Homology protein structure secondary. Medical search. Frequent questions

HSSP (Homology-derived Secondary Structure of Proteins) is a database that combines structural and sequence information about proteins. (wikipedia.org)
The first task performed by VLDP is to build the Laguerre, or weighted Voronoi, diagram of the data, typically a set of positions describing the molecular structure as provided by bio-structural techniques, e.g. crystallography, NMR spectroscopy or simulation (molecular dynamics, Monte-Carlo, etc. (nature.com)
Structure of the EGL-1/CED-9 complex revealed that EGL-1 adopts an extended alpha-helical conformation and induces substantial structural rearrangements in CED-9 upon binding. (nih.gov)
Three interesting score when comparing two structures for their structural similarity are the Cα RMSD , the all-atom RMSD and the TM Score . (tu-muenchen.de)
The non-structural proteins NS1 and NS5 of all four DENV strains show more than 65 percent similarity index in 3D structure analysis. (als-journal.com)
Structural and functional characterization of the kindlin-1 pleckstrin homology domain. (ox.ac.uk)
It has a structural and functional homology with matrix protein fibrillin-1 and fibrillin-2. (org.pk)
Results revealed the secondary, tertiary structural changes along with changes in free energy of folding, volume and accessible surface area. (uni-mysore.ac.in)
Thus, the structural changes in the mutated proteins impaired the normal function of GATA4. (uni-mysore.ac.in)
The modeled structure proves fairly resilient, with no significant changes at the secondary or tertiary structural levels. (elsevierpure.com)
However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
A novel DNA-binding motif shares structural homology to DNA replicationand repair nucleases and polymerases. (embl.de)
This new DNA-binding motif shares structuralhomology with T4 RNase H, E. coli endonuclease III and Bacillus subtilisDNA polymerase I. The structural homology suggests a mechanism forsubstrate recognition by these enzymes. (embl.de)
Structural and biophysical data show that ASTN-2 (but not ASTN-1) binds inositol triphosphates, suggesting a mechanism for membrane recognition or secondary messenger regulation of its activity. (ox.ac.uk)
Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. (beds.ac.uk)
Implicitly, this refers to a high level of similarity among comparable structural elements across the sequences so that a common structural fold among these homologs is maintained which, in turn, governs the general biological function of this homologous protein family. (beds.ac.uk)
The minimal essential sequences of yeast U1 can be drawn in a secondary structure which resembles metazoan U1 in four of seven structural domains. (umn.edu)
The structural and functional annotation of bu PAG2 shall allow the designing of mutants and inhibitors for dissection of the exact physiological role of the protein. (biomedcentral.com)
The viral genome encodes four structural capsid proteins (VP1 to VP4) and seven nonstructural (NS) proteins, the leader Lb/ab protease, and proteins encoded in the P2 (2B and 2C) and P3 (3A, 3B, 3C, and 3D) regions ( 9 ). (asm.org)
The secondary structural analysis further validates the stability owing to higher α-helices. (springeropen.com)
Domains of unknown function are proteins that have been identified experimentally but do not have a known functional or structural domain. (aquaticfood.org)
The current view of protein folding and stability is largely based on SAXS and DLS data13-16 and the extensive exposure of hydropho- a generic structural classification into native (N), compact dena- bic residues suggested by the finding that the heat capacity of the tured or molten globule (MG), and unfolded or denatured (D) MG state is midway between that of the N and D states7 have been conformational states1-10. (lu.se)
Inferences about hydration have usually been indirect (where the ous structural and dynamic information about the internal peptide chain is not, there is solvent) or have relied on uncertain (buried) and external (surface) hydration of globular proteins in premises. (lu.se)

