• To be useful, these nascent proteins must shield their shown hydrophobic residues and MGCD0103 pontent inhibitor adopt an accurate tertiary framework. (phytid.org)
  • Further, during binding experiments with 1-anilino-8-naphthalenesulfonate (ANS), the WT and N78D mutant showed relatively more solvent-exposed hydrophobic residues than the N146D and N78D/N146D mutants. (nih.gov)
  • 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)
  • These replacements also led to production of infective viruses that replaced the acidic residues introduced (E) by nonpolar amino acids, indicating that preservation of the hydrophobic interface is essential for virus replication. (asm.org)
  • The region that interacts with the terminal hydrophobic groups of the inhibitors gave versatile structures according to the structures of the terminal groups, showing that this region is structurally flexible. (rcsb.org)
  • These residues formed in the active site hydrogen bond networks, which were adaptable for the structures of the terminal hydrophobic groups of the inhibitors, with a small deformation or partial destruction according to the shapes and sizes of the inhibitors. (rcsb.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)
  • Shown to the right is a predicted tertiary structure of the protein. (wikipedia.org)
  • Learning recovers information about protein structure: secondary structure and residue-residue contacts can be extracted by linear projections from learned representations. (biorxiv.org)
  • Learning on full sequence diversity rather than individual protein families increases recoverable information about secondary structure. (biorxiv.org)
  • 3D fluorescence studies showed that the HSA structure was altered at the secondary and tertiary levels upon binding with the complexes. (rsc.org)
  • The crystal structure and AlphaFold-predicted model of the designed proteins via domain-recombination provided a molecular explanation for domain-based stepwise stabilization. (bvsalud.org)
  • The mutant protein showed altered polarity around tryptophan residues, changed quenching parameters and also noticeably altered secondary and tertiary structure compared to the w-t protein. (sciencecentral.in)
  • The pH stability of the w-t and mutant proteins varied at extreme acidic pH and the molten globule like structure of w-t at pH1 was absent in case of the mutant protein. (sciencecentral.in)
  • Thus, the results provide insight into the alterations of NDUFS3 protein structure caused by the mutations, affecting the overall integrity of the protein and finally leading to disruption of Complex-I assembly. (sciencecentral.in)
  • Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. (biomedcentral.com)
  • Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary structure prediction. (biomedcentral.com)
  • We propose a new template-based modelling method called ThreaderAI to improve protein tertiary structure prediction. (biomedcentral.com)
  • These results demonstrate that with the help of deep learning, ThreaderAI can significantly improve the accuracy of template-based structure prediction, especially for distant-homology proteins. (biomedcentral.com)
  • Protein structure is fundamentally important to understand protein functions. (biomedcentral.com)
  • Computational protein structure prediction remains one of the most challenging problems in structural bioinformatics. (biomedcentral.com)
  • TBM method predicts the structure of query protein by modifying the structural framework of its homologous protein with known structure in accordance with template-query alignment. (biomedcentral.com)
  • Hydroxyl-radical footprinting to probe equilibrium changes in RNA tertiary structure. (nyu.edu)
  • The addition of a precursor 13-residue oligosaccharide moiety GlcNAc2Man8Gluc3 to the nascent polypeptide chain occurs in the endoplasmic reticulum, following which the assembly folds and acquires its secondary, tertiary, and quaternary structure. (chromatographyonline.com)
  • A cooperative and competitive interaction between multiple enzymes, cell lines, and cell culture conditions causes processing of the oligosaccharide structure during which some of the already attached moieties like mannose are trimmed to yield a fiveâ residue core (Man3GlcNAc2), to which N-acetylglucosamine (GlcNAc), fucose, galactose, and N-acetylneuraminic acid (sialic acid or Neu5Ac) residues get added in a probabilistic fashion. (chromatographyonline.com)
  • The tertiary structure of GlxA revealed a unique domain arrangement, atypical spectroscopic properties compared to Gox and a lack of enzymatic activity with classical Gox substrates. (bl.uk)
  • We introduce multiple interface string alignment (MISA), a visualization tool to display coherently various sequence and structure based statistics at protein-protein interfaces (SSE elements, buried surface area, ΔASA , B factor values, etc). (bvsalud.org)
