR4 in complex with sucrose
Neil Saunders is wondering if there is some standard software to manage the data involved in structural genomics projects. Unfortunately most structural genomics laboratories (e.g. the JCSG, the TB consortium) have had to tackle this problem independently.. A couple of years back I worked on a LIMS system for stuctural genomics, which can be read about here. In theory the SQL schema and frontend are available for anyone, but there would be a fair amount of tweaking involved if another lab wanted to use it, and I think that would be the case for other systems. There have been efforts at the EBI to develop standard data models for structural genomics, though.. This is another example of the importance of data standardization in bioinformatics / post-genomic biology. Everyone in the structural genomics community agrees that standardization of the data is very important, because data mining of the results of thousands of individual experiments along the structural genomics pipeline might yield some ...
FFAS03 results for vfdb.0000010
Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley Deacon, John Wooley, Scott Lesley, Ian Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik. Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima. Science. 2009 Sep 18;325(5947):1544-9.. Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik. bNAber: database of broadly neutralizing HIV antibodies. Nucl. Acids Res. 2013; published on November 7, 2013.. Ye Y, Godzik A. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W582-5 ...
Non-Sequential Encoding Scheme for Multi-Level Cell (MLC) Memory Cells - Patent application
0072] A selected read/write sequence is next applied at step 238 to a set of the memory cells in the array using the selected encoding scheme. The sequence may be predetermined based on a baseline set of data, or may correspond to real-world R/W sequences experienced during normal device operation. During this operation, various types of data may be collected such as frequency statistics and total energy consumption data. The frequency statistics may correspond to the type of data in Table 2, and may generally reflect the relative occurrence of different multi-bit values that are written to the memory cells. The total energy consumption data may correspond to the data shown in FIG. 9 for the selected encoding scheme. Alternatively or additionally, data associated with different wear levels and their associated impact on operational life of the memory cells may be obtained ...
The impact of extremophiles on structural genomics (and vice versa) | Semantic Scholar
The advent of the complete genome sequences of various organisms in the mid-1990s raised the issue of how one could determine the function of hypothetical proteins. While insight might be obtained from a 3D structure, the chances of being able to predict such a structure is limited for the deduced amino acid sequence of any uncharacterized gene. A template for modeling is required, but there was only a low probability of finding a protein closely-related in sequence with an available structure. Thus, in the late 1990s, an international effort known as structural genomics (SG) was initiated, its primary goal to
The Ear: Evolved or Designed? - Part 1 | TASC
The difference between homologous and convergent evolution is in the supposed phylogenetic origin of the structures.. If two organisms which are thought to be closely related have a similar characteristic, they are called homologous and the similarities that they share are considered as evidence for their evolution. So creatures which are closely related would have homologous structures or homologous DNA because that is how they were determined to be related. Now when a creature has a characteristic or structure or DNA which is like that of another creature, but it has been assumed that they are not closely related, then these structures are called analogous and are said to be evidence of convergent evolution. So even though they have similar structures or similar DNA, they are not considered evidence for a close relationship because they have been predetermined to be unrelated.. Evolutionists use of homologous structures is a good example of circular reasoning. Circular reasoning is when the ...
PDB 2jz6 structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
2jz6: Solution structure of 50S ribosomal protein L28 from Thermotoga maritima. Northeast Structural Genomics Consortium target VR97.
Chiropractors Specialize In Bodys Structural Alignment, Relieving Stress And They Promote Healthy Lifestyle.
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The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function...
Structural genomics efforts have led to increasing numbers of novel, uncharacterized protein structures with low sequence identity to known proteins, resulting in a growing need for structure-based...
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
The publication AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. is placed in the Top 10000 of the best publications in CiteWeb. Also in the category Chemistry it is included to the Top 1000. Additionally, the publicaiton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. is placed in the Top 1000 among other scientific works published in 1996 ...
Domains & Structures - Site Guide - NCBI
The Related Structures tool allows users to find 3D structures from the Molecular Modeling Database (MMDB) that are similar in sequence to a query protein. Although the query protein may not yet have a resolved structure, the 3D shape of a similar protein sequence can shed light on the putative shape and biological function of the query protein.. ...
RCSB PDB for 4DXQ
4DXQ: Acid-Base Catalysis and Crystal Structures of a Least Evolved Ancestral GFP-like Protein Undergoing Green-to-Red Photoconversion.
The Protein Structure Series: Post - II - IDRACK: Blog
Second post in this series, necessary for a complete understanding of protein structures for computational analysis in the following posts.
"Structural modeling of ataxin-3 reveals distant homology to adaptins". Proteins. 50 (2): 355-70. doi:10.1002/prot.10280. PMID ... The protein encoded by the ATXN3 gene contains (CAG)n repeats in the coding region, and the expansion of these repeats from the ... Ataxin-3 is a protein that in humans is encoded by the ATXN3 gene. Machado-Joseph disease, also known as spinocerebellar ataxia ... Wang Q, Li L, Ye Y (Mar 2008). "Inhibition of p97-dependent protein degradation by Eeyarestatin I". The Journal of Biological ...
"Structural homology between rbs repressor and ribose binding protein implies functional similarity". Protein Science. 1 (7): ... The Ribose repressor (RbsR) is a bacterial DNA-binding transcription repressor protein and a member of the LacI/GalR protein ... an allosteric effector of the related LacI/GalR protein Catabolite Control Protein A (CcpA). RbsR in EcoGene RbsR in EColiWiki ... In Bacillus subtilis, RbsR was shown to interact with Histidine-containing protein (HPr), ...
Collagen, type XXIII, alpha 1
Collagen XXIII shows structural homology with collagen XIII and collagen XXV . Apart from having the characteristic structure ... Collagen Protein domain Transmembrane protein Non-small-cell lung carcinoma Prostate cancer Homotrimer Lipid raft Integrin, ... Both proteins co-localize on basal keratinocytes surface. Collagen XXIII plays a role as a biomarker for detection and ... Proteins which are included in this group present an amino-terminal cytoplasmic domain followed by a membrane-spanning ...
Mobarec JC, Sanchez R, Filizola M (2009). "Modern homology modeling of G-protein coupled receptors: which structural template ... "G Protein-Coupled Receptors - Modeling and Simulation" and "G Protein-Coupled Receptors in Drug Discovery". She is also an ... "Structural Aspects of Oligomerization in the Function of GPCRs - Marta Filizola". Grantome.com. Retrieved 2016-01-31. CS1 maint ... "G Protein-Coupled Receptors in Drug Discovery - Methods and , Marta Filizola , Springer". Springer.com. Retrieved 2016-01-24. " ...
This region shares homology with cholesterol-dependent cytolysins from Gram-positive bacteria. Perforin has structural and ... This protein is one of the main cytolytic proteins of cytolytic granules, and it is known to be a key effector molecule for T- ... Tschopp J, Masson D, Stanley KK (1986). "Structural/functional similarity between proteins involved in complement- and ... Perforin-1 is a protein that in humans is encoded by the PRF1 gene and the Prf1 gene in mice. Perforin is a pore forming ...
The C-terminal domain has an 'open fold' with no structural homology to other proteins. The dimer structure reveals the C- ... Qian D, Jiang L, Lu L, Wei C, Li Y (March 2011). "Biochemical and structural properties of cyanases from Arabidopsis thaliana ... Positively charged amino acids that make up the protein help form this site between subunits. This adjacent anion binding site ... Schlachter CR, Klapper V, Wybouw N, Radford T, Van Leeuwen T, Grbic M, Chruszcz M (July 2017). "Structural Characterization of ...
LC3 shares structural homology with ubiquitin, and therefore has been termed a ubiquitin-like protein. LC3 has a LDS (LIR ... Microtubule-associated proteins 1A/1B light chain 3B (hereafter referred to as LC3) is a protein that in humans is encoded by ... Overview of all the structural information available in the PDB for UniProt: Q9GZQ8 (Microtubule-associated proteins 1A/1B ... MAP1LC3B is a member of the highly conserved ATG8 protein family. ATG8 proteins are present in all known eukaryotic organisms. ...
... several integrin-like proteins were proposed based on structural homology with the metazoan receptors. Plants contain integrin- ... PIP3 and other phosphoinositides do the same thing to the Pleckstrin homology domains of proteins such as the kinase protein ... Other activated proteins interact with adaptor proteins that facilitate signaling protein interactions and coordination of ... most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellular response. Proteins ...
Ground squirrel hepatitis virus
The virus particles contain two major structural proteins, surface antigens (sAg) and core antigens (cAg). Both proteins were ... GSHV has greater nucleotide and amino acid homology with WHV than HBV, with 82% nucleotide and 78% amino acid homology between ... Two are for the genes encoding the structural proteins (surface antigens and core antigens), and the other two are unassigned. ... A protein is covalently bound to the 5' end of the minus strand which may be used as a primer for DNA synthesis. There are four ...
Chung SY, Subbiah S (October 1996). "A structural explanation for the twilight zone of protein sequence homology". Structure. 4 ... a de novo protein designed to adopt the alpha/beta-barrel packing)". Protein Engineering. 4 (7): 745-9. doi:10.1093/protein/4.7 ... a de novo polypeptide modelled on the alpha/beta-barrel proteins". Protein Engineering. 3 (4): 259-66. doi:10.1093/protein/3.4. ... The N/C-terminal and loop regions on TIM barrel proteins are capable of hosting structural inserts ranging from simple ...
"Phyre2: Protein Homology/analogY Recognition Engine V 2.0". Structural Bioinformatics Group, Imperial College, London. ... "Phyre: Protein Homology/analogY Recognition Engine". Structural Bioinformatics Group, Imperial College, London. Retrieved 22 ... Phyre and Phyre2 (Protein Homology/AnalogY Recognition Engine; pronounced as 'fire') are free web-based services for protein ... Like other remote homology recognition techniques (see protein threading), it is able to regularly generate reliable protein ...
... is a structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Homology ... SWISS-MODEL Homology modelling Protein structure prediction Protein structure prediction software CASP (Critical Assessment of ... Homology (or comparative) modelling methods make use of experimental protein structures ("templates") to build models for ... SWISS-MODEL pipeline comprises the four main steps that are involved in building a homology model of a given protein structure ...
This protein maintains structural similarity and sequence homology to the α-subunits of human leukocyte integrins. The αInt1p ... A plant protein with structural similarity to integrins contains the amino acid sequence Asn-Gly-Asp (NGD). ILRs play a role in ... This protein shares functional homology with mammalian integrins in that it connects the ECM to the intracellular matrix to ... Most commonly, ILRs resembles the β1 subunit found in integrin proteins. This structural similarity between ILRs and integrins ...
The degree of similarity with the latter proteins is insufficient to establish homology. As of early 2016, no crystal ... structural data is available for members of the BenE family. The generalized transport reaction catalyzed by BenE of A. ... These proteins are about 400 residues in length and probably span the membrane 12 times. Some members of the BenE family can ...
Although RpiA and RpiB catalyze the same reaction, they show no sequence or overall structural homology. According to Jung et ... This αβα motif is not uncommon in other proteins, suggesting possible homology with other enzymes. The separate molecules of ... The protein encoded by RPIA gene is an enzyme, which catalyzes the reversible conversion between ribose-5-phosphate and ... Rossmann MG, Moras D, Olsen KW (July 1974). "Chemical and biological evolution of nucleotide-binding protein". Nature. 250 (463 ...
Scholler JK, Kanner SB (1997). "The human p167 gene encodes a unique structural protein that contains centrosomin A homology ... protein binding. • structural molecule activity. • translation initiation factor activity. • receptor tyrosine kinase binding. ... Eukaryotic translation initiation factor 3 subunit A (eIF3a) is a protein that in humans is encoded by the EIF3A gene. ... "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3: 89. doi:10.1038/msb4100134 ...
