Bacteriophage T4: Virulent bacteriophage and type species of the genus T4-like phages, in the family MYOVIRIDAE. It infects E. coli and is the best known of the T-even phages. Its virion contains linear double-stranded DNA, terminally redundant and circularly permuted.Bacteriophages: Viruses whose hosts are bacterial cells.Bacteriophage T7: Virulent bacteriophage and type species of the genus T7-like phages, in the family PODOVIRIDAE, that infects E. coli. It consists of linear double-stranded DNA, terminally redundant, and non-permuted.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.T-Phages: A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Coliphages: Viruses whose host is Escherichia coli.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.Ribosomal Protein S6: A ribosomal protein that may play a role in controlling cell growth and proliferation. It is a major substrate of RIBOSOMAL PROTEIN S6 KINASES and plays a role in regulating the translation (TRANSLATION, GENETIC) of RNAs that contain an RNA 5' TERMINAL OLIGOPYRIMIDINE SEQUENCE.Protein S: The vitamin K-dependent cofactor of activated PROTEIN C. Together with protein C, it inhibits the action of factors VIIIa and Va. A deficiency in protein S; (PROTEIN S DEFICIENCY); can lead to recurrent venous and arterial thrombosis.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Leghemoglobin: A hemoglobin-like oxygen-binding hemeprotein present in the nitrogen-fixing root nodules of leguminous plants. The red pigment has a molecular weight approximately 1/4 that of hemoglobin and has been suggested to act as an oxido-reduction catalyst in symbiotic nitrogen fixation.Cytochromes b: Cytochromes of the b group that have alpha-band absorption of 563-564 nm. They occur as subunits in MITOCHONDRIAL ELECTRON TRANSPORT COMPLEX III.Phenylmethylsulfonyl Fluoride: An enzyme inhibitor that inactivates IRC-50 arvin, subtilisin, and the fatty acid synthetase complex.MercaptoethanolIce: The solid substance formed by the FREEZING of water.Smad3 Protein: A receptor-regulated smad protein that undergoes PHOSPHORYLATION by ACTIVIN RECEPTORS, TYPE I. Activated Smad3 can bind directly to DNA, and it regulates TRANSFORMING GROWTH FACTOR BETA and ACTIVIN signaling.Ribonuclease, Pancreatic: An enzyme that catalyzes the endonucleolytic cleavage of pancreatic ribonucleic acids to 3'-phosphomono- and oligonucleotides ending in cytidylic or uridylic acids with 2',3'-cyclic phosphate intermediates. EC 3.1.27.5.Chromatography, Affinity: A chromatographic technique that utilizes the ability of biological molecules to bind to certain ligands specifically and reversibly. It is used in protein biochemistry. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Smad4 Protein: A signal transducing adaptor protein and tumor suppressor protein. It forms a complex with activated RECEPTOR-REGULATED SMAD PROTEINS. The complex then translocates to the CELL NUCLEUS and regulates GENETIC TRANSCRIPTION of target GENES.BooksHydrogen Bonding: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Protein Conformation: 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).Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Sequence Alignment: 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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Molecular Dynamics Simulation: A computer simulation developed to study the motion of molecules over a period of time.Thermodynamics: A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)Awareness: The act of "taking account" of an object or state of affairs. It does not imply assessment of, nor attention to the qualities or nature of the object.Artifacts: Any visible result of a procedure which is caused by the procedure itself and not by the entity being analyzed. Common examples include histological structures introduced by tissue processing, radiographic images of structures that are not naturally present in living tissue, and products of chemical reactions that occur during analysis.Self Concept: A person's view of himself.Ego: The conscious portion of the personality structure which serves to mediate between the demands of the primitive instinctual drives, (the id), of internalized parental and social prohibitions or the conscience, (the superego), and of reality.Rationalization: A defense mechanism operating unconsciously, in which the individual attempts to justify or make consciously tolerable, by plausible means, feelings, behavior, and motives that would otherwise be intolerable.Search Engine: Software used to locate data or information stored in machine-readable form locally or at a distance such as an INTERNET site.Amyloid beta-Protein Precursor: A single-pass type I membrane protein. It is cleaved by AMYLOID PRECURSOR PROTEIN SECRETASES to produce peptides of varying amino acid lengths. A 39-42 amino acid peptide, AMYLOID BETA-PEPTIDES is a principal component of the extracellular amyloid in SENILE