  • Cysteine peptidases with a tertiary structure similar to that of the serine-type aspartyl dipeptidase are included in clan PC. (embl.de)
  • Proteins in the clan have an alpha/beta/alpha sandwich structure. (embl.de)
  • This has prompted speculation that proteins in clans CA and CE are related, and that members of one clan are derived from a circular permutation of the structure of the other. (embl.de)
  • The tertiary structure PP-fold is U shaped with an extended polyproline helix and an α helix connected by a β turn [ 7 ]. (hindawi.com)
  • The comparison presents that RSA has 73% of sequence similarity (Fig. S1 ), and high preservation of its tertiary structure (Fig. S2 ). (nature.com)
  • Bioinformatics approaches were used to predict the tertiary structure and cellular localization along with phylogenetic analysis of TPD52. (biomedcentral.com)
  • The aim of this study is to predict the tertiary structure of TPD52 for the first time to provide a deep insight towards a better understanding regarding the functional structure as well as the molecular basis of TPD52 as well as other members of the TPD family. (biomedcentral.com)
  • Plant defensins exhibit a conserved tertiary structure that consists of a triple-stranded antiparallel β-sheet and one α-helix that are stabilized into a compact shape by the disulfide bridges. (frontiersin.org)
  • Variations in the amino acids are reflected by small conformational changes in the tertiary structure that contribute to the broad range of biological activities in these proteins. (frontiersin.org)
  • The tertiary structure of the enzymes of the glycosylasparaginase precursor family is typical of the "N-terminal nucleophile" hydrolases in clan PB. (ebi.ac.uk)
  • More importantly, a similar assembly of the α/β-hydrolase fold domain tertiary structure among homologous members of the superfamily is required for correct trafficking of the proteins to their final destination. (hal.science)
  • Consideration of the tertiary structure of the glycosylated precursor and mature lectin showed that the entire series of processing events could occur without significant refolding of the initial translational product. (rupress.org)
  • Proteins play an important role in the construction of the body structure as well as in the gene expression of living beings. (cbsetuts.com)
  • This thesis consists of two distinct projects, one on the metastasis-associated laminin binding protein and the other on the putative copper chaperone NosL, both related by the common aim of investigation of the relationship between protein structure and function using nuclear magnetic resonance techniques. (montana.edu)
  • Furthermore, the peptide lacked the predicted alpha-helical content and tertiary structure as ascertained by nuclear magnetic resonance and by circular dichroism spectroscopy. (montana.edu)
  • To identify functional features and structural homologues of this protein, the structure of apo NosL Was solved using nuclear magnetic resonance techniques. (montana.edu)
  • AlphaFold's Protein Structure Database provides open access to protein structure predictions for the human proteome and 20 other organisms to accelerate scientific research. (ainews.one)
  • SEB has 2 distinct tightly "packed" domains that have a very complex tertiary structure. (medscape.com)
  • These observations are relevant to studies with Cys-less transporters utilized for the characterization of proteins with the substituted cysteine accessibility method and indicate that functional defects detected in a Cys-less protein, when the tertiary structure of the molecule is stressed, are not necessarily relevant to the wild-type protein. (elsevierpure.com)
  • Effective encoding of residue contact information is crucial for protein structure prediction since it has a unique role to capture long-range residue interactions compared to other commonly used scoring terms. (biomedcentral.com)
  • The residue contact information can be incorporated in structure prediction in several different ways: It can be incorporated as statistical potentials or it can be also used as constraints in ab initio structure prediction. (biomedcentral.com)
  • To seek the most effective definition of residue contacts for template-based protein structure prediction, we evaluated 45 different contact definitions, varying bases of contacts and distance cutoffs, in terms of their ability to identify proteins of the same fold. (biomedcentral.com)
  • The tertiary structure of proteins provides crucial information for understanding molecular mechanisms of biological functions. (biomedcentral.com)