In particular, the structural genes of cystoviruses are highly-similar to those used by a number of dsRNA viruses that infect ... Members of the Cystoviridae appear to be most closely related to the Reoviridae, but also share homology with the Totiviridae. ... The genome codes for 12 proteins. Viral replication is cytoplasmic. Replication follows the double-stranded RNA virus ... 14 kb in length and their protein and lipid outer layer. No other bacteriophage has any lipid in its outer coat, though the ...
FK506 binding protein 6, also known as FKBP6, is a human gene. The encoded protein shows structural homology to FKBP ... PDB: 3B7X; "RCSB Protein Data Bank - Structure Summary for 3B7X - Crystal structure of human FK506-Binding Protein 6". ... FKBP6 contains 3 α-helices and 11 β-sheet strands, and as a FK506-family protein, has been shown to be a potent ... Siekierka JJ, Hung SH, Poe M, Lin CS, Sigal NH (October 1989). "A cytosolic binding protein for the immunosuppressant FK506 has ...
The highly conserved Pleckstrin homology domain (PH) is a structural domain approximately 120 amino acids in length. It binds ... α-synuclein is the primary structural component of Lewy bodies, protein aggregates that are the hallmarks of Parkinson's ... it must first be activated by proteins such as Arf, Rho, Rac, and protein kinase C. The activity of phospholipase D is ... The protein may also undergo a conformational change upon PIP2 binding, but this has not been shown experimentally and would ...
Carnitine palmitoyltransferase II deficiency
The human homolog of the CPT II enzyme shows 82.2% amino acid sequence homology with the rat protein. Significant structural ... CPT II shares structural elements with other members of the carnitine acyltransferase protein family. The crystal structure of ... is a peripheral inner mitochondrial membrane protein ubiquitously found as a monomeric protein in all tissues that oxidize ... This gene is composed of 5 exons that encode a protein 658 amino acids in length. To date, sixty disease-causing mutations ...
have shown that the astacin sequence is inserted into the human bone morphogenetic protein (BMP) with significant homology. ... Tolloid-like protein 2 (TLL2) Gomis-Rüth FX, Trillo-Muyo S, Stöcker W (October 2012). "Functional and structural insights into ... Proteins containing the astacin domain include: Astacin-like metallo-endopeptidase (ASTL) Bone morphogenetic protein 1 (BMP1) ... The proteins are synthesised with N-terminal signal and pro-enzyme sequences, and many contain multiple domains C-terminal to ...
This fold is a common structural motif in fatty acid synthetic proteins and RhlA shows homology to transacylases. It has been ... The proteins encoded by rhlA and rhlB; RhlA and RhlB respectively, are expected to form a complex because of the operonic ... The hydroxyacyl-ACP substrate of RhlA is the product of FabG, a protein which encodes the NADPH-dependent β-keto-acyl-ACP ... Zhu K, Rock CO (May 2008). "RhlA converts beta-hydroxyacyl-acyl carrier protein intermediates in fatty acid synthesis to the ...
This protein is a voltage-dependent anion channel and shares high structural homology with the other VDAC isoforms. VDACs are ... Voltage-dependent anion-selective channel protein 2 is a protein that in humans is encoded by the VDAC2 gene on chromosome 10. ... VDACs have also been observed to interact with pro- or antiapoptotic proteins, such as Bcl-2 family proteins and kinases, and ... "Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ...
Microsomal epoxide hydrolase
"Structural insights into human microsomal epoxide hydrolase by combined homology modeling, molecular dynamics simulations, and ... Protein Engineering, Design and Selection" (PDF). Protein Eng. 5 (3): 197-211. doi:10.1093/protein/5.3.197. PMID 1409539. Ollis ... doi:10.1093/protein/5.3.197. PMID 1409539. Carr PD, Ollis DL (2009). "Alpha/beta hydrolase fold: an update". Protein and ... It is known that the N-terminal region of the enzyme is responsible for anchoring the protein to the cell membrane, while the C ...
This furcation is commonplace in the study of protein evolution. Structural features which are highly necessary for function ... Further, a homology model has been created for EPO based on the X-ray diffraction structure. The fold is highly conserved and ... In fact, when the calcium ion is removed, the protein precipitates out of solution. The protein contains only a single modular ... Structural Classification of Proteins) Source: The J. C. Segen Dictionary of Modern Medicine database. Molecular and Cellular ...
"Cooperation of breast cancer proteins PALB2 and piccolo BRCA2 in stimulating homologous recombination". Nature Structural & ... RAD51 is involved in the search for homology and strand pairing stages of the process. ... protein C-terminus binding. • protein binding. • four-way junction DNA binding. • identical protein binding. • ... This protein can interact with the ssDNA-binding protein RPA, BRCA2, PALB2 and RAD52. ...
Domain of unknown function
... whereas about one third possessed a novel protein fold. Some DUF families share remote sequence homology with domains that has ... Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The ... identified 238 DUFs in 355 essential proteins (in 16 model bacterial species), most of which represent single-domain proteins, ... As a result, these proteins and the DUF only become relevant when the cells starve. It is thus believed that many DUFs (or ...
"Refinement of protein structure homology models via long, all-atom molecular dynamics simulations". Proteins. 80 (8): 2071-9. ... Koehl, P.; Levitt, Michael (1999). "A brighter future for protein structure prediction". Nature Structural Biology. 6 (2): 108- ... These experiments can be used to reveal structural changes in a protein at the atomic level. SMD is often used to simulate ... In biophysics and structural biology, the method is frequently applied to study the motions of macromolecules such as proteins ...
... from Mycobacterium tuberculosis shows structural homology to the GNAT family of N-acetyltransferases". Protein Science. 12 (9 ... Identification of ovothiol A in Leishmania donovani and structural analysis of a novel thiol from Mycobacterium bovis". ...
By contrast, the putative jingmenvirus structural proteins that likely make up its capsids have no homology to known proteins. ... Homology has consistently been observed between the genes encoding non-structural proteins of jingmenviruses and flaviviruses, ... The JMTV genome has four segments, two of which contain genes with sequence homology to non-structural proteins found in ... whose protein product is processed by proteases, whereas the non-structural jingmenvirus proteins are encoded on two genome ...
Elastina - Wikipédia, a enciclopédia livre
extracellular matrix structural constituent. •protein binding. •extracellular matrix constituent conferring elasticity. • ... Dyksterhuis LB, Weiss AS (2010). «Homology models for domains 21-23 of human tropoelastin shed light on lysine crosslinking». ... Rosenbloom J (1984). «Elastin: relation of protein and gene structure to disease». Lab. Invest. 51 (6): 605-23. PMID 6150137. ... 2010). «Functional consequences of homocysteinylation of the elastic fiber proteins fibrillin-1 and tropoelastin». J. Biol. ...
Integral membrane protein
Homology modeling can be used to construct an atomic-resolution model of the "target" integral protein from its amino acid ... IMPs include transporters, linkers, channels, receptors, enzymes, structural membrane-anchoring domains, proteins involved in ... Integral polytopic proteinEdit. Main article: Transmembrane protein. The most common type of IMP is the transmembrane protein ( ... Integral monotopic proteinsEdit. Main article: Integral monotopic protein. Integral monotopic proteins are associated with the ...
Engelhardt H; Peters J (1998). "Structural research on surface layers: a focus on stability, surface layer homology domains, ... Gogarten, Johann Peter (1994). "Which is the Most Conserved Group of Proteins? Homology - Orthology, Paralogy, Xenology and the ... This proposal is also supported by other work investigating protein structural relationships and studies that suggest that ... Proteins related to the cytoskeleton components of other organisms exist in archaea, and filaments form within their cells, ...
They share amino acid sequence homology and core structural similarity to a specific class of major histones but also have ... who believed that transcription was activated by protein-DNA and protein-protein interactions on largely naked DNA templates, ... Nuclear protein Ataxia-Telangiectasia (NPAT), also known as nuclear protein coactivator of histone transcription, is a ... The first step of chromatin structure duplication is the synthesis of histone proteins: H1, H2A, H2B, H3, H4. These proteins ...
Brain-derived neurotrophic factor
positive regulation of non-membrane spanning protein tyrosine kinase activity. • transmembrane receptor protein tyrosine kinase ... Overview of all the structural information available in the PDB for UniProt: P23560 (Brain-derived neurotrophic factor) at the ... Fyn associates with the pICD-TrkB through its Src homology domain 2 (SH2) and is phosphorylated at its Y416 site. Once ... Binding proteins: IGFBP (1, 2, 3, 4, 5, 6, 7). *Cleavage products/derivatives with unknown target: Glypromate (GPE, (1-3)IGF-1) ...
Arqueas, a enciclopedia libre
Engelhardt H, Peters J (1998). "Structural research on surface layers: a focus on stability, surface layer homology domains, ... 2002). "Introns in protein-coding genes in Archaea". FEBS Lett. 510 (1-2): 27-30. PMID 11755525. doi:10.1016/S0014-5793(01) ... Jenney FE, Adams MW (2008). "The impact of extremophiles on structural genomics (and vice versa)". Extremophiles 12 (1): 39-50 ... Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH (2000). "Phylogenetic analyses of the constituents of Type III protein ...
LIG3, a enciclopedia libre
Nash RA, Caldecott KW, Barnes DE, Lindahl T (April 1997). "XRCC1 protein interacts with one of two distinct forms of DNA ligase ... "Homology and enzymatic requirements of microhomology-dependent alternative end joining". Cell Death Dis 6: e1697. PMC 4385936 ... "Eukaryotic DNA ligases: structural and functional insights". Annu. Rev. Biochem. 77: 313-38. PMC 2933818. PMID 18518823. doi ... interaction between DNA polymerase beta and the XRCC1 protein". EMBO J. 15 (23): 6662-70. PMC 452490. PMID 8978692.. ...
S100A6 - ويكيبيديا
"Molecular cloning of the cDNA for a growth factor-inducible gene with strong homology to S-100, a calcium-binding protein". J. ... "Structural and functional analysis of a growth-regulated gene, the human calcyclin". J. Biol. Chem. 262 (17): 8325-32. PMID ... S100 protein binding. • protein homodimerization activity. • ion transmembrane transporter activity. • ربط أيون الزنك. • ربط ... S100A6 (S100 calcium binding protein A6) هوَ بروتين يُشَفر بواسطة جين S100A6 في الإنسان. ...
protein binding. Cellular component. • extracellular region. • specific granule. • intracellular. • extracellular exosome. • ... Larrick JW, Lee J, Ma S, Li X, Francke U, Wright SC, Balint RF (November 1996). "Structural, functional analysis and ... The cathelicidin family shares primary sequence homology with the cystatin family of cysteine proteinase inhibitors, ... Patients with a high level of this protein were 3.7 times more likely to survive kidney dialysis for a year without a fatal ...
All CAS protein family members have common structural characteristics. CAS proteins have an amino terminal SH3 domain ... The CASS4 C-terminus has a short region of CAS family homology, but lacks obvious similarity at the level of primary amino acid ... structural constituent of cytoskeleton. • protein tyrosine kinase binding. Cellular component. • cytoplasm. • cell junction. • ... "Entrez Gene: Cas scaffolding protein family member 4".. *^ a b Tikhmyanova N, Little JL, Golemis EA (April 2010). "CAS proteins ...
Structural characteristics of the TCR. The TCR is a disulfide-linked membrane-anchored heterodimeric protein normally ... "A human T cell-specific cDNA clone encodes a protein having extensive homology to immunoglobulin chains". Nature. 308 (5955): ... UMich Orientation of Proteins in Membranes protein/pdbid-2hac - Zeta-zeta dimer of T cell receptor ... The TCR is composed of two different protein chains (that is, it is a heterodimer). In humans, in 95% of T cells the TCR ...