PLAQUES.Amyloid: A fibrous protein complex that consists of proteins folded into a specific cross beta-pleated sheet structure. This fibrillar structure has been found as an alternative folding pattern for a variety of functional proteins. Deposits of amyloid in the form of AMYLOID PLAQUES are associated with a variety of degenerative diseases. The amyloid structure has also been found in a number of functional proteins that are unrelated to disease.Centralized Hospital Services: The coordination of services in one area of a facility to improve efficiency.Amyloid Precursor Protein Secretases: Endopeptidases that are specific for AMYLOID PROTEIN PRECURSOR. Three secretase subtypes referred to as alpha, beta, and gamma have been identified based upon the region of amyloid protein precursor they cleave.Amyloid beta-Peptides: Peptides generated from AMYLOID BETA-PEPTIDES PRECURSOR. An amyloid fibrillar form of these peptides is the major component of amyloid plaques found in individuals with Alzheimer's disease and in aged individuals with trisomy 21 (DOWN SYNDROME). The peptide is found predominantly in the nervous system, but there have been reports of its presence in non-neural tissue.Alzheimer Disease: A degenerative disease of the BRAIN characterized by the insidious onset of DEMENTIA. Impairment of MEMORY, judgment, attention span, and problem solving skills are followed by severe APRAXIAS and a global loss of cognitive abilities. The condition primarily occurs after age 60, and is marked pathologically by severe cortical atrophy and the triad of SENILE PLAQUES; NEUROFIBRILLARY TANGLES; and NEUROPIL THREADS. (From Adams et al., Principles of Neurology, 6th ed, pp1049-57)
Simplified Representation of Protein Conformations for Rapid Simulation of Protein Folding. In: Journal of Molecular Biology. ... mit Patrice Koehl: Protein topology and stability define the space of allowed sequences. In: Proceedings of the National ... Protein Conformation, Dynamics and Folding by Computer Simulation. In: Annual Review of Biophysics and Bioengineering. Band 11 ... Protein Folding by Restrained Energy Minimization and Molecular Dynamics. In: Journal of Molecular Biology. Band 170, 1983, S. ...
It is calculated as the average sequence distance between residues that form native contacts in the folded protein divided by ... Zuo, G; Wang, J; Wang, W (2006). "Folding with downhill behavior and low cooperativity of proteins". Proteins. 63 (1): 165-73. ... which can be useful in classifying the fold of a novel sequence with some degree of homology to known sequences. Plaxco, Kevin ... and low contact order has been suggested as a predictor of potential downhill folding, or protein folding that occurs without a ...
"A database of protein structure families with common folding motifs". Protein Science. 1 (12): 1691-1698. doi:10.1002/pro. ... Sander, C.; Schulz, G. E. (1979). "Degeneracy of the information contained in amino acid sequences: Evidence from overlaid ... Rost, B.; Sander, C. (1993). "Prediction of Protein Secondary Structure at Better than 70% Accuracy". Journal of Molecular ... Holm, L.; Sander, C. (1993). "Protein Structure Comparison by Alignment of Distance Matrices". Journal of Molecular Biology. ...
"Protein folding funnels: a kinetic approach to the sequence-structure relationship". Proceedings of the National Academy of ... for the folding funnel hypothesis stating that the native state of a protein is a deep minimum of free energy for the protein's ...
... which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three ... Main article: Protein domain. Many proteins are composed of several protein domains, i.e. segments of a protein that fold into ... the SH3 domain binds to proline-rich sequences in other proteins). Sequence motif. Short amino acid sequences within proteins ... Most proteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native ...
"An empirical energy function for threading protein sequence through the folding motif". Proteins. 16 (1): 92-112. doi:10.1002/ ... Adhikari AN, Freed KF and Sosnick TR (2012). "De novo prediction of protein folding pathways and structure using the principle ... Kmiecik S and Kolinski A (2007). "Characterization of protein-folding pathways by reduced-space modeling". Proc. Natl. Acad. ... 3.3.co;2-l. Shen MY, Sali A (2006). "Statistical potential for assessment and prediction of protein structures". Protein Sci. ...
Yet, only the amino acid sequence is genetically coded. The mechanisms by which proteins fold are not completely known. He ... This is because, he said, a protein must undergo a process of folding to attain its characteristic three-dimensional shape ... attributed to genotype and that the chemically active aspect of a biologically active protein relies on more than the sequence ... the functional capability of a biologically active protein can be investigated purely using the genetically encoded sequence of ...