  • Among various structure-based terms, residue-residue contact potentials[ 21 - 23 ] are unique in that they capture long-range interactions in a protein structure[ 24 ]. (biomedcentral.com)
  • A proper encoding of residue contact information is crucial for structure prediction because in principle, a full distance map or a residue contact map has sufficient information for reconstructing the tertiary structure of a protein[ 25 ]. (biomedcentral.com)
  • · http://structbio.nature.com ness, secondary structure, tertiary fold, and side-chain packing. (lu.se)
  • For -lactalbu- min, only water molecules conserved in the human and baboon structures are shown (the structure of the bovine protein has not been reported). (lu.se)
  • This perspective focuses on two areas that have yielded new useful information during the last 20 years: (i) structure-activity relationship (SAR) studies of contact allergy based on the concept of hapten-protein binding and (ii) mechanistic investigations regarding activation of nonsensitizing compounds to contact allergens by air oxidation or skin metabolism. (cdc.gov)
  • Expert systems containing information about the relationship between the chemical structure and the ability of chemicals to haptenate proteins are available. (cdc.gov)
  • Molecular docking studies indicated that all three complexes primarily bind to HSA in subdomain IIA with amino acid residues such as Arg218 and Lys199 which are located at the entrance of Sudlow's site I. The in vitro cytotoxicities of complexes 1-3 against HeLa cells showed promising anticancer activity (IC 50 = 3.5, 3.9 and 16.9 μM for 1 , 2 and 3 , respectively). (rsc.org)
  • The molecular docking described the microenvironment of the interaction sites, rich in apolar residues. (nature.com)
  • Its molecular interactions were determined through KEGG analysis, and real-time PCR-based expression analysis was performed to assess its co-expression with another oncogenic cellular pathway (miR-223, KLF9, and PKCε) proteins in ovarian cancer. (biomedcentral.com)
  • SEB consists of 239 amino acid residues and has a molecular weight of 28 kd. (medscape.com)
  • EcoRI is a 377-amino-acid protein with a molecular weight of 31 kDa. (vedantu.com)
  • On determining far-UV circular dichroism and tryptophan (Trp) fluorescence spectra, significant secondary and tertiary structural changes were observed in the N146D and N78D/N146D mutants compared with WT and the N78D mutant. (nih.gov)
  • Serine residues are more likely to undergo phosphorylation than threonine or tyrosine residues. (wikipedia.org)
  • Indeed, we have shown previously that mutation of a tyrosine phosphorylation site in the long cytoplasmic loop of the β subunit impairs agrin-induced cytoskeletal anchoring and aggregation of mutant AChR in muscle cells ( Borges and Ferns, 2001 ). (jneurosci.org)
  • Its name is derived from its characteristic tyrosine (Y) residues at both the C and N terminals. (hindawi.com)
  • The crystal structures of the protein-tyrosine phosphatase SHP-1 catalytic domain and the complex it forms with the substrate analogue tungstate have been determined and refined to crystallographic R values of 0.209 at 2.5 A resolution and 0.207 at 2.8 A resolution, respectively. (umassmed.edu)
  • Despite low sequence similarity, the catalytic domain of SHP-1 shows high similarity in secondary and tertiary structures with other protein-tyrosine phosphatases (PTPs). (umassmed.edu)
  • Sequence alignment and structural analysis suggest that the residues in the WPD loop, especially the amino acid following Asp421, are critical for the movement of WPD loop on binding substrates and the specific activity of protein-tyrosine phosphatases. (umassmed.edu)
  • The JNK protein kinase is a member of the MAP kinase group that is activated in response to dual phosphorylation on threonine and tyrosine. (umassmed.edu)
  • These proteins share the same number of disulfide bridges (17) and a Cys34 thiol group 11 . (nature.com)
  • Defensins are small cationic peptides of 45-54 amino acid residues with a conserved signature of cysteines, which can form three to four disulfide bridges. (frontiersin.org)
  • The α/β-hydrolase fold superfamily of proteins is composed of structurally related members that, despite great diversity in their catalytic, recognition, adhesion and chaperone functions, share a common fold governed by homologous residues and conserved disulfide bridges. (hal.science)
  • an intramolecular disulfide bond between the Cys 66 and 298 residues, in the first and fourth extracellular loops, respectively, is present but not essential for function. (elsevierpure.com)
  • Preservation of the Cys66-Cys298 intramolecular disulfide bond was not required for stability of the K422C protein. (elsevierpure.com)