Brain-derived neurotrophic factor
positive regulation of non-membrane spanning protein tyrosine kinase activity. • transmembrane receptor protein tyrosine kinase ... Xu X, Ye L, Ruan Q (March 2009). "Environmental enrichment induces synaptic structural modification after transient focal ... Fyn associates with the pICD-TrkB through its Src homology domain 2 (SH2) and is phosphorylated at its Y416 site. Once ... Binding proteins: IGFBP (1, 2, 3, 4, 5, 6, 7). *Cleavage products/derivatives with unknown target: Glypromate (GPE, (1-3)IGF-1) ...
... epigenesis is a unidirectional movement from structural development in DNA to the functional maturation of the protein. " ... "DNA damage, homology-directed repair, and DNA methylation". PLoS Genet. 3 (7): e110. PMC 1913100 . PMID 17616978. doi:10.1371/ ... In general, proteins fold into discrete units that perform distinct cellular functions, but some proteins are also capable of ... Structural inheritance. For more details on this topic, see Structural inheritance. ...
Felix Rey, of the Pasteur Institute in Paris has constructed the 3D structure of the EFF1 protein and shown it does the ... Jamin, M, H Raveh-Barak, B Podbilewicz, FA Rey (2014) "Structural basis of eukaryotic cell-cell fusion" (Cell, Volume 157, ... About 800 million years ago, a minor genetic change in a single molecule called guanylate kinase protein-interaction domain ... part of a whole family of FF proteins. ... Homology. *Last universal common ancestor. *Macroevolution. * ...
Many proteins are composed of several protein domains, i.e. segments of a protein that fold into distinct structural units. ... "Advances in homology protein structure modeling". Current Protein & Peptide Science. 7 (3): 217-27. doi:10.2174/ ... Structural proteins. Structural proteins confer stiffness and rigidity to otherwise-fluid biological components. Most ... and membrane proteins. Almost all globular proteins are soluble and many are enzymes. Fibrous proteins are often structural, ...
Arthur M. Lesk
Lesk, Arthur M. (2001). Introduction to protein architecture: the structural biology of proteins. Oxford [Oxfordshire]: Oxford ... known as homology modelling. ... Schematic diagrams of protein structures. Lesk, along ... Lesk's work also involves the detailed comparison of proteins in different structural states as a means for understanding the ... "Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein ...
Bayer EA, Chanzy H, Lamed R, Shoham Y (October 1998). "Cellulose, cellulases and cellulosomes". Current Opinion in Structural ... April 2011). "Crystal structure and substrate-binding mode of cellulase 12A from Thermotoga maritima". Proteins. 79 (4): 1193- ... belonging to GH9 Family show highest sequence homology to metazoan endogenous cellulases. Algal cellulases are modular, ... protein structures) surrounding a central catalytic region which is the active-site. The enzyme is categorised as an ...
Proteins are classified into the chemokine family based on their structural characteristics, not just their ability to attract ... They are approximately 20-50% identical to each other; that is, they share gene sequence and amino acid sequence homology. They ... Cytokine proteins are classified as chemokines according to behavior and structural characteristics. In addition to being known ... All of these proteins exert their biological effects by interacting with G protein-linked transmembrane receptors called ...
It has been suggested that the evolution of the tetrapod limb from lobe-finned fishes is related to the loss of these proteins. ... Gegenbaur suggested a model of transformative homology - that all vertebrate paired fins and limbs were transformations of the ... "Some functional and structural characteristics of cetacean flippers and flukes" Pages 255-275 in: Norris KS (ed.) Whales, ... The genetic basis for the formation of the fin rays is thought to be genes coded for the production of certain proteins. ...
Complement component 1s
protein binding. • hydrolase activity. • metal ion binding. • identical protein binding. • serine-type endopeptidase activity. ... study by chemical cross-linking and three-dimensional homology modeling". Biochemistry. 34 (22): 7311-21. doi:10.1021/ ... "Structural and circular-dichroism studies on the interaction between human C1-esterase inhibitor and C1s". The Biochemical ... Complement component 1s (EC 188.8.131.52, C1 esterase, activated complement C1s, complement C overbar 1r, C1s) is a protein ...
One of the main ways that genomes are compared is by sequence homology. Homology is the study of biological structures and ... Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information ... Structural genomics. *Synthetic biology. *Systems biology. References. *^ a b c d e "NIH working definition of ... Other databases: Protein Data Bank, Ensembl and InterPro. *Specialised genomic databases: BOLD, Saccharomyces Genome Database, ...
عامل النمو شبيه الانسولين-1 - ويكيبيديا، الموسوعة الحرة
Rinderknecht E، Humbel RE (1978). "The amino acid sequence of human insulin-like growth factor I and its structural homology ... protein stabilization. • myotube cell development. • positive regulation of DNA replication. • myoblast proliferation. • ... protein kinase B signaling. • regulation of multicellular organism growth. • positive regulation of cell migration. • platelet ... Ras protein signal transduction. • cell proliferation. • positive regulation of mitotic nuclear division. • positive regulation ...
Thus, the S-layer protein can represent up to 15% of the whole protein content of a cell. S-layer proteins are poorly ... Series in Structural Biology. 7. Singapore: World Scientific Publishing. doi:10.1142/10084. ISBN 978-981-3141-81-0. .. ... In Gram-positive bacteria whose S-layers often contain surface layer homology (SLH) domains, the binding occurs to the ... protein-carbohydrate interactions and/or protein-protein interactions.. * ...
Some are simple structural molecules, like the fibers formed by the protein collagen. Proteins can bind to other proteins and ... By comparing the homology between different species' genomes, it is possible to calculate the evolutionary distance between ... 2002), I.3. Proteins: The Shape and Structure of Proteins *^ Alberts et al. (2002), I.3. Proteins: Protein Function Archived 25 ... without changing the structure of the protein itself). Protein structure is dynamic; the protein hemoglobin bends into slightly ...
Hazai E, Bikadi Z (2008). "Homology modeling of breast cancer resistance protein (ABCG2)". J Struct Biol. 162 (1): 63-74. doi: ... Overview of all the structural information available in the PDB for UniProt: Q9UNQ0 (Broad substrate specificity ATP-binding ... Click on genes, proteins and metabolites below to link to respective articles.[§ 1] [[File:. ... protein homodimerization activity. • transporter activity. • ATPase activity. • GO:0001948 protein binding. • ATP binding. • ...
The microscopic "hairs" of these cells are structural protein filaments that project out into the fluid. The hair cells are ... This serves as evidence of homology between related species. In humans, there is variability in these muscles, such that some ...
Homology searches revealed a close homology between caspases and the caspase-like proteins of Reticulomyxa (a unicellular ... The death folds are located in a structural domain of the caspases known as the pro-domain, which is larger in those caspases ... which is facilitated by binding to adaptor proteins via protein-protein interaction motifs that are collectively referred to as ... The adaptor protein FADD will recruit (by a Death domain-Death domain interaction) pro-Caspase 8 via the DED domain. This FasR ...
... structural proteins, polyamines, and proteins involved in nuclear import. Acetylation of these proteins can alter their ... HATs can be grouped into several different families based on sequence homology as well as shared structural features and ... Chromatin is a combination of proteins and DNA found in the nucleus, and it undergoes many structural changes as different ... Protein Chem. Advances in Protein Chemistry. 67: 181-99. doi:10.1016/S0065-3233(04)67007-0. ISBN 9780120342679. PMID 14969728. ...
3-Phosphoinositide-dependent protein kinase-1 (PDK1): structural and functional homology with the Drosophila DSTPK61 kinase. -...
3-Phosphoinositide-dependent protein kinase-1 (PDK1): structural and functional homology with the Drosophila DSTPK61 kinase.. ... PKB and PKC subfamily of protein kinases and a carboxy-terminal pleckstrin homology (PH) domain. The PDK1 gene is located on ... The activation of protein kinase B (PKB, also known as c-Akt) is stimulated by insulin or growth factors and results from its ... We recently identified a protein kinase, termed PDK1, that phosphorylates PKB at Thr308 only in the presence of lipid vesicles ...
Structural Biochemistry/Pleckstrin Homology Domain Leucine-rich Repeat Protein Phosphatase - Wikibooks, open books for an open...
Structural Biochemistry/Pleckstrin Homology Domain Leucine-rich Repeat Protein Phosphatase. From Wikibooks, open books for an ... The discovery of PHLPP, which stands for Pleckstrin Homology Domain Leucine-Rich Repeat Protein Phosphatase, contributes to the ... Homology_Domain_Leucine-rich_Repeat_Protein_Phosphatase&oldid=3117583" ... Cellular homeostasis requires balance between phosphorylation catalyzed by protein kinases and dephosphorylation catalyzed by ...
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and...
... a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology ... a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology ... and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates ... These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA ...
Structural homologies of cobalamin-binding proteins. Tryptic peptide mapping of intrinsic factor, transcobalamin and...
The results show that the homology between analogous proteins from different species is close for intrinsic factor and ... The results also suggest the existence of one or more regions which, with minor changes, are conserved among all proteins ... This implies a common evolutionary origin for all the cobalamin binding proteins studied. ... We have explored the structural features of cobalamin binding proteins by peptide mapping. The present report is a comparison ...
Prediction of protein structural classes for low-homology sequences based on predicted secondary structure | DR-NTU
Yang, J. Y., Peng, Z. L., & Chen, X. (2010). Prediction of protein structural classes for low-homology sequences based on ... Prediction of protein structural classes for low-homology sequences based on predicted secondary structure. ... Thus, it is a valuable method to predict protein structural classes particularly for low-homology amino acid sequences. ... Background: Prediction of protein structural classes (a, b, a + b and a/b) from amino acid sequences is of great importance, as ...
Sequence Similarity - 1BMX: HIV-1 CAPSID PROTEIN MAJOR HOMOLOGY REGION PEPTIDE ANALOG, NMR, 8 STRUCTURES Sequence...
... capsid protein major-homology-region peptide analogs by NMR spectroscopy. ... This allows for the easy identification of regions and types of structural flexibility present in a protein of interest. ... The PDBFlex database explores the intrinsic flexibility of protein structures by analyzing structural variations of the same ... HIV-1 CAPSID PROTEIN MAJOR HOMOLOGY REGION PEPTIDE ANALOG, NMR, 8 STRUCTURES. ...
Protein Structure Determination
Proteins play a crucial role in the world of research and their structures are, therefore, of great interest to the researcher ... Homology Modeling. This enables researchers to obtain a three-dimensional picture of a protein. It needs prior knowledge of the ... https://en.wikibooks.org/wiki/Structural_Biochemistry/Proteins/Protein_Structure_determination_methods ... Protein modeling based on this template depends on the fact that protein structure is highly conserved in most cases. ...
Structure Cluster - 1BMX: HIV-1 CAPSID PROTEIN MAJOR HOMOLOGY REGION PEPTIDE ANALOG, NMR, 8 STRUCTURES 3D Similarity...
... capsid protein major-homology-region peptide analogs by NMR spectroscopy. ... Structural Similarities for the Entities in PDB 1BMX. The following structural similarities have been found using the jFATCAT- ... HIV-1 CAPSID PROTEIN MAJOR HOMOLOGY REGION PEPTIDE ANALOG, NMR, 8 STRUCTURES. ... Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics 26: 2983-2985 ...
PDB 2v1l structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
... a conserved hypothetical protein from a Vibrio cholerae pathogenicity island, reveals homology to human p32. ... The Scottish Structural Proteomics Facility: targets, methods and outputs. Oke et al. (2010) ... Sequence domains: Protein of unknown function (DUF2787) Structure domains: Protein of unknown function DUF2787 ... Crystal structure of VC1805, a conserved hypothetical protein from a Vibrio cholerae pathogenicity island, reveals homology to ...
Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis | PNAS
C) COQ9 structural homology sequence scheme with FadR, a TFR family member (PDB 3anp) (32). (D) Individual and structural ... The crystal structure reveals that COQ9 retains the two main structural domains of TFR family proteins: a HTH and a small ... Our work reveals that COQ9 shares striking structural homology to members of the TetR family of regulators (TFRs)-a small ... Although we likely have not yet identified a bona fide endogenous ligand for COQ9, its structural homology, along with its ...
3-Day Protein Structural Bioinformatics Course
Morphing conformational changes to view as animations in PE: see Protein Morpher. *Homology (comparative) modeling: ... How to use Protein Explorer to visualize structural features of proteins and protein-ligand interactions. ... Protein Structural Bioinformatics 3-Day Course in 3D Macromolecular Visualization & Analysis with Protein Explorer Washington ... Is Structural Genomics the answer? Not in the next few years. *Intrinsicially unstructured proteins: About 10% of proteins are ...
2007 Protein Structural Bioinformatics Course
Homology (Comparative) Modeling *Jmol in Scientific Journals *FirstGlance in Jmol: Nature Structural and Molecular Biology *" ... Introduction to Structural Bioinformatics. Review of Protein Chemistry and Structure. * Central Dogma: DNA mRNA Protein. * 20 ... Is Structural Genomics the answer? Not in the next few years. *Intrinsicially unstructured proteins: About 10% of proteins are ... Sequence specific recognition DNA bases by zinc finger domain of protein *Hydrophobic protein-protein interaction *Nonspecific ...
PLEKHB2 - Pleckstrin homology domain containing, family B (Evectins) member 2, isoform CRA b - Homo sapiens (Human) - PLEKHB2...
Gene3D Structural and Functional Annotation of Protein Families. More...Gene3Di. 184.108.40.206, 1 hit. ... Protein. Similar proteins. Species. Score. Length. Source. A0A024QZ35. Pleckstrin homology domain-containing family B member 2 ... Protein. Similar proteins. Species. Score. Length. Source. A0A024QZ35. Pleckstrin homology domain-containing family B member 2 ... Protein. Similar proteins. Species. Score. Length. Source. A0A024QZ35. Pleckstrin homology domain-containing family B member 2 ...
Fermt2 - Pleckstrin homology domain containing, family C (With FERM domain) member 1 - Mus musculus (Mouse) - Fermt2 gene &...
Gene3D Structural and Functional Annotation of Protein Families. More...Gene3Di. 220.127.116.11. 2 hits. ... Protein. Similar proteins. Organisms. Length. Cluster ID. Cluster name. Size. Q3TLE2. Q8CIB5. Mus musculus (Mouse). 680. ... Protein. Similar proteins. Organisms. Length. Cluster ID. Cluster name. Size. Q3TLE2. Q96AC1. A0A024R687. K7B954. A0A2I2YNQ6. ... Protein. Similar proteins. Organisms. Length. Cluster ID. Cluster name. Size. Q3TLE2. Q96AC1. A0A024R687. K7B954. A0A2I2YNQ6. ...
Homology modeling and molecular dynamics simulations of the active state of the nociceptin receptor reveal new insights into...
... is a class A G protein-coupled receptor (GPCR) in the opioid receptor family. Although NOP shares a significant homology with ... An inactive-state homology model of NOP was also built using a multiple template approach. Molecular dynamics simulation of the ... Homology modeling and molecular dynamics simulations of the active state of the nociceptin receptor reveal new insights into ... Previously reported homology models of the NOP receptor, based on the inactive-state GPCR crystal structures, give limited ...
Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode
Protein Binding * S-Adenosylmethionine / chemistry * Sequence Homology, Amino Acid* * Structural Homology, Protein ... To the best of our knowledge, this is the first study to report a reliable homology model of LIAS protein. This study will ... A homology model for LIAS protein was generated using X-ray crystallographic structure of Thermosynechococcus elongatus BP-1 ( ... Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode J Theor Biol. 2017 ...
Frontiers | Perspectives in Peptide-Based Vaccination Strategies for Syndrome Coronavirus 2 Pandemic | Pharmacology
... membrane or nucleocapsid proteins. Herein, we aim to highlight the molecular basis of the infection and recent peptide-based ... SARS-CoV-2 immunogenic regions are mainly distributed, as well as for other coronaviruses, across structural areas such as ... Structural Proteins, Homologies and Differences Between Human Coronaviruses. All coronaviruses encode for four or five ... proteins (Liang et al., 2020). Viral structural proteins are components of the mature viruses, while non-structural proteins ...
Crystal structure of HutZ, a heme storage protein from Vibrio cholerae: A structural mismatch observed in the region of high...
In the absence of experimentally solved protein structures, homology modeling is widely used to predict a structure based on ... Structural comparison between HutZ and HugZ. Structural superimposition revealed that the HutZ monomer shared high structural ... Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci. 2006; ... Structural modeling of HutZ and its variants. Anfinsens dogma  states that a proteins native structure is determined by ...
Molecules | Free Full-Text | Structural Probing and Molecular Modeling of the A3 Adenosine Receptor: A Focus on Agonist Binding
... which belong to the G protein-coupled receptor (GPCR) superfamily. The human A3AR (hA3AR) subtype is implicated in several ... A3AR and discuss the challenges associated with an accurate prediction of the receptor extracellular vestibule through homology ... Keywords: G protein-coupled receptor; site-directed mutagenesis; homology modeling; adenosine receptor; structure-activity ... Structural Probing and Molecular Modeling of the A3 Adenosine Receptor: A Focus on Agonist Binding. Antonella Ciancetta. ...
IJMS | Free Full-Text | Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate...
... the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which ... That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of ... In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural ... In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to ...
The situation is this: I have a sequence-structure coordinate file of , a protein with , 85 % homology to the protein I want to ... structural hypothesis from sequence data? We have Sybyl, but Ive , been unable to get the Homology modeler to produce adequate ... own database with many similar proteins and just the resolved protein , with homology. Any suggestions or references would be ... Homology modelling. Andrej Sali sali at tamika.harvard.edu Wed Oct 12 17:44:12 EST 1994 *Previous message: Homology modelling ...
An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium...
An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium ... An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium ... An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium ... An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium ...
Collagen, type XXIII, alpha 1 - wikidoc
2.1 Protein structure. *2.2 Structural homology. *2.3 Shedding. *3 Interaction with integrin α2β1 ... Structural homology. File:Comparison of collagens XXIII, XIII and XXV.png Comparison of collagens XXIII, XIII and XXV ... Collagen XXIII shows structural homology with collagen XIII and collagen XXV . Apart from having the characteristic ... Both proteins co-localize on basal keratinocytes surface. Clinical significance. Collagen XXIII plays a role as a biomarker for ...
The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins...
The high-resolution structure of a filamentous flexible plant virus shows that there is structural homology between its coat ... protein and the nucleoproteins of an unrelated group of enveloped RNA animal viruses. ... 5) In the last paragraph of the Introduction and in the first paragraph of the subsection "Structural homology between CP from ... Suggest: The structure of a flexuous-helix plant virus shows homology of its capsid protein with the nucleoprotein of animal ...
Structural basis of a potent human monoclonal antibody against Zika virus targeting a quaternary epitope | PNAS
1976) Exploring structural homology of proteins. J Mol Biol 105:75-95. ... The E protein consists of DI (red), DII (yellow), DIII (blue), and transmembrane domain (TM; tan). The fusion loop of E protein ... Protein Sequence Alignment and Annotation.. Protein sequence alignments were conducted using the program CLUSTALW of the web ... The structure of the E protein (35) was fitted independently into each of the three E protein locations within the icosahedral ...
Crystal structure of alkyl hydroperoxidase D like protein PA0269 from Pseudomonas aeruginosa: Homology of the AhpD-like...
... and one structural water molecule. A comparison of five other related hypothetical proteins from various species, assigned to ... Thus, this hypothetical protein was assigned to the AhpD-like protein family with peroxidase-related activity. The functional ... The protein has an all-helical fold with a chain topology similar to a known AhpD from Mycobacterium tuberculosis despite a low ... However, in the P. aeruginosa protein, helices H3, H4 of this motif are located at the N-terminal part of the chain, while in M ...
IUCr) Acta Crystallographica Section F Volume 63, Part 4, April 2007
Preliminary structural studies on the leucine-zipper homology region of the human protein Bap31. ... A truncated form of biotin carboxyl carrier protein containing the C-terminal half fragment (BCCPΔN76) and the biotin protein ... Crystallization and preliminary X-ray crystallographic studies of the biotin carboxyl carrier protein and biotin protein ligase ... have been cloned and the proteins have been expressed in Escherichia coli. Both proteins have been crystallized in the presence ...
X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family
Structure and sequence relationships and homology modeling. In an effort to annotate the function of these two related proteins ... We have predicted the protein to be a solute-binding protein based on structure and binding cavity. Fold and structural ... Principles of protein-protein interactions. Proc Natl Acad Sci U S A. 1996;93 :13-20. doi: 10.1073/pnas.93.1.13. [PubMed] [ ... X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family. ...
PDB 2qtw structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
The self-inhibited structure of full-length PCSK9 at 1.9 A reveals structural homology with resistin within the C-terminal ... The self-inhibited structure of full-length PCSK9 at 1.9 A reveals structural homology with resistin within the C-terminal ... The Crystal Structure of PCSK9 at 1.9 Angstroms Resolution Reveals structural homology to Resistin within the C-terminal domain ...
Autoregulation of yeast ribosomal proteins discovered by efficient search for feedback regulation | Communications Biology
We used the yeast collection of genes fused to GFP as a rapid screen for examples of feedback regulation in ribosomal proteins ... We tested 95 ribosomal protein genes and found a wide continuum of effects, with 30% showing at least a 3-fold reduction in ... Further analyses showed that the intron in the 5 UTR of RPS22B is required for regulation, presumably because the protein ... Here, the authors screen for feedback regulation of ribosomal proteins by overexpressing a non- regulatable version of a gene ...