The need to fold proteins correctly is a big restriction on the evolution of protein sequences. It has been proposed that the ... Similarly, binding proteins may spend some proportion of their time bound to off-target proteins. These reactions or ... Sup35p is a yeast protein involved in recognising stop codons and causing translation to stop correctly at the ends of proteins ... Knocking out a regulatory protein such as a chromatin regulator may lead to more effective capacitance than knocking out a ...
Disadvantages include the need for a single protein for analysis and the requirement that the protein sequence is located, at ... Results showed altered fingerprints and therefore altered levels of folding in the proteins. So, they concluded that ... De novo peptide sequencing Protein mass spectrometry Proteomics Mass spectrometry in the biological sciences James, P.; ... Once formed, a peptide-mass fingerprint can be used to search in databases for related protein or even genomic sequences, ...
However, the molecular architecture and folding conformation of these proteins are all very similar. Dendrotoxins possess a ... sequence identity as well as identical disulfide bonds. Despite the structural homology between these two proteins, ... Dendrotoxins are basic proteins that possess a net positive charge when present in neutral pH. Most of the positively charged ... Dendrotoxins are ~7kDa proteins consisting of a single peptide chain of approximately 57-60 amino acids. Several homologues of ...
... sequence-similar structures within different protein folds". Protein Science. 10 (2): 285-292. doi:10.1110/ps.31901. PMC ... BNR/Asp-box repeat is a repetitive sequence of amino acids contained in some proteins. Members of this family contain multiple ... Human genes encoding proteins containing this domain include: NEU1 NEU2 NEU3 RELN SORCS1 SORCS2 SORCS3 SORL1 SORT1 Gaskell, A; ... These repeats are found in a variety of non-homologous proteins, including bacterial ribonucleases, sulphite oxidases, reelin, ...
The new polypeptide then folds into a functional three-dimensional protein molecule. ... The ribosome mediates the formation of a polypeptide sequence based on the mRNA sequence. The mRNA sequence directly relates to ... Protein synthesis. Main article: Protein biosynthesis. Cells are capable of synthesizing new proteins, which are essential for ... linear molecules (chromosomes) with histone proteins RNA/protein synthesis coupled in the cytoplasm RNA synthesis in the ...
... which explains the fast protein folding. This is also described as protein folding directed within funnel-like energy ... this suggests local amino acid sequences which form stable interactions and serve as nucleation points in the folding process". ... "protein folding is sped up and guided by the rapid formation of local interactions which then determine the further folding of ... including any possible folding redundancy). Therefore, if a protein were to attain its correctly folded configuration by ...
The new polypeptide then folds into a functional three-dimensional protein molecule. Unicellular organisms can move in order to ... The ribosome mediates the formation of a polypeptide sequence based on the mRNA sequence. The mRNA sequence directly relates to ... The subunit protein of microfilaments is a small, monomeric protein called actin. The subunit of microtubules is a dimeric ... The ER has two forms: the rough ER, which has ribosomes on its surface that secrete proteins into the ER, and the smooth ER, ...
Removal of nucleic acids from laboratory protein preparations allowing for protein folding and structure-function studies. ... The enzyme is also active against double-stranded DNA and RNA and all sequences will be ultimately cleaved. The enzyme has a ... Research on the mechanisms of protein folding. Heins JN, Suriano JR, Taniuchi H, Anfinsen CB (1967). "Characterization of a ... was solved very early in the history of protein crystallography, in 1969, deposited as now-obsolete Protein Data Bank file 1SNS ...
Using SAPS, a Statistical Analysis of Protein Sequence software, amino acid bias was able to be determined. Isoform one is rich ... This nearly neutral pH enables the protein to fold properly and inhibits denaturation. The twenty most conserved amino acids, ... The high levels of cysteine residues contributes to the numerous disulfide bonds found in the mature protein's folded structure ... These domain are important to maintaining a properly folded protein and its function. Visit Carpenter syndrome for more ...
Most peroxisomal matrix proteins contain a short sequence, usually three amino acids at the extreme carboxy tail of the protein ... PEX5 imports folded proteins into the peroxisome, shuttling between the peroxisome and cytosol. PEX5 interacts with a large ... A few peroxisomal matrix proteins have a different, and less conserved sequence, at their amino termini. This PTS2 signal is ... In biochemical protein targeting, a peroxisomal targeting signal (PTS) is a region of the peroxisomal protein that receptors ...