The links to the Web sites in the following list focus on protein sequences. (dummies.com)
This entailed mining available transcriptomic and/or genomic sequence datasets for the presence of homologues of known TIMPs, predicting secondary structures of defined protein sequences, systematic phylogenetic analyses and assessment of differential expression of genes encoding putative TIMPs in the developmental stages of A. suum , N. americanus and Schistosoma haematobium which infect the mammalian hosts. (biomedcentral.com)
A total of 15 protein sequences with high homology to known eukaryotic TIMPs were predicted from the complement of sequence data available for parasitic helminths and subjected to in-depth bioinformatic analyses. (biomedcentral.com)
It is based on an alignment of the target sequence and one or more template sequences with known secondary structures. (tu-muenchen.de)
There are also many other features provided by MODELLER like de novo modelling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, and so on. (tu-muenchen.de)
The coding sequences (CDs) and protein sequences of newly reported dengue strains (DENV 1, DENV 2, DENV 3, and DENV 4) were obtained from the National center for Biotechnology Information (NCBI) nucleotide and protein databases. (als-journal.com)
Among the conspicuous characteristics featuring its hyperthermophilic adaptation are overrepresentation of purine bases in protein coding sequences, higher GC-content in tRNA/rRNA sequences, distinct synonymous codon usage, enhanced usage of aromatic and positively charged residues, and decreased frequencies of polar uncharged residues, as compared to those in mesophilic organisms. (biomedcentral.com)
Pairwise comparison of 105 orthologous protein sequences shows a strong bias towards replacement of uncharged polar residues of mesophilic proteins by Lys/Arg, Tyr and some hydrophobic residues in their Nanoarchaeal orthologs. (biomedcentral.com)
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)
First, the sequences carrying point mutations are modeled on a given template structure, and subsequently, molecular dynamics simulations are carried out for 10 ns. (hindawi.com)
Furthermore, against the backdrop that the number of well-studied proteins continues to grow at a slow rate, it necessitates for a search methodology to dive deeper into the sequence similarity space to connect the unknown sequences to the well-studied ones, albeit more distant, for biological function postulations. (beds.ac.uk)
In contrast, the essential 5′ and 3′ terminal domains correspond to phylogenetically conserved sequences and/or structures previously implicated in RNA:RNA and RNA:protein interactions. (umn.edu)
M ODELLER can also perform multiple comparison of protein sequences and/or structures, clustering of proteins, and searching of sequence databases. (salilab.org)
10.4194/AFS37 - Unknown or hypothetical proteins exist, but they have yet to be identified or correlated to gene sequences. (aquaticfood.org)
Phylogenetic analyses of RRV envelope glycoprotein E2 and nonstructural protein nsP3 nucleotide sequences segregated the RRV isolates obtained in 2016 and 2017 outbreaks into 2 distinct sublineages, suggesting that each outbreak was caused by a different strain of RRV. (cdc.gov)

The secondary structure was predicted using the PSIPRED and GOR4 prediction methods, the lowest energy CYP7B1 model was generated using MOE, and then this model was assessed in terms of stereochemical quality and the side chain environment using RAMPAGE, Verify3D and ProSA. (nih.gov)
For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. (nature.com)
Chia-Tzu Ho, Yu-Wei Huang, Chia-Hua Lo, Wei-Cheng Lo * (2021, Nov). Discovering the ultimate limits of protein secondary structure prediction. (nctu.edu.tw)
A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction. (nctu.edu.tw)
The influence of dataset homology and a rigorous evaluation strategy on protein secondary structure prediction. (nctu.edu.tw)
A simple strategy to enhance the speed of protein secondary structure prediction without sacrificing accuracy. (nctu.edu.tw)
Yun-Tzai Lee, Tz-Hsiang Su, Wei-Cheng Lo , Ping-Chiang Lyu* and Shih-Che Sue* (2012, Aug). Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein. (nctu.edu.tw)
The prediction performance of Dicer cleavage site improved significantly from 66% to 86% when we integrated secondary structure information. (biomedcentral.com)
Given the availability of 3D structures of these homologous proteins, the prediction of PAG structure from its amino acid sequence at high confidence levels is implicit. (biomedcentral.com)

An extensive bioinformatics analysis of the coronavirus replicase proteins by Snijder et al. (pdfroom.com)
A secondary goal that should be sought by a bioinformatics facility is to make algorithms and analysis methods accessible for non-computational biologists. (lu.se)

Characterization of the dead ringer gene identifies a novel, highlyconserved family of sequence-specific DNA-binding proteins. (embl.de)
Although homology-modeled structures may often not be accurate enough to allow characterization of protein-protein or protein-inhibitor interactions at the atomic level, they can suggest which sequence regions or individual amino acids are essential functional components of the protein. (biomedcentral.com)