  • The structural and functional properties compared with WT protein were investigated, respectively, by static light scattering (SLS), circular dichroism (CD), and fluorescence spectroscopy and by determining chaperone activity with the use of three substrates. (nih.gov)
  • The results show that the deamidation of N146 but not of N78 have profound effects on the structural and functional properties of alphaB-crystallin. (nih.gov)
  • 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)
  • ThreaderAI first employs deep learning to predict residue-residue aligning probability matrix by integrating sequence profile, predicted sequential structural features, and predicted residue-residue contacts, and then builds template-query alignment by applying a dynamic programming algorithm on the probability matrix. (biomedcentral.com)
  • DtpA is shown through enzymology and structural analysis to be a member of the dye-decolourising peroxidase (DyP) family. (bl.uk)
  • In other words, amino acids are the structural elements of all proteins . (ainews.one)
  • 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)
  • Proteins that undergo maturation in the ER are stabilized SOS2 by chaperones such as calnexin and calreticulin, which are structurally related and identify glycosylated, nonnative proteins through lectin-like domains. (phytid.org)
  • The results show that nonnative proteins are more structured and less solvent exposed than commonly believed. (lu.se)
  • Learning the natural distribution of evolutionary protein sequence variation is a logical step toward predictive and generative modeling for biology. (biorxiv.org)
  • Our study suggests that domain-based modular engineering can minimize the sequence space for calculations in computational design and experimental errors, thereby offering useful guidance for multidomain protein engineering. (bvsalud.org)
  • Glycosylation refers to a sequence of events that take place in the Golgi body and the endoplasmic reticulum of the cells of the expression system (predominantly mammalian) that lead to post-translational addition and processing of carbohydrate or glycan moieties to the protein backbone (usually serine- or threonineâ linked glycosylation for O-linked glycans and asparagineâ linked glycosylation for N-linked glycans) (6). (chromatographyonline.com)
  • was estimated as the portion of putatively disordered SwissProt proteins with lengths between 0.9L and 1.1L. TribeMCL clustering was used to reduce effects of sequence redundancy in estimation of font. (pepas.org)
  • We observe that TR is a better method when the sample size is small and test protein sequences are sufficiently similar to the training sequence. (bvsalud.org)
  • Based on primary sequence comparisons, β subunits are predicted to be modular structures composed of five domains (A-E) that are related to the large family of membrane-associated guanylate kinase proteins. (jneurosci.org)
  • By examining the amino acid sequence from the various proteins, mutations were found to be prevalent in conserved residues within the α/β-hydrolase fold of the homologous proteins. (hal.science)
  • Contrary to previous findings on a synthetic peptide corresponding to residues 205-229, this sequence within the context of the 200-295 construct demonstrated no laminin binding activity. (montana.edu)
  • These two Prdx6's have only 8% difference in their primary sequence (with 19 amino acids) with no apparent modification at any of the key conserved residues. (jascoinc.com)
  • The RNA chain is decoded and translated by ribosomes to produce a polypeptide sequence, otherwise known as a protein. (ainews.one)
  • For example, the sequence AUG (in the mRNA) is a codon that specifies the amino acid methionine, which almost always specifies the beginning of a protein. (ainews.one)
  • The spike glycoprotein sequence was retrieved from protein data bank (PDB) database. (ijpsonline.com)
  • Using chimeric proteins in which CD4 is fused to the large intracellular loop of each of the AChR subunits we found that agrin induced clustering of only chimeras containing the β subunit loop. (jneurosci.org)
  • Each subunit has a large intracellular loop between the third and fourth transmembrane domains that is the likely site for regulated interactions with postsynaptic scaffolding proteins. (jneurosci.org)
  • The major component of the bacterial flagellum is definitely a thin filament of 12C25 nm in diameter, which is known as the flagellar filament and is made of protein subunit called flagellin. (pepas.org)
  • with residues from each subunit in Cavity 1. (proteopedia.org)
  • Protein fold of the peptidase unit for members of this family resembles that of archaean proteasome subunit B, the type example of clan PB. (ebi.ac.uk)