... a comprehensive resource for histones and histone fold-containing proteins". Proteins. doi:10.1002/prot.20814. PMID 16345076. ... The curated set is supplemented by an automatically extracted set of histone sequences from the non-redundant protein database ... Baxevanis AD, Landsman D (1997). "Histone and histone fold sequences and structures: a database". Nucleic Acids Res. PMID ... The Histone Database is a comprehensive database of histone protein sequences including histone variants, classified by histone ...
The morpheein model does not require gross changes in the basic protein fold. The conformational differences that accompany ... It is generally taught that a given amino acid sequence will have only one physiologically relevant (native) quaternary ... Garel, J.-R. (1980). "Sequential Folding of a Bifunctional Allosteric Protein". Proceedings of the National Academy of Sciences ... Protein function is dependent on the oligomeric form; therefore, the protein's function can be regulated by shifting the ...
Corpas, Manuel (2006). Folding patterns in protein sequences. librarysearch.manchester.ac.uk (PhD thesis). University of ... Her research concerns protein sequence alignment and protein analysis. Inspired by the creation of PROSITE, Attwood developed a ... As well as being a biocurator she has co-developed tools to align and visualise protein sequences and structures, including ... Coletta, Alain Nava (2009). Characterisation of low-complexity regions in protein sequences. librarysearch.manchester.ac.uk ( ...
This is a case of a protein changing its own primary sequence from the sequence originally encoded by the DNA of a gene. ... Once the protein has been transconformed to the prion folding it changes function. In turn it can convey information into new ... Although this is a form of protein affecting protein sequence, not explicitly covered by the central dogma, there are not many ... This is an example of protein directly editing DNA sequence, as well as increasing the sequence's heritable propagation. ...
in protein sequences protein folding code (Berezovsky, Grosberg & Trifonov 2000) Proteins are composed of modules. The newly ... Protein modularity could also give an answer to the Levinthal's paradox, i.e. the question how a protein sequence can fold in a ... Trifonov's concept of protein modules tries to address the questions of proteins evolution and protein folding. In 2000, ... in RNA sequences RNA-to-protein translation code (triplet code) Every triplet in the RNA sequence corresponds (is translated) ...
Chaperone - proteins that assist other proteins in folding or unfolding Folding funnel Anfinsen's dogma Levinthal, Cyrus (1969 ... this suggests local amino acid sequences which form stable interactions and serve as nucleation points in the folding process ... which explains the fast protein folding. This is also described as protein folding directed within funnel-like energy ... "protein folding is sped up and guided by the rapid formation of local interactions which then determine the further folding of ...
Tertiary protein folding is dependent on hydrophobic forces from amino acids throughout the sequence of the protein. Chaotropic ... Macromolecular structure and function is dependent on the net effect of these forces (see protein folding), therefore it ... This is used in protein purification processes, to remove undesired proteins from solution A chaotropic agent is a substance ... For example, a chaotropic agent reduces the amount of order in the structure of a protein formed by water molecules, both in ...
It is composed of 244 individually folded protein domains connected by unstructured peptide sequences. These domains unfold ... The protein's in vivo half-life, the time it takes for half of the amount of protein in a cell to break down after its ... Titin /ˈtaɪtɪn/, also known as connectin, is a protein that, in humans, is encoded by the TTN gene. Titin is a giant protein, ... myosin-binding protein C, calmodulin 1, CAPN3, and MURF1 Mutations anywhere within the unusually long sequence of this gene can ...
... carbohydrate recognition and analysis of the b-prims fold". Protein Science. 8 (1): 13-24. doi:10.1110/ps.8.1.13. PMC 2144112. ... "Km+, a mannose-binding lectin from Artocarpus inegrifolia: amino acid sequence predicted tertiary structure, ... Protein Expression and Purification. 21 (1): 134-140. doi:10.1006/prep.2000.1353. PMID 11162398.. ... where he is a full professor of cell and molecular biology and head of the Center for Protein Chemistry of Hemocentro de ...
... an alpha-helical protein with over 50% sequence identity to an all-beta protein. Proteins 24:502-513. ... NMR structures of two designed proteins with high sequence identity but different fold and function. Yanan He, Yihong Chen, ... We recently designed two proteins, GA88 and GB88, with 88% sequence identity but different folds and functions [Alexander et al ... The basic idea was to design a pair of proteins with maximal sequence identity but retaining their different wild-type folds. ...
The Self-Folding Proteins, by SJET LLC, are single strands of material with sequences of fold angles. When they are thrown into ... the air randomly, they self-assemble into the 3D protein structure! ...