They are classified into 5 groups according to substrate specificity and internal homology: collagenases, gelatinases, stromelysins, membrane-type MMPs, and others, including matrilysins 8 . (bvsalud.org)

A molecular modeling of the structure of L. miliaris Hb, on the other hand, allows us to conclude that the residues Glu43β(CD2) and Glu101β(G3) are not essential in the maintenance of the tetrameric form, supporting our findings and allowing us to rule out the hypothesis proposed in the literature for the Hb of Liophis miliaris and other species of snakes. (eurekaselect.com)
VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
In turn, fold conservation implies the conservation of a sequence pattern of hydrophilic/hydrophobic and size-restricted residues within the protein family. (beds.ac.uk)
A molecular model of the FMDV 3A protein, derived from the nuclear magnetic resonance (NMR) structure of the poliovirus 3A protein, predicted a hydrophobic interface spanning residues 25 to 44 as the main determinant for 3A dimerization. (asm.org)
Replacements L38E and L41E, involving charge acquisition at residues predicted to contribute to the hydrophobic interface, reduced the dimerization signal in the protein ligation assay and prevented the detection of dimer/multimer species in both transiently expressed 3A proteins and in synthetic peptides reproducing the N terminus of 3A. (asm.org)
The fACCD were found 16.18-82.47 kDa proteins having 149-750 amino acid residues. (springeropen.com)
Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. (pdfroom.com)

More generally, the input to the program are restraints on the spatial structure of the amino acid sequence(s) and ligands to be modeled. (salilab.org)
The primary amino acid sequence of a protein is a translated version from its gene sequence which carries important messages and information concealed therein. (springeropen.com)

A simplistic similarity approach in the case of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc.) is not justified and a pertinent source for mistaken homologies. (beds.ac.uk)
Based on our previous work of dissecting the hidden markov model (HMMER) based similarity score into fold-critical and the non-globular contributions to improve homology inference, we propose a framework-dissectHMMER, that identifies more fold-related domain hits from standard HMMER searches. (beds.ac.uk)
Briefly, the technical problems as to how to recognize non-globular parts in the domain model, resolve contradictory HMMER2/HMMER3 results and evaluate fold-related domain hits for homology, are addressed in this work. (beds.ac.uk)
A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand �-sheet holding two �-helices of three and four turns that are oriented antiparallel to the �-strands. (pdfroom.com)
This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold. (pdfroom.com)

Polymorphisms that slightly vary native peptides or inflammatory processes set the stage for abnormal protein folding and amyloid fibril deposition. (medscape.com)
Amyloid fibrils are formed by proteins or peptides, that under certain conditions self-assemble into characteristic fibrillar structures [ 1 ] . (encyclopedia.pub)

Native or wild-type quaternary protein structure is usually born from a single translated protein sequence with one ordered conformation with downstream protein interactions. (medscape.com)
PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). (bvsalud.org)

Foot-and-mouth disease virus (FMDV) nonstructural protein 3A plays important roles in virus replication, virulence, and host range. (asm.org)
The coronavirus replication cycle begins with the translation of the 29-kb positive-strand genomic RNA to produce two large polyprotein species (pp1a and pp1ab), which are subse- quently cleaved to produce 15 or possibly 16 nonstructural proteins (nsp's) (11). (pdfroom.com)

To evaluate the potential impact of CYP7B1 mutations identified in SPG5 on binding and protein function, a comparative model of cytochrome P450 7B1 (CYP7B1) was constructed using human CYP7A1 as a template during model construction. (nih.gov)
MODELLER is used for homology or comparative modelling of protein three-dimensional structures. (tu-muenchen.de)
To predict ARDs in the intestinal microbiota, we developed a method based on protein homology modelling (see Methods) that we termed pairwise comparative modelling (PCM). (nature.com)
M ODELLER is most frequently used for homology or comparative protein structure modeling: The user provides an alignment of a sequence to be modeled with known related structures and M ODELLER will automatically calculate a model with all non-hydrogen atoms. (salilab.org)
These include related protein structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc . (salilab.org)