  • NH2-terminal sequencing of the abundant precursors confirmed that the intact subunit of concanavalin A was formed by the reannealing of two fragments, since the alignment of residues 1-118 and 119-237 was reversed in the final form of the lectin identified in the chase and the precursor first labeled. (rupress.org)
  • The S1 subunit (PDB I.D-6VSB) of the spike protein being reported to acts as receptor binding domain (RBD), binding to ACE-2 receptor with higher affinity. (ijpsonline.com)
  • We show the networks generalize by adapting them to variant activity prediction from sequences only, with results that are comparable to a state-of-the-art variant predictor that uses evolutionary and structurally derived features. (biorxiv.org)
  • It is definitely known that principal amino-acid sequences dictate the tertiary buildings of proteins, but how foldable in to the indigenous condition occurs may be the subject matter of intense investigation still. (phytid.org)
  • Assessment of Ndc80p sequences Rabbit Polyclonal to SHP-1 from 29 organisms reveals the 1st 100 residues of the protein are poorly conserved among fungi and mainly absent from higher eukaryotes.61 Flagellum This the locomotion organelle is a long, whip-like extension, which enables particular cells or unicellular organisms to swim. (pepas.org)
  • Predicting protein properties from amino acid sequences is an important problem in biology and pharmacology. (bvsalud.org)
  • We compare the effectiveness of these models in predicting the binding affinity and expression of SARS-CoV-2 spike protein sequences. (bvsalud.org)
  • We also explore how effective these predictive methods are when trained on laboratory-created data and are tasked with predicting the binding affinity of the in-the-wild SARS-CoV-2 spike protein sequences obtained from the GISAID datasets. (bvsalud.org)
  • By now you get the idea that cells generate proteins, which are sequences of amino acids. (ainews.one)
  • Although protein structures have been solved by experiments at an increasing rate, a flood of new sequences have been determined even more rapidly due to the advance of sequencing technologies[ 6 , 7 ]. (biomedcentral.com)
  • 61 Full size and truncated Ndc80p are populated almost equally, suggesting low conformational stability of the N-terminal website of this protein. (pepas.org)
  • The aggregated views MISA/SSE, MISA/BSA, MISA/ΔASA, and so forth, make it trivial to identify commonalities and differences between chains, to infer key interface residues, and to understand where conformational changes occur upon binding. (bvsalud.org)
  • Optimization of protein thermostability is a key step in the development of industrial enzymes and biologics. (bvsalud.org)
  • These enzymes are involved in the processing of poly-ubiquitin precursors as well as that of ubiquinated proteins. (embl.de)
  • In these reactions, precursor proteins converted themselves into active enzymes that were not peptidases. (ebi.ac.uk)
  • In the organism major part of the body components is protein by nature and the enzymes carrying out almost all biological activities are also proteins. (cbsetuts.com)
  • In the prescribed buffer and chemical reactions, many of the enzymes show 100% activity. (vedantu.com)
  • A total of five major Open Reading Frames (ORF) were found in COVID-19: the ORF 1a/b region coding replicase and other enzymes, the spike or S protein ORF, M or membrane glycoprotein ORF, E or small membrane protein ORF and the N or nucleocapsid ORF ( fig. 1 )[ 5 ]. (ijpsonline.com)
  • 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)
  • Here we show that these mutations in the cholinesterase homologous region alter the folding properties of the α/β-hydrolase fold domain, which are reflected in defects in protein trafficking, folding and function, and ultimately result in retention of the partially processed proteins in the endoplasmic reticulum. (hal.science)
  • We have applied GMMA to a previously published experiment reporting on >54,000 variants of green fluorescent protein (GFP), each with known fluorescence output, and each carrying 1-15 amino acid substitutions (Sarkisyan et al. (bvsalud.org)
  • This paper shows the importance of applying inner filter correction over the entire fluorescence spectrum prior to any conclusion regarding changes in the polarity of the fluorophore microenvironment, also demonstrates the convergence of the results obtained from the treatment of fluorescence data using the area below the spectrum curve and the intensity in a single wavelength. (nature.com)
  • Proteins denatured by guanidinium chloride are not fully solvent exposed but contain strongly perturbed occluded water. (lu.se)
  • The identification of amino acid substitutions that both enhance the stability and function of a protein is a key challenge in protein engineering. (bvsalud.org)