... the selective packaging of eleven distinct genomic RNA segments requires virus-encoded protein NSP2 to alter the RNA structures ... Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments. ... Thank you for submitting your article "Protein-mediated RNA folding governs sequence-specific interactions involved in genome ... The resulting pET-28b-NSP2 construct was verified by sequencing and used for protein expression in BL21(DE3) E.coli as ...
Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue ... Repressor protein cI,Maltose-binding periplasmic protein The fusion protein of Repressor protein (residues 1-20), linker, and ... MALTODEXTRIN-BINDING PROTEIN 562 87 6D66 1 A Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1 9606 ... Maltose binding protein 562 103 4OGM 1 A Maltose ABC transporter periplasmic protein, pilin protein chimera SEE REMARK 999 1496 ...
Determination of alpha-helix propensity within the context of a folded protein. Sites 44 and 131 in bacteriophage T4 lysozyme. ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1DYA Legend Entity #1 , Chains: A T4 LYSOZYME protein, length: 164 (BLAST ... DETERMINATION OF ALPHA-HELIX PROPENSITY WITHIN THE CONTEXT OF A FOLDED PROTEIN: SITES 44 AND 131 IN BACTERIOPHAGE T4 LYSOZYME. ...
... prediction of protein three-dimensional folds, 2) discrimination between sequences of gene introns and exons, and 3) ... and distribution of defined attributes in the amino acid or nucleotide sequence. We have tested this approach on three ... identification of putative RNA genes in genomic sequences. ... General global sequence descriptors have been developed which ... Global Description of Amino Acid & Nucleotide Sequences: Application to Predicting Protein Folds, Intron-Exon Discrimination ...
In addition, although the F-type fold is distinctive for FTLs, a structure-based search revealed apparently unrelated proteins ... with minor sequence similarity to FTLs, that displayed the FTLD fold. In general, the phylogenetic analysis of FTLD sequences ... fold) and unique carbohydrate- and calcium-binding sequence motifs. This novel lectin family comprises widely distributed ... Furthermore, the extraordinary variability of FTL sequences (isoforms) that are expressed in a single individual has revealed ...
Protein & Peptide Letters. Title: Study on the Influences of Palindromes in Protein Coding Sequences on the Folding Rates of ... and protein coding sequences do carry the information which can influence the folding rates of peptide chains or protein ... and protein coding sequences do carry the information which can influence the folding rates of peptide chains or protein ... Study on the Influences of Palindromes in Protein Coding Sequences on the Folding Rates of Peptide Chains", Protein & Peptide ...
To investigate how protein folding is affected by sequence connectivity five topological variants of the ribosomal protein S6 ... Keywords:NATURAL SCIENCES; Chemistry; Biochemistry; protein folding; protein stability; two-state folding; S6; chevron plot; ... Folding of the Ribosomal protein S6 :The role of sequence connectivity, overlapping foldons, and parallel pathways. by Haglund ... The results show that the folding nuclei of the wild-type and permutant proteins comprises a common motif of one ?-helix ...
a) Sequence alignment of the N-terminal region of the D. melanogaster Expansion protein with orthologous proteins found in the ... Keywords: Expansion protein; Smad homology domain 2; MH2 domain; Smad/FHA protein superfamily; protein-protein interaction; ... Sequence alignment and secondary-structure prediction. Sequences corresponding to Expansion proteins were retrieved from the ... In the Smad proteins the H2 region and the β8 strand are implicated in protein-protein interactions by β-sheet augmentation, ...
Protein folding depends on sequence[edit]. As Anfinsen demonstrated in the 1960s, proteins acquire their structure by ... Proteins can fold into domains[edit]. A significant number of proteins, especially large proteins, have a structure divided ... Most proteins require no external factors in order to fold (although specialized protein exist in cells, called chaperones, ... Proteins do so much that its important to note what proteins dont do. Currently there are no known proteins that can directly ...
HYPOTHETICAL 65.0 KDA PROTEIN IN COX14-COS3 INTERGENIC REGION PRECURSOR1-Ethyl-Pyrrolidine-2,5-DioneCadmium IonFlavin-Adenine ... 1RQ1: Structure Of Ero1p, Source Of Disulfide Bonds For Oxidative Protein Folding In The Cell. ... Hypothetical 65.0 KDA Protein in Cox14-cos3 Intergenic Region Precursor(Gene symbol: ERO1) ...