There are 12193 ARID domains in 12162 proteins in SMART's nrdb database. (embl.de)
A novel class of DNA-binding domains has been established from at leastsixteen recently identified DNA-binding proteins. (embl.de)
We show that dri encodes a nuclear protein that contains asequence-specific DNA-binding domain that bears no similarity to knownDNA-binding domains. (embl.de)
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. (bvsalud.org)

The problems of protein fold recognition and remote homology detection have recently attracted a great deal of interest as they represent challenging multi-feature multi-class problems for which modern pattern recognition methods achieve only modest levels of performance. (videolectures.net)
1.00 means the two compared structures are in about the same fold and therefore the predicted model has a correct topology. (tu-muenchen.de)
The annexin-like domain is closest in fold to repeat three of human annexin V and similarly binds calcium, and yet shares no sequence homology with it. (ox.ac.uk)
The proposed framework-dissectHMMER, is faithful to the original inception of the sequence homology concept while improving upon the existing HMMER search tool through the rescue of statistically evaluated false-negative yet fold-related domain hits to the query sequence. (beds.ac.uk)
In simple terms, the highest abstraction of a biological function is conferred by the protein fold. (beds.ac.uk)
Yeast U1 snRNA (568 nucleotides) is 3.5-fold larger than its mammalian counterpart (164 nucleotides) and contains apparent sequence homology only at the 5′ and 3′ ends. (umn.edu)
Considering the widely acknowledged Accordingly, theoretical models of the MG state invariably invoke importance of protein-solvent interactions for stability and fold- a substantial internal hydration20-22. (lu.se)
· http://structbio.nature.com ness, secondary structure, tertiary fold, and side-chain packing. (lu.se)

Cytochrome P460 was shown to have a good sequence homology with MCCP Bath along with a similar predicted highly beta sheet secondary structure which suggests an evolutionary history between the two proteins. (essex.ac.uk)
Mainly, with the high degree of evolutionary conservation in the innate immunity of the gut and similarities in the enteric epithelial structure, Manduca sexta can serve as a model for human gut inflammation. (uni-giessen.de)
In this work, we generated and optimized a new synthetic fusion protein using an evolutionary approach. (hindawi.com)
The present study unveils the structure-function and evolutionary aspects of 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) proteins of fungal origin. (springeropen.com)

Given the tight relation between protein structure and function, we present a set of methods to analyze protein topology, implemented in the VLDP program, relying on Laguerre space partitions built from series of molecular dynamics snapshots. (nature.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)
Out of the variety of methods to be used for this topic, we chose homology modeling as a first approach to our goal. (tu-muenchen.de)
The hydration of nonnative states is central to protein folding and stability but has been probed mainly by indirect methods. (lu.se)

This sequence is composed of 18 hydrophilic amino acids which does not share significant homology to any existing native protein. (hku.hk)
CEBPα protein was an unstable hydrophilic protein with a transmembrane structure and phosphorylation/dephosphorylation. (hbnxb.net)
The in-silico investigation documented the protein`s hydrophilic nature with predominantly alpha (α) helices in its secondary structure. (aquaticfood.org)

The 3D and 2D structures of DENV strains (1-4) show some similarity and dissimilarity index, however the four DENV strains differ in their 2D structure's alpha helix (H), random coil, and number of amino acids. (als-journal.com)
on the other hand, there are many cases of nearly identical structures known, sharing no sequence similarity at all [ 3 ]. (hindawi.com)
The early general expression ofdri and the similarity of DRI and homeodomain in vitro DNA-bindingspecificity compound the problem of understanding the in vivo specificityof action of these proteins. (embl.de)
Amyloid forming proteins do not share any similarity in sequence or native structure, albeit amyloid fibrils are characterized by a common structure, known as "cross-β" structure. (encyclopedia.pub)
The sequence homology concept [ 1 - 3 ] is collectively founded upon the inductive reasoning that a homologous protein group (as an antecedent) shares a high level of sequence similarity (as a consequent) [ 4 - 8 ]. (beds.ac.uk)
This measure comes along with the caveat of possibly high sequence similarity does not necessarily imply homology. (beds.ac.uk)