BioinformaticsSequencesPleckstrin homologySimilarityEscherichiaRemote homology detectionGenesStructures of proteinsHighly conservedCharacterizationKinaseFunctional homologyInteractionsAlignmentsModels of proteinsMotifsPeptidesComputationalBiologyResiduesPeptideReceptorAnalogous proteinsMRNACatalyticTertiaryGeneProtein'sSite-directed muChemistryEvolutionaryPutativeRecombinantFunctionMembrane proteinDomainAlignmentMammalianHomologousAllergenic proteinsSequence identityCrystallographyMoleculesSilicoMetabolismInteractionHomolog proteinsSimulationsGenomics ConsortiumModelingSecondary structureEffector proteinsRibosomal proteinsTransmembrane proteinsLocalizationGeneticsActinClassification of proteinsMotifStructure predictionGlobularYeastAbstractPrediction of protein structuralConformationalHypothetical proteinsBiologicalExpression
- In this day of exploding bioinformatics information from genomics and proteomics, it is ever more important to be conversant with macromolecular three-dimensional structure, and how it relates to protein and nucleic acid function and drug design. (umass.edu)
- Protein Explorer integrates several key bioinformatics servers, and has been adopted by numerous bioinformatics resources . (umass.edu)
- It progresses rapidly to powerful tools that will be of interest to specialists in protein structure and bioinformatics. (umass.edu)
- Adopted by Nature Structural and Molecular Biology and other bioinformatics resources . (umass.edu)
- Introduction to Structural Bioinformatics. (umass.edu)
- An Introduction to Structural Bioinformatics The practical application of molecular modelling techniques to study protein sequence, structure and function will be the focus of a hands-on workshop - An Introduction to Structural Bioinformatics: From Sequence to Structure to Function of Prteins - to be held in York 19-20 March 1998. (bio.net)
- The course on Applied Pharmaceutical Structural Bioinformatics teaches how to solve practical problems in pharmacology, life sciences and bioinformatics using free software and databases relating to the structure of functional proteins and drug targets. (uu.se)
- The course covers bioinformatics for nucleotide and amino acid sequences and structural bioinformatics. (uu.se)
- Introduction to Structural Bioinformatics in the pharmaceutical field. (uu.se)
- Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors. (ncbs.res.in)
- Results: Bioinformatics and comparative genomics tools were applied to determine a core of 7668 shared protein families in all Botrytis species, which grouped them in two distinct phylogenetic clades. (wur.nl)
- The MPI Bioinformatics toolkit for protein sequence analysis. (mpg.de)
- T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. (nih.gov)
- These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. (nih.gov)
- These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. (nih.gov)
- Background: Prediction of protein structural classes (a, b, a + b and a/b) from amino acid sequences is of great importance, as it is beneficial to study protein function, regulation and interactions. (ntu.edu.sg)
- Results: We propose a new method to predict protein structural classes on the basis of features extracted from the predicted secondary structures of proteins rather than directly from their amino acid sequences. (ntu.edu.sg)
- Conclusion: The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the predicted secondary structure sequences, which is capable of characterizing the sequence order information, local interactions of the secondary structural elements, and spacial arrangements of a helices and b strands. (ntu.edu.sg)
- Thus, it is a valuable method to predict protein structural classes particularly for low-homology amino acid sequences. (ntu.edu.sg)
- Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (hindawi.com)
- Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (hindawi.com)
- Researchers at the Institute of Food Safety in Wageningen, The Netherlands, screened transgenic proteins in GM food crops for the presence of short amino acid sequences identical to those in known allergens, and to find out if these are involved in binding IgE, the class of antibodies produced in allergic reactions. (i-sis.org.uk)
- This includes methods, databases and software for analysis and management of amino acid and nucleotide sequences, secondary and tertiary structures of proteins, methods and tools for homology modelling of protein 3D structure, and molecular dynamics simulations and molecular docking. (uu.se)
- We analyzed the SARS-CoV-2 spike (S) protein amino acid sequence extracted from 11,542 viral genomic sequences submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database through April 27, 2020. (preprints.org)
- Consistent with prior reports, we found a major S protein mutation, D614 to G614, that was represented in 56% of all the analyzed sequences. (preprints.org)
- One hope was that the sequences would lead to a greater understanding of how genes and their encoded proteins function. (biomedicalcomputationreview.org)
- And as the number of known gene sequences grew, many scientists realized they could not catch up simply by determining protein structures one by one. (biomedicalcomputationreview.org)
- Fortunately, unlike sequences, which are nearly infinite in number, "there may be a finite number of different shapes that proteins actually adopt to perform their functions in the cell," says Ian Wilson, DPhil , professor of structural biology at The Scripps Research Institute and director of the Joint Center for Structural Genomics (JCSG). (biomedicalcomputationreview.org)
- This envelope-spanning protein has three transmembrane sequences, and interacts with TagL on the cytoplasmic side, and TssJ on the C-terminal, periplasmic side  . (kenyon.edu)
- In their study, the researchers concentrated their analysis on the olfactomedin domain of the sequences because of extreme differences in sequence lengths among the olfactomedin-related proteins. (mcponline.org)
- On the basis of the frequently high conservation among enzymes responsible for the post-translational modification of specific antimicrobials, we performed an in silico screen for novel thuricin CD-like gene clusters using the TrnC and TrnD radical SAM proteins as driver sequences to perform an initial homology search against the complete non-redundant database. (plos.org)
- In this work, we establish an integrated sys-tem of neural networks (called Real-SPINE) for real-value prediction and apply the method to pre-dict residue-solvent accessibility and backbone w dihedral angles of proteins based on information derived from sequences only. (psu.edu)
- TPRpred: A tool for prediction of TPR-, PPR- and SELI-like repeats from protein sequences. (mpg.de)
- The 556-residue monomeric enzyme comprises a catalytic domain that is most similar to the PKA, PKB and PKC subfamily of protein kinases and a carboxy-terminal pleckstrin homology (PH) domain. (nih.gov)
- The discovery of PHLPP, which stands for Pleckstrin Homology Domain Leucine-Rich Repeat Protein Phosphatase, contributes to the cast of phosphate-controlling enzymes in cell signaling. (wikibooks.org)
- Growth factor receptor-binding protein 10 (Grb10) is a pleckstrin homology and Src homology 2 (SH2) domain-containing protein that interacts with several receptor tyrosine kinases, including the insulin receptor (IR) and the IGF-1 receptor (IGF1R) ( 5 , 6 ). (diabetesjournals.org)
- Grb10 negatively regulates insulin or IGF-1 signaling by binding to the kinase domain of the tyrosine-phosphorylated IR or IGF1R, mainly via its SH2 domain and partly a region between the pleckstrin homology domain and the SH2 domain (BPS) ( 9 , 12 - 14 ). (diabetesjournals.org)
- Clostridial neurotoxins are comprised of botulinum (BoNT) and tetanus (TeNT), which share significant structural and functional similarity. (nih.gov)
- This similarity is striking and suggests that the gene that encodes these proteins has been transferred between the two groups of viruses during evolution. (elifesciences.org)
- The degree of 3-dimensional shape similarity between proteins. (bioportfolio.com)
- Thus there is value in use of active-site structural templates as a complementary approach to sequence-based methods and more global methods, but none of the similarity-based methods is sufficient to provide a rigorous determination of activity. (biomedcentral.com)
- The major capsid protein (B345) was found to be glycosylated, implying a strong similarity to proteins from other dsDNA viruses. (asm.org)
- Thus, overall amino-acid similarity with an allergenic protein, i.e., 35% identity within a run of 80 amino acids, might be suspect. (i-sis.org.uk)
- The amino acid sequence of a protein is compared with all known allergenic proteins retrieved from the protein databases to identify stretches of 80 amino acids with more than 35% similarity, or small identical runs of at least 6 amino acids. (i-sis.org.uk)
- Through the use of homology modeling and structure threading, NDR1 was predicted to have a high degree of structural similarity to Arabidopsis LATE EMBRYOGENESIS ABUNDANT14, a protein implicated in abiotic stress responses. (plantphysiol.org)
- NB-LRR R proteins have been historically divided into two subgroups, based on the N-terminal presence of either a coiled-coil (CC) domain or a domain with similarity to the Toll IL-1 receptor (TIR) family of proteins (for review, see Takken and Tameling, 2009 ). (plantphysiol.org)
- Based on the similarity between the TIGR ( t rabecular-meshwork i nducible g lucocorticoid r esponse) (also known as myocilin) and olfactomedin protein families identified throughout the length of the TIGR protein, we have identified more distantly related proteins to determine the elements essential to the function/structure of the TIGR and olfactomedin proteins. (mcponline.org)
- and class C contains only the Drosophila SR-C. Class D, E, and F receptors have only recently been identified, and none of these show any structural similarity with class A, B, or C receptors (see Figure ⇓ for classes and structures). (ahajournals.org)
Remote homology detection3
- SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. (mendeley.com)
- We introduce a greedy algorithm for filtering and enrichment of dynamic fragment libraries, compiled with remote-homology detection methods such as HHfrag. (ebscohost.com)
- Remote homology detection of proteins using 3D models enriched with physicochemical properties. (ebscohost.com)
- We used the yeast collection of genes fused to GFP as a rapid screen for examples of feedback regulation in ribosomal proteins by overexpressing a non-regulatable version of a gene and observing the effects on the expression of the GFP-fused version. (nature.com)
- We tested 95 ribosomal protein genes and found a wide continuum of effects, with 30% showing at least a 3-fold reduction in expression. (nature.com)
- Autoregulation by one of the proteins in the operon is typically sufficient to control the expression of all the other genes in the operon by translational coupling, where translation of an upstream gene in an operon is required for translation of the downstream genes. (nature.com)
- Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes , and which usually results in protein folding into a specific three-dimensional structure that determines its activity. (wikipedia.org)
- By 1990s, five different LOX genes (LOX, LOXL1, LOXL2, LOXL3, and LOXL4) encoding proteins were identified which shared a highly conserved C terminal domain and a diverse N-terminal. (springer.com)
- Genomewide association screens for AD that Tanzi's group is currently conducting are generating signals from genes involved in the molecular skirmishes that have evolved between host and microbes, as well as from genes whose proteins signal to activate the innate immune system. (alzforum.org)
- So a group of scientists embarked on a strategic plan to uncover the three-dimensional structures of all the proteins that these genes encode. (biomedicalcomputationreview.org)
- Analysis of the thuricin CD-associated gene cluster revealed the presence of genes encoding two highly unusual SAM proteins (TrnC and TrnD) which are proposed to be responsible for these unusual post-translational modifications. (plos.org)
- Fifteen novel thuricin CD-like gene clusters were identified, based on the presence of TrnC and TrnD homologues in the context of neighbouring genes encoding potential bacteriocin structural peptides. (plos.org)
- The phenotypes of both mutants clearly indicate that the genes are involved in the localization of determinants in the form of mRNA and protein. (genetics.org)
Structures of proteins2
- Protein modeling based on this template depends on the fact that protein structure is highly conserved in most cases. (news-medical.net)
- Very interestingly, structural superimposition of HutZ and its homologous protein HugZ, a heme oxygenase from Helicobacter pylori , exhibited a structural mismatch of one amino acid residue in β6 of HutZ, although residues involved in this region are highly conserved in both proteins. (pubmedcentralcanada.ca)
- Although the N-terminal domain of olfactomedin is divergent ( 2 ), the C-terminal domain is highly conserved among the TIGR and olfactomedin proteins. (mcponline.org)
- Optimized method for TAG protein homology modeling: In silico and experimental structural characterization. (crg.eu)
- Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. (nature.com)
- Here we report the structural and functional characterization of skeletal muscles from sAnk1 knockout mice (KO). (jove.com)
- This book is essential reading for all researchers, biochemists and crystallographers working with membrane proteins, who are interested by the structural characterization of their favorite protein and who wish to follow the expression, migration, modifications and recycling of a membrane protein. (springer.com)