... secretory proteins contain signals in addition to the canonical signal sequence and the rate of folding. ... Based on this proposal, we hypothesized that a cytoplasmic protein containing a mutation that slows its rate of folding would ... It was proposed previously that the basis for this precise discrimination is the slow folding rate of secretory proteins, ... No export of the mutant protein was observed, even in a prl strain. We then examined binding of the mutant λ repressor to SecB ...
... From evolutionary interference, function ... A novel sequence alignment algorithm based on deep learning of the protein folding code. Bioinformatics. (2020, in press) PDF ... protein sequence comparison has provided crucial biological insights. While many sequence alignment algorithms have been ... To address this critical problem, we introduce a computational algorithm that performs protein Sequence Alignments from deep- ...
Although comprised of only 68 residues, it likely interacts with at least two other proteins in the mature phage and with DNA. ... Protein W (gpW) from bacteriophage lambda is required for the stabilization of DNA within the phage head and for attachment of ... Molecular Sequence Data * Nuclear Magnetic Resonance, Biomolecular* * Protein Folding* * Protein Structure, Quaternary ... The solution structure of bacteriophage lambda protein W, a small morphogenetic protein possessing a novel fold J Mol Biol. ...
The Three Folding Problems[edit]. The Folding Code[edit]. In the late 1980s, scientists discovered that there is a sequence of ... Based on the complexity of protein folding, there are 3 major problems of protein folding: The folding code, structure ... Protein Folding Problem[edit]. The Protein Folding Problem is the obstacle that scientists confront when they try to predict 3D ... Mechanisms of protein folding There were two different mechanism used to describe the folding of single-domain proteins. Some ...
PSI-BLAST searches do not identify sequence similarities to known TIM-barrel proteins, and sensitive profile-profile searches ... De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.. Huang PS#1,2, Feldmeier K#3, ... Despite efforts for over 25 years, de novo protein design has not succeeded in achieving the TIM-barrel fold. Here we describe ... De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy ...
... neither protein forms knots. Strikingly, when sequence-dependent non-native interactions between amino acids are introduced, ... In folding simulations that exclusively promote the formation of native contacts, ... can favor their folding into a native state of non-trivial topology (which is a global property). Some of the mechanisms that ... one observes knotting events but only for the natively-knotted protein. The results support the importance of non-native ...
... protein structure and folding; and molecular interactions and dynamics.. Author(s): Lippert, Ross. ... It covers subjects such as the sequence alignment algorithms: dynamic programming, hashing, suffix trees, and Gibbs sampling. ... Furthermore, it focuses on computational approaches to: genetic and physical mapping; genome sequencing, assembly, and ...
... protein structure and folding; and molecular interactions and dynamics.. Author(s): Lippert, Ross. ... It covers subjects such as the sequence alignment algorithms: dynamic programming, hashing, suffix trees, and Gibbs sampling. ... Furthermore, it focuses on computational approaches to: genetic and physical mapping; genome sequencing, assembly, and ... the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into ...
Our sequence pattern discovery and analysis approach unveiled protein regions of significant interest. AMYPdb is freely ... AMYPdb is a comprehensive online database aiming at the centralization of bioinformatic data regarding all amyloid proteins and ... Molecular Sequence Data * Protein Folding * Sequence Homology, Amino Acid Substances * Amyloid beta-Protein Precursor ... Our sequence pattern discovery and analysis approach unveiled protein regions of significant interest. AMYPdb is freely ...
2010) Sequence-specific random coil chemical shifts of intrinsically disordered proteins. J Am Chem Soc 132(51):18000-18003. ... Many regulatory proteins contain disordered recognition motifs that fold upon binding to their cellular targets, by mechanisms ... 5D); an n-fold change in the population of helix corresponds to the same n-fold change in kON. A direct correlation between the ... 2007) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447(7147):1021-1025. ...
I can generate a Go board and a sequence of strictly valid moves because I know the rules for Go. With certain limited high ... I disagree on protein folding- It seems to me that AlphaGo Zero is a great analogy to the protein folding problem: If you have ... those rules dont exist as such for protein folding. In other words if I generate 1000 protein folds, I dont know which ones ... DeepMind has already begun using AlphaGo Zero to study protein folding and has promised it will soon publish new findings.. ...
Simplified Representation of Protein Conformations for Rapid Simulation of Protein Folding. In: Journal of Molecular Biology. ... mit Patrice Koehl: Protein topology and stability define the space of allowed sequences. In: Proceedings of the National ... Protein Conformation, Dynamics and Folding by Computer Simulation. In: Annual Review of Biophysics and Bioengineering. Band 11 ... Protein Folding by Restrained Energy Minimization and Molecular Dynamics. In: Journal of Molecular Biology. Band 170, 1983, S. ...