The viral particle is composed of a protein capsid that contains a positive-sense RNA molecule of about 8,500 nucleotides that is infectious and encodes a single polyprotein, which is processed in infected cells by cis - and trans -acting viral proteases ( 55 ) to yield different polypeptide precursors and the mature viral proteins ( 9 , 62 ). (asm.org)
NS proteins are involved in crucial aspects of the viral cycle and pathogenesis, such as rearrangements of intracellular membranes required for endomembrane recruitment and the lysis of host cells ( 1 , 12 , 14 , 18 , 73 ). (asm.org)
However, the development of reliable HDV RNA assays is challenged by viral heterogeneity (at least 8 different genotypes and several subgenotypes), intra-host viral diversity, rapid viral evolution, and distinct secondary structure features of HDV RNA. (cdc.gov)

A detailed understanding of the molecular biology of parasitic helminths, and in particular of the structure and function of key genes and gene products playing essential roles in host-parasite interactions, could provide a basis for the design of novel therapeutics. (biomedcentral.com)
Hydrophobicity was one of the most important physicochemical properties, due to the fact that it is involved in protein interactions, for example, by forming hydrophobic cores. (hindawi.com)
The physicochemical characteristics, subcellular localization, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein are all available from this in silico perspective. (aquaticfood.org)
Protein-protein interactions are investigated using the STRING software and resulted that VP128 putative protein interacts strongly with the GlpX type protein Fructose-1,6-bisphosphatase. (aquaticfood.org)

The deduced properties are the existence and count of water aggregates, possible passage ways and constrictions, the structure, connectivity, stability and depth of the water network. (nature.com)
Amyloidosis results from the accumulation of pathogenic amyloids-most of which are aggregates of misfolded proteins-in a variety of tissues. (medscape.com)

Examples of function annotation using dissectHMMER, including the function discovery of an uncharacterized membrane protein Q9K8K1_BACHD (WP_010899149.1) as a lactose/H+ symporter, are presented. (beds.ac.uk)
In addition, primary and secondary structure analysis and functional annotation studies were also performed. (biomedcentral.com)

As a test-case, the membrane protein FepA is investigated in its full environment, yielding a more precise description of the protein surface. (nature.com)
Membrane proteins, such as those operating transport through the membrane in a controlled way, are prone to show interesting topological properties related to their function. (nature.com)
Our study uses classical algorithms such as space partitions and Dijkstra paths search 9 , applied in an original and novel way by taking into account the full representation of a membrane protein including the solvent and the lipid bilayer (Fig. 1 ). (nature.com)
The FepA membrane protein is surrounded by a lipid bilayer separating the extracellular medium and the periplasm. (nature.com)
The traits potentially attributable to the symbiotic/parasitic life-style of the organism include the presence of apparently weak translational selection in synonymous codon usage and a marked heterogeneity in membrane-associated proteins, which may be important for N. equitans to interact with the host and hence, may help the organism to adapt to the strictly host-associated life style. (biomedcentral.com)
Structure of astrotactin-2: a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development. (ox.ac.uk)
The vertebrate-specific proteins astrotactin-1 and 2 (ASTN-1 and ASTN-2) are integral membrane perforin-like proteins known to play critical roles in neurodevelopment, while ASTN-2 has been linked to the planar cell polarity pathway in hair cells. (ox.ac.uk)
The perforin-like domain differs from that of other members of the membrane attack complex-perforin (MACPF) protein family in ways that suggest ASTN-2 does not form pores. (ox.ac.uk)
in poliovirus (PV), the interaction between the RNA replication complex and intracellular membranes appears to be accomplished by proteins 3A and 2C, which have membrane-binding properties ( 11 , 60 ). (asm.org)
They have been defined as monotropic integral membrane proteins located primarily in the endoplasmic reticulum (COX-1) and the perinuclear envelope (COX-2). (medscape.com)

The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)

Yet, this assumption is poorly supported by empirical evidence due to the distant homologies between known ARDs (mostly from culturable bacteria) and ARDs from the intestinal microbiota. (nature.com)
AtPNP-A has distant sequence homology with human ANP, a protein that forms amyloid fibrils in vivo . (encyclopedia.pub)
Worse, as we delve deeper into sequence search space, high sequence divergence among the distant homologs will inevitably corrupt the homology signal. (beds.ac.uk)

In the absence of experimentally determined protein structures, a homology-based model may serve as a good starting point for investigation of sequence-structure-function relationships. (biomedcentral.com)