- Dr. Isabelle Mus-Veteau is a biochemist and biophysicist specialist in membrane protein characterization. (springer.com)
- 3-Phosphoinositide-dependent protein kinase-1 (PDK1): structural and functional homology with the Drosophila DSTPK61 kinase. (nih.gov)
- The activation of protein kinase B (PKB, also known as c-Akt) is stimulated by insulin or growth factors and results from its phosphorylation at Thr308 and Ser473. (nih.gov)
- We recently identified a protein kinase, termed PDK1, that phosphorylates PKB at Thr308 only in the presence of lipid vesicles containing phosphatidylinositol 3,4,5-trisphosphate (Ptdlns(3,4,5)P3) or phosphatidylinositol 3,4-bisphosphate (Ptdlns(3,4)P2). (nih.gov)
- Human PDK1 is homologous to the Drosophila protein kinase DSTPK61, which has been implicated in the regulation of sex differentiation, oogenesis and spermatogenesis. (nih.gov)
- Here, we discuss three candidate cell surface proteins that are suitable for homology modeling: human norepinephrine transporter (hNET), anaplastic lymphoma kinase (ALK), and neurotrophic tyrosine kinase receptor 2 (NTRK2 or TrkB). (frontiersin.org)
- A detailed evaluation of homology models expands on three chosen cell surface protein candidates: human norepinephrine transporter (hNET), anaplastic lymphoma kinase (ALK), and neurotrophic tyrosine kinase receptor type 2 (NTRK2, commonly known as TrkB). (frontiersin.org)
- Protein kinase C inhibitors. (freepatentsonline.com)
- Novel 3-amino/hydroxy-4- 4-benzoylphenylcarboxylamino/oxy -azepanes and their homologies as protein kinase inhibitors. (freepatentsonline.com)
- To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). (nature.com)
- Upon ligand occupancy changes, chemoreceptors transmit signals across the inner membrane that modulate the autophosphorylation activity of a homodimeric histidine kinase CheA, which is coupled to receptor control by an adaptor protein CheW. (nature.com)
- An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium meliloti FixK. (uni-bielefeld.de)
- Participants will be enabled to incorporate computer visualization and qualitative analysis of 3D structure of protein, DNA, RNA, and protein-ligand interactions into their teaching and research. (umass.edu)
- How to use Protein Explorer to visualize structural features of proteins and protein-ligand interactions. (umass.edu)
- s findings reveal how the virus particles assemble, and the interactions between the coat protein and the ssRNA. (elifesciences.org)
- Decreasing physical errors in protein structures plays major role in the development of targeting agents and understanding of chemical interactions at the molecular level. (frontiersin.org)
- 226] Jayashree S, Murugavel P, Sowdhamini R, Srinivasan N. (2019) Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions. (ncbs.res.in)
- Specificity and stability of transient protein-protein interactions. (ncbs.res.in)
- The interaction may be modified by endocytosis of the receptors, cleavage by proteolysis and through interactions of surfactant proteins. (labome.org)
- Starting from an amino acid sequence, I-TASSER first generates three-dimensional (3D) atomic models from multiple threading alignments and iterative structural assembly simulations. (nih.gov)
- Background: Protein sequence profile-profile alignment is an important approach to recognizing remote homologs and generating accurate pairwise alignments. (ebscohost.com)
- 227] Pritha Ghosh, Teerna Bhattacharya, Oommen K. Mathew and R. Sowdhamini (2019) PASS2 version 6 a database of structure based sequence alignments of protein domain superfamilies in accordance with SCOPe. (ncbs.res.in)
Models of proteins1
- Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. (psu.edu)
- Specific protein motifs also point to a degree of homology with mammalian integrins, well-characterized proteins involved in adhesion and signaling. (plantphysiol.org)
- TagL is a protein, required for T6S activity, that contains PG-binding motifs and likely acts as a cell wall binding agent  . (kenyon.edu)
- Karavanich and Anholt ( 2 ) first compared the olfactomedin-related proteins from rat, mouse, human, and frog and identified several conserved motifs. (mcponline.org)
- More than half of the Bic-D protein consists of heptad repeats distributed throughout, and no other protein motifs are apparent. (genetics.org)
- Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides , or sometimes oligopeptides . (wikipedia.org)
- Molecular dynamics (MD) simulations are powerful computational tools in structural biology, widely used for understanding conformational changes in proteins, and the folding of peptides. (cityofhope.org)
- In a follow-up study published September 2004 , a new webtool was used to predict potential allergenicity of proteins and peptides according to the current recommendations of the FAO/WHO Expert Consultation, as outlined in the Codex Alimentarius [4, 5]. (i-sis.org.uk)
- Homology modeling is a systematic computational process where the most similar protein sequence, of a known crystal structure, is used for construction of a new model by replacing the equivalent amino acids on an equivalent backbone. (frontiersin.org)
- SMi's In Silico ADMET conference will bring together structural biologists, computational chemists, physicochemists from pharmaceutical and biotech industry and academia to discuss the current state of ADMET prediction. (smi-online.co.uk)
- This timely topic involves a comparison of different computational chemistry approaches (QSAR, QSPR and protein structure-based design). (smi-online.co.uk)
- The detailed computational investigation of the canine lysyl oxidase protein was analyzed in silico with respect to its physicochemical properties, secondary and tertiary structure predictions and functional analysis using standard bioinformatic tools. (springer.com)
- Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. (hindawi.com)
- Our lab is focused on developing physics-based, state-of-the-art multiscale computational methods to study the conformational dynamics of proteins and in drug design. (cityofhope.org)
- One of the major bottlenecks in using the existing computational methods to study dynamics of proteins is the limitation in time scale and the narrow conformational search afforded by these methods. (cityofhope.org)
- We are developing coarse-grain computational methods to sample the various kinetic states of the protein dynamics, followed by fine-grain computational methods to capture the detailed atomic-level structural changes and calculate the thermodynamic properties. (cityofhope.org)
- Techniques for prediction of secondary protein structure with computational tools and review of the Pfam and PROSITE databases. (uu.se)
- Thus, researchers reasoned that it might be possible to unveil the universe of protein structures through a combination of experimental structure determination and computational structure prediction. (biomedicalcomputationreview.org)
- Protein structures are the final frontiers in understanding the human biology at the molecular level. (frontiersin.org)
- The Plant Protein Club's principal objective is to promote the exchange of ideas and expertise between communities specialising in protein structure, plant biology and their industrial applications. (bio.net)
- Structural determination in traditional structural biology laboratories can't possibly keep up, researchers say. (biomedicalcomputationreview.org)
- Residues 24-62 of the putative catalytic region of P. aeruginosa have a higher sequence identity of 33% where the functional activity is supplied by a proton relay system of five residues, Glu36, Cys48, Tyr50, Cys51, and His55, and one structural water molecule. (biomedcentral.com)
- In this study, the N‐terminal region (residues 1-339) of the human formin homology domain‐containing protein 1 (FHOD1) was purified and crystallized from 20%( w / v ) PEG 4000, 10%( v / v ) glycerol, 0.3 M magnesium chloride and 0.1 M Tris-HCl pH 8.0. (ingentaconnect.com)
- Proteins are large biomolecules , or macromolecules , consisting of one or more long chains of amino acid residues . (wikipedia.org)
- The sequence of amino acid residues in a protein is defined by the sequence of a gene , which is encoded in the genetic code . (wikipedia.org)
- Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification , which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. (wikipedia.org)
- VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
- Residues 93 and 323 within the major capsid protein, located in the vicinity of the threefold spikes, allow the CPV capsids to bind canine TfR ( 25 ). (asm.org)
- Several residues have been identified as essential to the function and/or structure of the human TIGR protein based on their degree of conservation across the family and their implication in the pathogenesis of primary open-angle glaucoma. (mcponline.org)
- Prediction of protein functional residues from sequence by probability density estimation. (mpg.de)
- These proteins contain domains of extensive heptad repeats in which the hydrophobic residues are preferentially located at positions 1 and 4 ( M c L achlan and K arn 1983 ). (genetics.org)
- All teneurins, especially in mouse, are type II transmembrane proteins that are composed of a large extracellular C terminal domain of ~2400 amino acid residues, a single transmembrane helical domain of ~30 hydrophobic residues and an intracellular N terminal domain of ~300-375 residues. (wikipedia.org)
- The 4 cysteine residues assist in protein folding, however, they are absent in Ten-m2 and Ten-m3. (wikipedia.org)
- We have explored the structural features of cobalamin binding proteins by peptide mapping. (semanticscholar.org)
- Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors . (wikipedia.org)
- In addition to the linear and conformational peptide epitopes, glycans (carbohydrate chains linked to the protein) have also been shown to be major IgE binding sites in allergenic glycoproteins. (i-sis.org.uk)
- 9. The pharmaceutical composition of claim 4 , wherein the cupredoxin peptide is part or all of a protein selected from the group consisting of an azurin, pseudoazurin, plastocyanin, rusticyanin, Laz, auracyanin, stellacyanin and cucumber basic protein. (google.com)
- Adenosine is an endogenous modulator exerting its functions through the activation of four adenosine receptor (AR) subtypes, termed A 1 , A 2A , A 2B and A 3 , which belong to the G protein-coupled receptor (GPCR) superfamily. (mdpi.com)
- In this review, we showcase selected modeling-based and guided strategies that were applied to elucidate the binding of agonists to the A 3 AR and discuss the challenges associated with an accurate prediction of the receptor extracellular vestibule through homology modeling from the available X-ray templates. (mdpi.com)
- 2004. Cannabinoid CB1 receptor protein expression in the rat choroid plexus: a possible involvement of cannabinoids in the regulation of cerebrospinal fluid. (springer.com)
- 2000. Crystal structure of rhodopsin: A G protein-coupled receptor. (springer.com)
- 2008. Crystal structure of the ligand-free G-protein-coupled receptor opsin. (springer.com)
- In this study, we show that pancreas-specific knockout of growth factor receptor-binding protein 10 (Grb10), which is highly expressed in pancreas and islets, leads to elevated insulin/IGF-1 signaling in islets, enhanced β-cell mass and insulin content, and increased insulin secretion in mice. (diabetesjournals.org)
- Antibodies have also been shown to induce a conformational change or rearrangement of viral capsid proteins, causing the receptor binding site to become inaccessible ( 33 ). (asm.org)
- Investigating the effect of key mutations on the conformational dynamics of toll‐like receptor dimers through molecular dynamics simulations and protein structure networks. (ncbs.res.in)
- This field has made significant advances since the elucidation of the first 3-D structure of a recombinant G Protein Coupled Receptor (GPCR), rhodopsin, with the structure of several more GPCRs having been solved in the past five years. (springer.com)
- The Potato Nucleotide-Binding Leucine-Rich Repeat (NLR) Immune Receptor Rx1 is a Pathogen Dependent DNA-Deforming Protein. (dur.ac.uk)
- In both cases the cis-regulatory segment resides in the 5' UTR of the gene as shown by placing that segment of the mRNA upstream of GFP alone and demonstrating it is sufficient to cause repression of GFP when the protein is over-expressed. (nature.com)
- The encoded protein is part of the spliceosome complex and functions in the second catalytic step of mRNA splicing. (genecards.org)
- The catalytic mechanism requires two peroxidases, AhpC and AhpD, where AhpD plays the role of an essential adaptor protein. (biomedcentral.com)
- A comparison of five other related hypothetical proteins from various species, assigned to the alkyl hydroperoxidase D-like protein family, shows they contain the same conserved structural motif and catalytic sequence Cys-X-X-Cys. (biomedcentral.com)
- The LTQ cofactor is conserved in all LOX like proteins and is essential for the catalytic activity of LOX. (springer.com)
- One of the methods that have been proposed is a multiobjective optimization, in which protein stability and catalytic activity are simultaneously optimized [ 4 , 5 ]. (hindawi.com)
- Several methods have been proposed to design novel stable proteins, such as multi-objective optimization, in which protein stability and catalytic activity are simultaneously optimized. (hindawi.com)
- PTPs having closely related catalytic domains also tend to be similar in overall structural topology. (asm.org)
- In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. (mdpi.com)
- Genetic analysis reveals links between lipid A structure and expression of the outer membrane protein gene, ropB, in Rhizobium leguminosarum. (uni-bielefeld.de)
- p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence. (uniprot.org)
- section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. (uniprot.org)