  • We present a Global Multi-Mutant Analysis (GMMA) that exploits the presence of multiply-substituted variants to identify individual amino acid substitutions that are beneficial for the stability and function across a large library of protein variants. (bvsalud.org)
  • Stability is critical for the proper functioning of all proteins. (bvsalud.org)
  • Domain-level analysis of designed protein variants with similar structures but different thermal profiles showed that the independent enhancement of the thermostability of a constituent domain improves the overall stability of the whole multidomain protein. (bvsalud.org)
  • These moieties are critical in terms of their role in in-vivo safety and efficacy (pharmacodynamics and pharmacokinetics), protein folding, protein targeting and trafficking, ligand binding, stability, protein halfâ life regulation, and immunogenicity (8). (chromatographyonline.com)
  • The loss of activity of both mutant PCFTs was shown to be due to impaired protein stability and expression. (elsevierpure.com)
  • The hydration of nonnative states is central to protein folding and stability but has been probed mainly by indirect methods. (lu.se)
  • 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)
  • In the last decades, HOX proteins have been extensively studied due to their pivotal role in transcriptional events. (mdpi.com)
  • Overexpression of constitutive active DREB2A which had a transcriptional activation domain between residues 254 and 335 resulted in significant drought stress tolerance through regulates expression of many water stress-inducible genes [ 9 ]. (biomedcentral.com)
  • Processing of the precursor proteins exposes an N-terminal threonine residue that is the nucleophile in catalysis ( Aronson, 2004 ). (ebi.ac.uk)
  • Proteolytic events included removal of a peptide from the surface of the precursor molecule that connected the NH2- and COOH-termini of the mature protein. (rupress.org)
  • The globular protein is made up of alpha helices, beta sheets, and 3/10 helices. (vedantu.com)
  • To cause sensitization, a chemical must bind to macromolecules (proteins) in the skin. (cdc.gov)
  • At the neuromuscular junction, the acetylcholine receptor (AChR) is specifically clustered in the postsynaptic membrane via interactions with rapsyn and other scaffolding proteins. (jneurosci.org)
  • However, it remains unclear where these proteins bind on the AChR and how the interactions are regulated. (jneurosci.org)
  • Replacements that favored (Q44R) or impaired (Q44D) the polar interactions predicted between residues Q44 and D32 did not abolish dimer formation of transiently expressed 3A, indicating that these interactions are not critical for 3A dimerization. (asm.org)
  • Protein-protein interactions among SARS-CoV-2 spike protein, human receptors and antibodies are key determinants of the potency of this virus and its ability to evade the human immune response. (bvsalud.org)
  • the E-value for the Peptidase_C54 domain shown below is 2.3e-39. (embl.de)
  • This is a group of cysteine peptidases which constitute MEROPS peptidase family C54 (Aut2 peptidase family, clan CA), which are a group of proteins of unknown function. (embl.de)
  • A cysteine peptidase is a proteolytic enzyme that hydrolyses a peptide bond using the thiol group of a cysteine residue as a nucleophile. (embl.de)
  • The only peptidase reactions known to be catalysed by proteins in the family at the time were autolytic cleavage events. (ebi.ac.uk)
  • Congenital hypothyroidism mutations affect common folding and trafficking in the α/β-hydrolase fold proteins. (hal.science)
  • To address whether correct folding of the common domain is required for protein export, we inserted the thyroglobulin mutations at homologous positions in two correlated but simpler α/β-hydrolase fold proteins known to be exported to the cell surface: neuroligin3 and acetylcholinesterase. (hal.science)
  • Accordingly, mutations at conserved residues may be transferred amongst homologous proteins to produce common processing defects despite disparate functions, protein complexity and tissue-specific expression of the homologous proteins. (hal.science)
  • Accumulating evidence shows that tRNA expression and mutations are associated with various diseases such as neurological pathologies and cancer development3,4. (cdc.gov)
  • Serine protease present on cell membrane, is used by SARS-CoV-2 for associating spike protein to enable its fusion with host cells[ 12 - 14 ]. (ijpsonline.com)
  • Molten globule proteins preserve most of the native internal hydration sites and have native-like surface hydration. (lu.se)
  • The mechanism by which MuSK signaling regulates the interaction of the AChR with scaffolding proteins that localize it in the postsynaptic membrane, however, remain unknown. (jneurosci.org)