The quantitative evaluation of protein structure quality was verified with Volume Area Dihedral Angle Reporter server. (uni-mysore.ac.in)

2,4 To date, mutations in LTBP2 gene are reported to cause microspherophakia, 4 microspherophakia with ectopia lentis 5 and secondary glaucoma. (org.pk)
6 LTBP2 gene (LTBP2 [MIM *602091]) has 36 exons encoding 1821 amino acid proteins with multi-domain structures. (org.pk)
Pathogenic mutations in the gene encoding the giant skeletal muscle protein titin (TTN) are associated with several muscle disorders, including cardiomyopathy, recessive congenital myopathies and limb-girdle muscular dystrophy (LGMD) type10. (biomedcentral.com)
Yak was used as the experimental object to clone the yak CCAAT/Enhancer binding protein alpha( CEBPα ) gene, predicted its protein structure and function, isolated yak adipocyte, and detected the expression of CEBPα in different tissues of yak and yak fat expression during cell induction and differentiation. (hbnxb.net)
The exact structure and function of the gene product is unknown due to limitations on obtaining purified pregnancy associated glycoprotein preparations. (biomedcentral.com)

This database has the information of the alignment of all available homologs of proteins from the PDB database As a result of this, HSSP is also a database of homology-based implied protein structures. (wikipedia.org)

Amyloid fibrils are protein polymers comprising identical monomer units (homopolymers). (medscape.com)
[ 5 ] Only 10% of amyloidosis deposits consist of components such as glycosaminoglycans (GAGs), apolipoprotein-E (apoE), and serum amyloid P-component (SAP), while nearly 90% of the deposits consist of amyloid fibrils that are formed by the aggregation of misfolded proteins. (medscape.com)
[ 6 ] In humans, about 23 different unrelated proteins are known to form amyloid fibrils in vivo. (medscape.com)

KIN17, which is known as a DNA and RNA binding protein, is highly expressed in numerous types of human cancers and was discovered to participate in several vital cell behaviors, including DNA replication, damage repair, regulation of cell cycle and RNA processing. (spandidos-publications.com)
Latent transforming growth factor beta binding protein 2 (LTBP2) plays a critical role in the development of connective tissue structure and function. (org.pk)
The first residue of the PWWP motif modulates HATH domain binding, stability, and protein-protein interaction. (nctu.edu.tw)
A homology model of the ligand binding domain of the α7 nicotinic receptor is constructed based on the acetylcholine-binding protein crystal structure. (elsevierpure.com)
The hypothesis that the acetylcholine-binding protein template is in the activated or desensitized state, and the absence of a bound agonist in the simulation suggests that the structure may also be relaxing from this state to the activatable state. (elsevierpure.com)
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)
Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. (embl.de)
Other proteins containing the conserved motifinclude yeast SWI1, two human retinoblastoma binding proteins, and othermammalian regulatory proteins. (embl.de)
Gelretardation and optimal binding site screens revealed that the in vitrosequence specificity of DRI is strikingly similar to that of manyhomeodomain proteins, although the sequence and predicted secondarystructure do not resemble a homeodomain. (embl.de)
The papillomaviral DNA replication initiation protein E1 has origin recognition and ATP-dependent DNA melting and helicase activities, and it consists of a DNA-binding domain and an ATPase/helicase domain. (cshl.edu)
Here we present the crystal structure of the monomeric HPV-18 E1 DNA-binding domain refined to 1.8-A resolution. (cshl.edu)

A novel fusion protein tag, named 'NE' - was designed as a tool for detection and purification of recombinant protein. (hku.hk)
When expressed as a recombinant protein in transfected cells, PV 3A cofractionates with endoplasmic reticulum markers ( 66 ), and its single transient expression can disrupt the secretory apparatus ( 23 ) and decrease major histocompatibility complex (MHC) class I expression ( 22 ). (asm.org)

These findings shed new light on hydrophobic stabilization of proteins. (lu.se)
Whereas the N state has been character- taken to imply that hundreds of water molecules penetrate the MG ized at high resolution, many aspects of the D and MG states are protein (except for a relatively small hydrophobic core)5,7,8,17-19. (lu.se)