Pro-sequence-assisted protein folding Previous article in issue: Pro-sequence-assisted protein folding ... Strain RB-44 Complete Genome Sequence Using PacBio Single-Molecule Real-Time Sequencing Technology, Genome Announcements, 2014 ... is synthesized by the action of the Luxl protein. OHHL is thought to bind to the LuxR protein, allowing it to act as a positive ...
  • We recently described the design and preliminary characterization of two small proteins, G A 88 and G B 88, with 88% sequence identity but different monomeric folds and functions ( 15 ). (pnas.org)
  • We show that binding of the rotavirus-encoded non-structural protein NSP2 to viral ssRNAs results in the remodeling of RNA, which is conducive to formation of stable inter-segment contacts. (elifesciences.org)
  • The PDBFlex database explores the intrinsic flexibility of protein structures by analyzing structural variations of the same protein across the archive. (rcsb.org)
  • This allows for the easy identification of regions and types of structural flexibility present in a protein of interest. (rcsb.org)
  • Members of several lectin families characterized by unique sequence motifs and structural folds such as C-type lectins (CTLs) ( 6 ), peptidoglycan binding proteins ( 7 ), ficolins ( 8 ), pentraxins (PXNs) ( 9 ), galectins ( 10 ), and most recently, F-type lectins (FTLs) ( 11 - 14 ) have been implicated in immune surveillance and homeostasis. (frontiersin.org)
  • As similar overlap between competing nuclei is also seen in other proteins, I hypothesise that the coupling of several small nuclei into extended 'super nuclei' represents a general principle for propagating folding cooperativity across large structural distances. (openthesis.org)
  • Based on the structural similarities to the MH2 fold, it is proposed that the N α -MH2 domain should be classified as a new member of the Smad/FHA superfamily. (iucr.org)
  • It is theorized that prions may be able to act as a structural template for other chemically (but not structurally) identical proteins, but they can't function as a native template for protein synthesis de novo . (wikibooks.org)
  • While many sequence alignment algorithms have been developed, existing approaches are often incapable of detecting hidden structural relationships in the "twilight zone" of low sequence identity. (gatech.edu)
  • The key idea is to implicitly learn the protein folding code from many thousands of structural alignments. (gatech.edu)
  • Other proteins are responsible for transporting chemicals in and out of cells, while others are structural parts of the cell. (rationalwiki.org)
  • ORF2 is approximately 1.8 kb long, which may transform into 60 kDa major structural protein VP1 with the following functions: self-assembly and capsid formation, receptor recognition, host specificity, strain diversity, and immunogenicity [ 7 ]. (hindawi.com)
  • learn about the wide range of functions which can be performed by proteins - such as enzymes, signalling proteins, membrane bound transport proteins and structural proteins. (york.ac.uk)
  • Students will be expected to rationalise and understand the behaviour of different proteins based on their structural features. (york.ac.uk)
  • These results shed light on the structural basis of the translational pausing and provided a practical tool for industrial protein fermentation. (deepdyve.com)
  • We design, optimize, and develop methods to change proteins and nucleic acids to enable studies of the physical and structural properties that are essential for their function. (nih.gov)
  • PSI-BLAST searches do not identify sequence similarities to known TIM-barrel proteins, and sensitive profile-profile searches indicate that the design sequence is distant from other naturally occurring TIM-barrel superfamilies, suggesting that Nature has sampled only a subset of the sequence space available to the TIM-barrel fold. (nih.gov)
  • So for example the TIM b/a barrel Fold ----- TIM beta/alpha-barrel (31) has 31 superfamilies and its Ribulose-phosphate binding barrel ---------- Ribulose-phoshate binding barrel (4) has 4 families. (bioinformatics.org)
  • Moreover, the distribution of proteins among these folds is highly non-homogeneous -- some folds and superfamilies are extremely abundant, but most are rare. (antievolution.org)
  • Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins , by Andreas D. Baxevanis and B. F. Francis Ouellette , Wiley-Interscience, ISBN: 0471383910. (nyu.edu)
  • Binding of the RBD to 23S rRNA in the late stages of ribosome subunit maturation would position the ATP-binding duplex destabilization fragment of the protein for interaction with rRNA in the peptidyl transferase cleft of the subunit, allowing it to "melt out" unstable secondary structures and allow proper folding. (stanford.edu)
  • What is the folding mechanism? (wikibooks.org)
  • Here we show that the disordered transactivation domain of the transcription factor c-Myb binds to the KIX domain of the transcriptional coactivator cAMP-response element binding (CREB-binding) protein (CBP) by a mechanism that involves elements of conformational selection and induced fit. (pnas.org)