  • 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)
  • It was found to be membrane associated with a mononuclear Cu site and possess a Cys-Tyr redox cofactor capable of housing a protein radical, comparable to the fungal galactose oxidase (Gox). (bl.uk)
  • The ABCG2 multidrug transporter or abc subfamily G member 2 is a membrane protein from the A TP- B inding C assette (ABC) transporter family, specifically the G-subfamily. (proteopedia.org)
  • Endocytic trafficking dynamically regulates neuronal plasma membrane protein presentation and activity, and plays a central role in excitability and plasticity. (umassmed.edu)
  • Over the course of my dissertation research I investigated endocytic mechanisms regulating two neuronal membrane proteins: the anesthetic-activated potassium leak channel, KCNK3, as well as the psychostimulant-sensitive dopamine transporter (DAT). (umassmed.edu)
  • Taken together, these results demonstrate that novel, non-classical endocytic mechanisms dynamically control the plasma membrane presentation of these two important neuronal proteins. (umassmed.edu)
  • Analysis of the transcriptome identified several orthologues required for intra-erythrocytic survival and erythrocyte invasion, including the rhoptry neck protein 2 (RON2) and the apical membrane antigen-1 (AMA-1). (biomedcentral.com)
  • Normal neuromuscular junction showing a presynaptic terminal with a motor nerve ending in an enlargement (bouton terminale): Synaptic cleft and postsynaptic membrane with multiple folds and embedded with several acetylcholine receptors. (medscape.com)
  • The enzyme also shows specificity to the tRNA. (cbsetuts.com)
  • To analyze the properties of the active site in this enzyme, we determined the tertiary structures of pdAroAT complexed with nine different inhibitors. (rcsb.org)
  • Author Manuscript and RNA repair protein AlkB-derived enzyme mixture was first used to remove methylations at the Watson-Crick face. (cdc.gov)
  • The transferase component of debranching enzyme then transfers the 3 (green) glucose residues from the short branch to the end of an adjacent branch of the glycogen molecule. (medscape.com)
  • K-Pro is a new database designed for collecting and storing experimental kinetic data on monomeric proteins, with a two-state folding mechanism. (bvsalud.org)
  • The PP-fold family comprises neuropeptide Y (NPY), peptide YY (PYY), and pancreatic polypeptide (PP). They are composed of a chain of 36 amino acids residue and share amino acid homology, amidated C-terminal ends. (hindawi.com)
  • There are over thirty families in the clan, and tertiary structures have been solved for members of most of these. (embl.de)
  • Cysteine peptidases can be grouped into fourteen different clans, with members of each clan possessing a tertiary fold unique to the clan. (embl.de)
  • Clan CA includes proteins with a papain-like fold. (embl.de)
  • Clan CE includes proteins with an adenain-like fold. (embl.de)
  • Clan CL includes proteins with a sortase B-like fold. (embl.de)
  • Lower fold recognition accuracy was observed when inaccurate threading alignments were used to identify common residue contacts between protein pairs. (biomedcentral.com)
  • In the case of threading, alignment accuracy strongly influences the fraction of common contacts identified among proteins of the same fold, which eventually affects the fold recognition accuracy. (biomedcentral.com)
  • The largest deterioration of the fold recognition was observed for β-class proteins when the threading methods were used because the average alignment accuracy was worst for this fold class. (biomedcentral.com)
  • When results of fold recognition were examined for individual proteins, we found that the effective contact definition depends on the fold of the proteins. (biomedcentral.com)
  • Residue contacts defined by Cβ−Cβ distance of 7.0 Å work best overall among tested to identify proteins of the same fold. (biomedcentral.com)
  • We also found that effective contact definitions differ from fold to fold, suggesting that using different residue contact definition specific for each template will lead to improvement of the performance of threading. (biomedcentral.com)
  • Specificity is predominantly directed towards residues that occupy the S1 binding pocket, so that caspases cleave aspartyl bonds, legumains cleave asparaginyl bonds, and gingipains cleave lysyl or arginyl bonds. (embl.de)
  • I) A cofactor-A dimer (yellowish and gray) with conserved putative binding residues (crimson). (phytid.org)
  • As a result, isomerization of proline residues (peptidyl-prolyl isomerases) and the correct development of disulphide bonds (proteins disulphide isomerases) frequently bind and stabilize nonnative protein (Leroux, 2001). (phytid.org)