As with many pattern recognition problems, there are multiple feature spaces or groups of attributes available, such as global characteristics like the amino-acid composition (C), predicted secondary structure (S), hydrophobicity (H), van der Waals volume (V), polarity (P), polarizability (Z), as well as attributes derived from local sequence alignment such as the Smith-Waterman scores. (videolectures.net)
By 1964, after recognition of this basic structure, Bergstrom and colleagues successfully synthesized series 2 prostaglandins from arachidonic acid using sheep seminal fluid. (medscape.com)

Researching Cytochrome c' structure and function 2016 - p/t PhD Biological Sciences, University of Essex. (essex.ac.uk)
The aim of this research is to elucidate the structure and function of the c-beta of Methylococcus capsulatus Bath (MCCP Bath) and to study its ability to bind to and discriminate between gaseous ligands in comparison to the more conventional four-alpha-helical cytochromes c. (essex.ac.uk)
The present review was the first, to the best of our knowledge, to systematically summarize and clarify the relevance between KIN17 and tumor development from different aspects ( Table I ), including the structure, function, expression level and regulatory mechanisms of KIN17, so as to explore the potential of KIN17 as a tumor diagnostic and prognostic biomarker and as a potential therapeutic target. (spandidos-publications.com)
Many mechanisms of protein function contribute to amyloidogenesis, including "nonphysiologic proteolysis, defective or absent physiologic proteolysis, mutations involving changes in thermodynamic or kinetic properties, and pathways that are yet to be defined. (medscape.com)
function and secondary structure]] of our protein we will determine the 3D structure as well as how much influence one, or several, SNPs has/have on this structure. (tu-muenchen.de)
Still, the distribution of ACCD in fungal species is limited which consequently limits our understanding of the structure-function aspects of the fungal ACCD (fACCD). (springeropen.com)
Evidence suggests that COX-1 and COX-2 are similar in structure and function but that they exist as 2 distinct enzymatic entities. (medscape.com)

In the present study, we conducted a large-scale investigation of TIMP proteins of a range of neglected human parasites including the hookworm Necator americanus , the roundworm Ascaris suum , the liver flukes Clonorchis sinensis and Opisthorchis viverrini , as well as the schistosome blood flukes. (biomedcentral.com)

Topology is a prominent aspect of both morphology and functioning of proteins. (nature.com)

In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)

It is helpful in the lock and key hypothesis where a drug molecule binds with a protein. (mcnsolutions.net)
Monoclonal anti-Δ42PD1 antibody is an affinity purified mouse immunoglobulin, IgG1, which binds to Δ42PD1 protein. (hku.hk)

These highly ordered structures are characterized by extreme stability, while conflicting evidence has emerged about the ability of proteases to fragment them [ 2 ] [ 3 ] . (encyclopedia.pub)

The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. (embl.de)
and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. (embl.de)

Tissue inhibitors of metalloproteases (TIMPs) are a multifunctional family of proteins that orchestrate extracellular matrix turnover, tissue remodelling and other cellular processes. (biomedcentral.com)

This structure is refined in a 10 ns molecular dynamics simulation. (elsevierpure.com)

The optimization was guided by directed evolution based on hydrophobicity scores, molecular weight, and secondary structure predictions. (hindawi.com)

Organisms1

Chemicals and Drugs12

Analytical, Diagnostic and Therapeutic Techniques and Equipment16

Phenomena and Processes32

Disciplines and Occupations2

Information Science17

Health Care1

Structural23

Sequences16

Prediction9

Bioinformatics2

Characterization2

Substrate Specificity1

Residues7

Amino Acid Seq2

Globular5

Peptides2

Conformation2

Nonstructural2

Comparative5

Domains4

Fold8

Evolutionary4

Methods5

Hydrophilic3

Similarity6

Viral3

Interactions4

Aggregates2

Annotation2

Membrane10

Encodes2

Distant3

Experimentally1

Quantitative1

Gene5

Homologs1

Amyloid fibrils3

Binding11

Recombinant protein2

Hydrophobic2

Recognition2

Function7

Investigation1

Topology1

Biological1

Binds2

Stability1

Alpha helices2

Extracellular1

Molecular Dynamics Simulation1

Predictions1