- Collagen α-1 (XXIII) chain is a protein encoded by COL23A1 gene , which is located on chromosome 5q35 in humans, and on chromosome 11B1+2 in mice. (wikidoc.org)
- Although less well-studied, autoregulation also occurs for proteins involved in post-transcriptional steps of gene expression. (nature.com)
- In most of those cases, both transcription factors and RNA-binding proteins, the normal function of the protein is to bind DNA or RNA and often to regulate gene expression. (nature.com)
- There are also examples of proteins whose primary function is not in gene regulation but that have a secondary role in regulating their own expression. (nature.com)
- Many of these are proteins that bind to RNA, but whose primary functions are not involved in controlling gene expression. (nature.com)
- The homology suggests gene transfer between eukaryotic (+) and (-)ssRNA viruses. (elifesciences.org)
- Murphy K, O'Sullivan O, Rea MC, Cotter PD, Ross RP, Hill C (2011) Genome Mining for Radical SAM Protein Determinants Reveals Multiple Sactibiotic-Like Gene Clusters. (plos.org)
- This method uses the gene for azurin from P. aeruginosa as an expression system for azurin or heterologous proteins in P. aeruginosa or heterologous cells. (google.com)
- This gene encodes an RNA binding protein. (genecards.org)
- RBM17 (RNA Binding Motif Protein 17) is a Protein Coding gene. (genecards.org)
- Angiogenin is a protein of 14.1 kDa encoded by ANG gene and belongs to a superfamily of pancreatic ribonuclease A. Angiogenin is an effective stimulator of new blood vessels formation. (omicsonline.org)
- Ataxin-3 is a protein that in humans is encoded by the ATXN3 gene. (wikipedia.org)
- The protein encoded by the ATXN3 gene contains (CAG)n repeats in the coding region, and the expansion of these repeats from the normal 13-36 to 68-79 is the cause of Machado-Joseph disease. (wikipedia.org)
- In most of these proteins, the coiled-coil domains are flanked by protein domains that control the protein's distribution or specific function. (genetics.org)
- Methods commonly used to study protein structure and function include immunohistochemistry , site-directed mutagenesis , X-ray crystallography , nuclear magnetic resonance and mass spectrometry . (wikipedia.org)
- Review of Protein Chemistry and Structure. (umass.edu)
- Before the PSI launched, determining the structure of a relatively complex protein was a major task, requiring the efforts of a graduate student for several months or even years, says Keith Hodgson, PhD , professor of chemistry at Stanford and head of the JCSG structure determination unit. (biomedicalcomputationreview.org)
- Inhibition of p97-dependent protein degradation by Eeyarestatin I". The Journal of Biological Chemistry. (wikipedia.org)
- What is the relationship between a proteins evolutionary rate and its degree? (slideserve.com)
- SCOPmap: Automated assignment of protein structures to evolutionary superfamilies. (ebscohost.com)
- Thus a significant drawback to the use of evolutionary-based protein structure classifications is the difficulty in assigning new proteins to unique positions in the. (ebscohost.com)
- Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information. (ebscohost.com)
- In this work, we generated and optimized a new synthetic fusion protein using an evolutionary approach. (hindawi.com)
- Presumably, sequence elements conserved across long evolutionary times are likely to be essential to the structural or functional success of a protein family ( 7 ). (mcponline.org)
- Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. (elifesciences.org)
- Evolutionary covariation based structural model of E. coli YidC. (elifesciences.org)
- For this reason recombinant proteins are often produced in the necessary quantity, and then impurities removed, followed by refolding of the protein and crystallographic study. (news-medical.net)
- The recombinant TAG protein was expressed and purified to determine oligomeric state using size exclusion chromatography, which showed the existence of TAG protein as monomer (mwt ∼21kDa). (crg.eu)
- The Plant Protein Club is a pre-competitive science and technology club with membership drawn from industry, academia and government which aims to stimulate efficient progress in the fundamental understanding, use and manipulation of native and recombinant plant proteins to mee the needs of industry. (bio.net)
- In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information. (mdpi.com)
- The iterative threading assembly refinement (I-TASSER) server is an integrated platform for automated protein structure and function prediction based on the sequence-to-structure-to-function paradigm. (nih.gov)
- The function of the protein is then inferred by structurally matching the 3D models with other known proteins. (nih.gov)
- This protocol provides new insights and guidelines for designing of online server systems for the state-of-the-art protein structure and function predictions. (nih.gov)
- This protein family includes a few representative members: the first, carboxymuconolactone decarboxylase, is involved in biodegradation of monocyclic aromatic carbon sources, the second, alkyl hydroperoxidase, is related to protecting against oxidative stress and the third has an unknown function. (biomedcentral.com)
- Pfam has two large series of functionally uncharacterized families, known as Domains of Unknown Function (DUFs) and Uncharacterized Protein Families (UPFs). (pubmedcentralcanada.ca)
- The Pfam protein family DUF178 (ID: PF02621) consists of 61 proteins of unknown function, 59 from bacteria and 2 from archaebacteria [ 2 ]. (pubmedcentralcanada.ca)
- In this intensive course students will investigate the interrelationships existing amongst protein sequence, structure, and function through the lens of a structural bioinformaticist. (brandeis.edu)
- Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes . (wikipedia.org)
- and attribute function to unknown proteins. (bio.net)
- The examples will demonstrate how modern software and modelling can inform research into protein function. (bio.net)
- 3-D Structural Analysis of Protein Interaction Networks Gives New Insight Into Protein Function, Network Topology and Evolution. (slideserve.com)
- Oliver Daumke of the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) is investigating the function and spatial structure of these EHD proteins. (eurekalert.org)
- The FFAS03 server provides a web interface to the third generation of the profileï¿½profile alignment and fold-recognition algorithm of fold and function assignment system (FFAS) [L. Rychlewski, L. Jaroszewski, W. Li and A. Godzik (2000), Protein Sci. (ebscohost.com)
- It plays an important role in protein sequence database search, protein structure prediction, protein function prediction, and phylogenetic. (ebscohost.com)
- The ubiquitin-like modifier (UBL) SUMO (Small Ubiquitin-Like Modifier) regulates protein function. (wur.nl)
- Two features in particular stand out: the turrets, which are proposed to function in host recognition and DNA translocation, and two electron-dense layers sandwiched between the protein capsid and the packaged genome that may be composed of lipids ( 30 ) (Fig. 1 ). (asm.org)
- 1998, Kinetic steps for alpha-helix formation Proteins: Structure, Function and Genetics, 33: (3) 343-357. (cityofhope.org)
- Thus, while there appears to be conservation in terms of specificity, function, and activation of signaling through both EDS1 and NDR1 in terms of R protein structure, the full mechanism(s) associated with these pathways is unknown. (plantphysiol.org)
- The basic structure consists of thirteen proteins necessary for function  . (kenyon.edu)
- These proteins have a high degree of conservation across type six secretion systems, and have been experimentally determined to be required for T6SS function, but their exact purpose remains unclear  . (kenyon.edu)
- Despite continued interest in the olfactomedin domain-containing (ODC) proteins, the native function has not been determined for any of these proteins. (mcponline.org)
- Protein domain prediction is important for protein structure prediction, structure determination, function annotation, mutagenesis analysis and protein engineering. (psu.edu)
- The three other deletions result in proteins with full zygotic function, but with affected ovarian function. (genetics.org)
- Bic-D and Egl proteins are found in a complex ( M ach and L ehmann 1997 ) and are likely to function together, but how they do it remains to be elucidated. (genetics.org)
- To test the functional importance of the heptad repeat domains in Bic-D, and to further understand its function, we have undertaken a structure-function analysis of the Bic-D protein. (genetics.org)
- Barclay A. Signal regulatory protein alpha (SIRPalpha)/CD47 interaction and function. (labome.org)
- The main function of proteins containing this domain appears to be to act as accessory clathrin adaptors in endocytosis, epsin is able to recruit and promote clathrin polymerisation on a lipid monolayer, but may have additional roles in signalling and actin regulation. (wikipedia.org)
- Casein-degrading serine protease autotransporter of enterobacteriaceae (SPATE) subfamily protein SigA, an outer membrane protein, exerts both cytopathic and enterotoxic effects especially cytopathic to human epithelial cell type-2 (HEp-2) and is shown to be highly immunogenic. (hindawi.com)
- We determined that TMEM14C, an inner mitochondrial membrane protein that is enriched in vertebrate hematopoietic tissues, is essential for erythropoiesis and heme synthesis in vivo and in cultured erythroid cells. (jove.com)
- The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. (elifesciences.org)
- This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. (elifesciences.org)
- Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion. (elifesciences.org)
- Further experiments also identified the amino acids in the YidC protein that interact with the newly built membrane protein, thus revealing where it might leave the YidC protein and be inserted into the membrane. (elifesciences.org)
- This central lipid plug is reminiscent of those reported for other membrane protein oligomers such as bacteriorhodopsin9. (nih.gov)
- She organized two international summer schools on membrane protein production for structural analysis and two international congresses on membrane biophysics. (springer.com)
- PDP: protein domain parser. (rcsb.org)
- A similar protein domain is also present in E. coli Fnr and is essential for the oxygen-regulated activity of this protein. (uni-bielefeld.de)
- Proteins which are included in this group present an amino-terminal cytoplasmic domain followed by a membrane-spanning hydrophobic domain and at least one extracellular triple-helical collagenous domain alternated with short non-collagenous domains. (wikidoc.org)
- Crystal structure analysis of the apo form of catabolite control protein A reveals the three-helix bundle of the DNA-binding domain. (iucr.org)
- In the crystal packing, this domain interacts with the binding site for the corepressor protein. (iucr.org)
- Topics covered range from analysis of protein structure to domain classification, phylogeny, structural modeling, interaction site prediction, and structure-based drug design. (brandeis.edu)
- 2017): "Structural insights into the activation mechanism of dynamin-like Eps15-homology domain proteins. (eurekalert.org)
- We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein. (hindawi.com)
- To understand the structural basis of ZIP4 dysfunction caused by the AE-causing mutations and to facilitate drug discovery of ZIP4 inhibitors, we previously solved the crystal structure of the extracellular domain (ECD) of a mammalian ZIP4 ( 10 ), demonstrating that ZIP4-ECD is a crucial regulatory domain for optimal zinc transport. (sciencemag.org)
- The ZIP family consists of thousands of integral membrane proteins throughout the three kingdoms of life, and all of its members share a conserved transmembrane domain (TMD) with eight transmembrane helices (TMs). (sciencemag.org)
- Calponin homology (CH) domain profile. (pdbj.org)
- Thus, homology modeling studies suggest a potential mechanism whereby the D614G mutation may confer a competitive advantage at the furin binding domain that may contribute to the rise of the D614G SARS-CoV-2 mutant. (preprints.org)
- Our previous work has established that the relationship between the TIGR ( t rabecular-meshwork i nducible g lucocorticoid r esponse) (also known as myocilin) and olfactomedin proteins is evident not only in the C-terminal olfactomedin domain but also in the N-terminal domain of both proteins ( 1 ). (mcponline.org)
- curate, hybrid domain prediction server (DOMAC) that integrates homology modeling, domain parsing and ab initio methods together. (psu.edu)
- The preliminary implementation of the server [under the name: FOLDpro =-=(25)-=-] participated in the domain evaluation in the seventh edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7) (26,27). (psu.edu)
- Here we describe an accurate protein domain prediction server (DOMAC) combining both template-based and ab initio methods. (psu.edu)
- 221] Iyer MS, Joshi AG, Sowdhamini R. Genome-wide survey of remote homologues for protein domain superfamilies of known structure reveals unequal distribution across structural classes. (ncbs.res.in)
- 2005), could cooperate with the SH2-like domain to enhance clustering of RTK-GIV complexes at the PM. We propose that the SH2-like domain is key to achieve targeting and proximity of GIV to RTKs, which allows GIV to integrate incoming signals from these receptors and modulate them via activation of G proteins in the vicinity of the receptors. (nih.gov)
- Previously we noted a structural homology between the NB domain of NLRs and DNA replication origin-binding Cdc6/Orc1 proteins. (dur.ac.uk)