  • The interaction of the intrinsically disordered phosphorylated kinase-inducible domain (pKID) of the cAMP-response element binding (CREB) protein with the KIX domain of a general transcriptional coactivator CREB-binding protein (CBP) provides an example of the induced-fit mechanism. (pnas.org)
  • By what mechanism do they fold? (powershow.com)
  • Finally, I showed that perhaps all members in the PDZ family could fold via a three state folding mechanism. (diva-portal.org)
  • An additional study discovered that the specific section of the En-HD called the helix-turn-helix motif (HTH) behaves as an independent folding domain. (wikibooks.org)
  • In Protein Folding, Misfolding, and Disease: Methods and Protocols , experts in the field present a collection of current methods for studying the analysis of protein folding and misfolding, featuring strategies for expressing and refolding recombinant proteins which can then be utilized in subsequent experiments. (springer.com)
  • OHHL is thought to bind to the LuxR protein, allowing it to act as a positive transcriptional activator in an autoinduction process that physiologically couples cell density (and growth phase) to the expression of the bioluminescence genes. (wiley.com)
  • Proteins don't act as fundamental energy reserves in most organisms, as their metabolism is slower and inefficient compared to sugars or lipids. (wikibooks.org)
  • In addition to their catalytic functions, proteins can transmit and commute signals from the extracellular environment, duplicate genetic information, assist in transforming the energy in light and chemicals with astonishing efficiency, convert chemical energy into mechanical work, and carry molecules between cell compartments. (wikibooks.org)
  • Some of these proteins were characterized by circular dichroism (CD) spectroscopy under acidic conditions but had a propensity to aggregate near neutral pH. (pnas.org)
  • Currently, the group uses single-molecule fluorescent energy transfer confocal microscopy, ultrafast polarised fluorescence spectroscopy, and NMR spectroscopy in oriented systems to elucidate the folding in vitro of the protein flavodoxin. (wur.nl)
  • All they can do is group together, forming a droplet of oil in the middle of the protein--with a surrounding shell of soluble amino acids. (indiana.edu)
  • Nevertheless, we also found that the translational pausing optimization increases the fitness of the expression host, and thus benefits the recombinant protein production, independent from the soluble expression. (deepdyve.com)
  • Click molecule labels to explore molecular sequence information. (nih.gov)
  • Researchers used single-molecule experiments to examine coil to globule transition of proteins and have demonstrated that the denatured state showed steady expansion as the concentration of denaturant was increased. (wikibooks.org)
  • The paradigm for N-AHL production is in the bioluminescence (lux) phenotype of Photobacterium fischeri (formerly classified as Vibrio fischeri ) where the signalling molecule N -(3-oxohexanoyl)-L-homoserine lactone (OHHL) is synthesized by the action of the Luxl protein. (wiley.com)
  • Search proteins in UniProtKB for this molecule. (uniprot.org)
  • In this sense, most natural folds can be considered to be only marginally stable. (pnas.org)
  • According to Gruebele, the proteins studied in vivo using the new technique were more stable, their thermal denaturation was more gradual and their folding kinetics were slower than the same proteins studied in vitro. (bio-medicine.org)
  • Gruebele said that in living cells, "You really expect a lot of heterogeneity, that there would be a lot of differences among different areas of the cell, that there might be areas of the cell where the protein might be very stable, and other places where it's very unstable. (bio-medicine.org)
  • These proteins are very stable, easy to express and purify and their folding reaction is reversible under most laboratory conditions. (diva-portal.org)
  • Now, two scientists from Howard Hughes Medical Institute have counted a non-trivial number of other proteins that can switch between two stable folds. (evolutionnews.org)
  • Exploration and discussion of detector technology, signals and signal processing, spectral separation methods and physical mechanisms used to determine protein associations and protein diffusion in cells are integrated throughout the course. (bu.edu)
  • Up to date and authoritative, Protein Folding, Misfolding, and Disease: Methods and Protocols offers researchers the tools necessary to move ahead in this vital field. (springer.com)
  • p>An evidence describes the source of an annotation, e.g. an experiment that has been published in the scientific literature, an orthologous protein, a record from another database, etc. (uniprot.org)
  • be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein. (uniprot.org)