- Cliff M, Harris R, Barford D, Ladbury J, Williams M. Conformational diversity in the TPR domain-mediated interaction of protein phosphatase 5 with Hsp90. (labome.org)
- The epsin N-terminal homology (ENTH) domain is a structural domain that is found in proteins involved in endocytosis and cytoskeletal machinery. (wikipedia.org)
- This domain is approximately 150 amino acids in length and is always found located at the N-termini of proteins. (wikipedia.org)
- Proteins containing this domain have been found to bind PtdIns(4,5)P2 and Ins(1,4,5)P3 suggesting that the domain is a membrane-interacting module. (wikipedia.org)
- At that homology level, there are likely to be only a few gaps in the alignment, the alignment is likely to be accurate, and the template's 3D structure is likely to be close to the actual target structure. (bio.net)
- DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. (bio.net)
- (1) The choice of template(s) and initial alignment are the first challenges in homology modeling. (frontiersin.org)
- Summary: Sequence-to-structure alignment in template-based protein structure modeling for remote homologs remains a difficult problem even following the correct recognition of folds. (ebscohost.com)
- Real-SPINE is trained with a large data set of 2640 protein chains, sequence profiles generated from multiple seq-uence alignment, representative amino-acid prop-erties, a slow learning rate, overfitting protection, and predicted secondary structures. (psu.edu)
- The phylogenetic relationship of canine lysyl oxidase with a vast range of mammalian species indicates that the protein was very well conserved throughout the course of evolution. (springer.com)
- In mammalian cells, the Zrt/Irt-like protein (ZIP) family [solute carrier family 39A (SLC39A)] and the ZnT family are responsible for zinc influx and efflux, respectively ( 3 - 5 ). (sciencemag.org)
- Derived homologous models of different single point variants with model evaluations suggested that Pro 140 of HutZ, corresponding to Phe 215 of HugZ, might have been the main contributor to the structural mismatch. (pubmedcentralcanada.ca)
- However, the existing threading tools perform poorly on remote homologous proteins. (ebscohost.com)
- Hcp, or Hemolysin Coregulated Protein, is homologous to the major tail protein, gpV, in phage  . (kenyon.edu)
- VgrG, or Valine-Glycine Repeat Protein G, is homologous to the gp27/gp5 complex, or the tailspike of bacteriophage T4  . (kenyon.edu)
- These two proteins complex in a manner homologous to the T4 sheath  . (kenyon.edu)
- They screened 33 transgenic proteins for continuous runs of at least 6 amino acids identical to known allergenic proteins. (i-sis.org.uk)
- One of the first steps in assessing if a protein is potentially allergenic is to compare its amino acid sequence with those of known allergenic proteins stored in computer databases, using available computer algorithms. (i-sis.org.uk)
- 85% homology (% sequence identity? (bio.net)
- When choosing templates, both sequence identity and structure quality are important for homology modeling and pose the first of many challenges in the modeling process. (frontiersin.org)
- The primary structure, or amino acid sequence identity, of the proteins between paralogs is ~60% identical and between orthologs is ~90%, whilst between vertebrates and Drosophila or C. elegans is only 33-41% identical. (wikipedia.org)
- Cryoelectron microscopy is a variant at temperatures at or below that of liquid nitrogen and can visualize protein structures at very high resolution, though is less than that of methods like NMR spectroscopy or crystallography. (news-medical.net)
- This protein was the first to have its structure solved by X-ray crystallography . (wikipedia.org)
- Structure determination consists of multiple steps including cloning, expressing, and purifying a protein, finding appropriate conditions for crystallizing the protein, performing structural analysis by techniques such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, and analyzing the resulting data. (biomedicalcomputationreview.org)
- thus it results in very detailed data on atomic arrangement within a rigid protein with other neighboring ions, ligands and molecules, but may not work so well with proteins which have large flexible domains and therefore do not form precisely ordered crystalline structures. (news-medical.net)
- Proteins perform a vast array of functions within organisms , including catalysing metabolic reactions , DNA replication , responding to stimuli , providing structure to cells and organisms , and transporting molecules from one location to another. (wikipedia.org)
- Comparing the active and inactive protein structures, they discovered that EHD molecules flip open when they bind to the membrane, exposing specialized regions. (eurekalert.org)
- and some of these membrane proteins act as channels that allow molecules to enter and leave the cell, while others allow the cell to communicate with its surroundings. (elifesciences.org)
- These heptad repeats usually mediate the packaging of one helix against another, forming coiled-coil structures made up of two or three protein molecules and resulting in homo- or heterodimers, or in multimers. (genetics.org)
- This development offers the possibility to complement the repertoire of in silico ADMET methods with protein-structure based approaches. (smi-online.co.uk)
- Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism . (wikipedia.org)
- Digestion breaks the proteins down for use in the metabolism. (wikipedia.org)
- Several aspects of ADMET relevant processes such as plasma protein binding, active transport, cytochrome P450 inhibition, metabolism and induction will be discussed in molecular detail. (smi-online.co.uk)
- Zrt/Irt-like proteins (ZIPs) play fundamental roles in metal metabolism/homeostasis and are broadly involved in numerous physiological and pathological processes. (sciencemag.org)
- Cholesterol and its numerous oxygenated derivatives (oxysterols) profoundly affect the biophysical properties of membranes, and positively and negatively regulate sterol homoeostasis through interaction with effector proteins. (biochemj.org)
- Sequence analysis and structural predication of virion-associated viral proteins suggest that they may have roles in DNA packaging, penton formation, and protein-protein interaction. (asm.org)
- Homology modeling, also known as comparative modeling, is used for constructing protein models based on template structures of homolog proteins. (frontiersin.org)
- Since discovery of teneurins in Drosophila, many other laboratories have independently described the Ten-a and Ten-m/Odz homolog proteins in different vertebrates. (wikipedia.org)
- Known structures for this family include the trimer Mycobacterium tuberculosis AhpD [ 1 - 3 ], the hexameric protein TTHA0727 from Thermus thermophilus [ 4 ] and some additional hexameric hypothetical proteins from thermophilic and methanobacteria from structural genomics consortium efforts. (biomedcentral.com)
- Here optimized molecular modeling approaches were used to provide a structural scaffold of TAG. (crg.eu)
- This residue shift also emphasized a limitation of the traditional template selection criterion for homology modeling. (pubmedcentralcanada.ca)
- In the absence of known crystal structures, researchers rely on homology modeling to construct template-based theoretical structures for drug design and testing. (frontiersin.org)
- Homology modeling of hNET can be improved using template models of dopamine and serotonin transporters instead of the leucine transporter (LeuT). (frontiersin.org)
- The extracellular domains of ALK and TrkB are yet to be exploited by homology modeling. (frontiersin.org)
- In this perspective article, we have highlighted the main structural issues in homology modeling of three candidate cell surface proteins for neuroblastoma targeted therapy. (frontiersin.org)
- In the next section, we emphasize the challenges faced in each step in the homology modeling process. (frontiersin.org)
- While the technical aspects of this manuscript favor an audience of specialists working on drug discovery and homology modeling of these three targets, the same principles of model evaluation and challenging issues can be applied for other homology models. (frontiersin.org)
- Despite the lack of crystal structures for CB1, protein-based homology modeling approaches and molecular docking methods can be used in the design and discovery of cannabinoid analogues. (springer.com)
- Summary: The protein structure prediction approaches can be categorized into template-based modeling (including homology modeling and threading) and free modeling. (ebscohost.com)
- The structures of Fab fragments not determined crystallographically were predicted by homology modeling according to the amino acid sequence. (asm.org)
- Structural and phylogenetic modeling of highly pathogenic avian influenza virus (H5N8), EG-CA285, from migratory birds, Egypt, 2016. (cdc.gov)
- To gain insight into the consequences of the D614G mutation, homology modeling using a multi-template threading mechanism with ab initio structural refinement was performed for a region of the S protein (S591 to N710) spanning the D614G mutation and the S1 furin cleavage site. (preprints.org)
- then used a combination of theoretical modeling and other experiments to identify the amino acids in the YidC protein that bind to the ribosome: as expected, the binding takes place where the newly formed protein chain exits the ribosome. (elifesciences.org)
- Infection with Pseudomonas syringae pv tomato DC3000 expressing the bacterial effector proteins AvrRpt2, AvrB, and AvrPphB activates resistance by the aforementioned R proteins. (plantphysiol.org)
- Ribosomal proteins are expressed as part of transcription units (operons) composed of other ribosomal proteins. (nature.com)
- The functions of collagen XXIII are still unknown, although it is believed that they could be similar to other transmembrane proteins, such as collagen XIII . (wikidoc.org)
- Furthermore, cellular localization of collagen XXIII was determined by immunofluorescence staining, using an antibody that recognizes the carboxyl terminus of the protein. (wikidoc.org)
- Deletion of sAnk1 did not change the expression and localization of SR proteins in 4-6 month old sAnk1 KO mice. (jove.com)
- Possible indirect effects on translation and splicing were excluded by demonstrating nuclear localization of the protein and splicing proficiency of the mutant. (genetics.org)
- Localization of the Bicaudal-D (Bic-D) protein to the presumptive oocyte is required for the accumulation of Bic-D and other mRNAs to the pro-oocyte. (genetics.org)
- In his talk at the 9th International Conference AD/PD, which unfolded 11-15 March in the Czech capital of Prague, Moir, a feisty Aussie at the Genetics and Aging Research Unit at Massachusetts General Hospital in Charlestown, came to the defense of the much maligned protein. (alzforum.org)
- Formins are key regulators of actin cytoskeletal dynamics that constitute a diverse protein family that is present in all eukaryotes examined. (ingentaconnect.com)
- Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton , which form a system of scaffolding that maintains cell shape. (wikipedia.org)
Classification of proteins1
- The automatic classification of proteins into groups is one of the major objectives for mining the increasing amount of data released by genomic and metagenomic sequencing projects. (ebscohost.com)
- However, in the P. aeruginosa protein, helices H3, H4 of this motif are located at the N-terminal part of the chain, while in M. tuberculosis AhpD, the corresponding helices H8, H9 are situated at the C-terminus. (biomedcentral.com)
- [email protected]: a high-throughput protein structure prediction server based on remote homologue recognition. (ebscohost.com)
- At the same time, protein structure prediction helps fill in the gaps between known and unknown structures, bringing us closer to knowing the "structure of everything. (biomedicalcomputationreview.org)
- The internal diameter of the tubule suggests that the T6SS can theoretically transport globular proteins up to 50 kDa  . (kenyon.edu)
- By now it is well documented that proteins with a large degree tend to be essential proteins in yeast. (slideserve.com)
- ABSTRACT Proteins can move freely in three-dimensional space. (psu.edu)
Prediction of protein structural2
- Proteins are allosteric nanomachines whose conformational dynamics confer their functional versatility. (cityofhope.org)
- That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. (mdpi.com)
- p>This section provides any useful information about the protein, mostly biological knowledge. (uniprot.org)
- Like other biological macromolecules such as polysaccharides and nucleic acids , proteins are essential parts of organisms and participate in virtually every process within cells . (wikipedia.org)
- In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
- and ultimately develop innovative strategies for delivering useful structural information to the greater biological community. (biomedicalcomputationreview.org)
- Lectins are specific carbohydrate-binding proteins: - Enormous diversity of carbohydrates have biological significance: Different monosaccharides can be joined to one another through any several -OH groups. (wikibooks.org)
- The fact that they can regulate their own expression is not surprising given the advantages of such feedback processes, it only requires that the gene's own DNA or RNA be included in the target list for the protein. (nature.com)
- Is there a relationship between a proteins connectivity and expression profile? (slideserve.com)
- Grb10 is expressed in insulin target tissues such as fat and muscle, but the highest expression of this protein is in pancreas of adult mice ( 11 ). (diabetesjournals.org)
- in 1999 from the original name, Ten-a, and the major site of the protein expression being in the nervous system. (wikipedia.org)