  • A few WRKY proteins which show slight variations in the heptapeptide WRKYGQK motif can not bind the W box and may bind the WK box (TTTTCCAC) [ 14 - 17 ]. (biomedcentral.com)
  • It is composed mostly of long alpha-helices with several coil regions and strands dispersed throughout the length of the protein. (wikipedia.org)
  • Plant receptor proteins that trigger defense responses can recognize effectors, and the functions of several plant receptor proteins function have been reported. (biomedcentral.com)
  • Viruses belonging to the largest cluster acquired an amino acid substitution in the receptor binding domain of the Spike protein (position 486), evolved faster and spread longer and more widely. (bvsalud.org)
  • Herein, we demonstrate that multidomain proteins can be stabilized significantly using domain-based engineering followed by the recombination of the optimized domains. (bvsalud.org)
  • 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)
  • This primary polypeptide chain may achieve tertiary or quarternary configuration in order to produce a functional protein molecule. (cbsetuts.com)
  • Phylogenetic analysis showed that these genes were clustered into clades corresponding to the doublesex/Mav-3 (DM) genes of vertebrates. (researchsquare.com)
  • Orthologues identified by transcriptome sequencing were characterized using phylogenetic, ab initio protein modelling and comparative and population-based methods. (biomedcentral.com)
  • The differences between the two genes is due seemingly random segments of non-conserved and semiconserved residues scattered throughout the two alignments. (wikipedia.org)
  • Comparison of these active site structures showed that the active site of pdAroAT consists of two parts with contrary properties: rigidity and flexibility. (rcsb.org)
  • Overall, this study identified two secreted proteins in T. horrida that induce cell death or are involved in defense machinery in non-host plants. (biomedcentral.com)
  • 2002). Cellular quality control chemical substance or Physical strains that are as a result of heat range adjustments, contact with proteotoxic realtors, or other circumstances that are conducive to proteins misfolding induce a ubiquitous, defensive, cellular tension response. (phytid.org)
  • Furthermore, we screened 597 secreted proteins from the T. horrida genome, some of which induced expression in host-pathogen interaction processes. (biomedcentral.com)
  • Although PPL is present in the bloodstream, no information is found on the interaction between PPL and rat serum albumin (RSA), the most abundant protein with the function of transporting endo/exogenous molecules. (nature.com)
  • Comparison of the binding activity of the JNK isoforms demonstrated that the JNK proteins differ in their interaction with ATF2, Elk-1 and Jun transcription factors. (umassmed.edu)
  • [ 3 ] Illingworth and Cori isolated the glycogen from the tissues of this patient and showed that it had extremely short outer chains. (medscape.com)
  • TCAIM is a protein that in humans is encoded by the TCAIM gene (T-cell activation inhibitor, mitochondrial). (wikipedia.org)
  • The protein contains a mitochondrial signal peptide localizing it to the mitochondrial matrix. (wikipedia.org)
  • The high isoelectric point of the Human protein provides further evidence for the mitochondrial localization due to the high pH of the mitochondrial matrix. (wikipedia.org)
  • Mitochondrial transcription element A (TFAM), a member of an HMG protein family, is essential for maintenance of mitochondrial DNA, potentially playing a histone-like architectural part for maintenance of mitochondrial DNA.79 As both these functions, transcription regulation and histone, are associated with intrinsic disorder, (S)-Mapracorat TFAM potentially behaves as an intrinsically disordered protein as well. (pepas.org)
  • The study of protein folding plays a crucial role in improving our understanding of protein function and of the relationship between genetics and phenotypes. (bvsalud.org)
  • We decellularized the metastatic lung sections, measured the micromechanics of the tumor ECM, and stained the sections for ECM proteins, proliferation, and cell death markers. (ibecbarcelona.eu)
  • [ 13 ] The toxin binds directly to the major histocompatability complex (MHC) class II proteins on target cells, subsequently stimulating the proliferation of large numbers of T lymphocytes. (medscape.com)
  • The polypeptide chain is the primary configuration of a protein in which the amino acids may be linked in the linear array by an organized system within the cell. (cbsetuts.com)
  • The polypeptide chain may be converted into protein through post-translational processing. (cbsetuts.com)
  • Hydrolysis involves usually a catalytic triad consisting of the thiol group of the cysteine, the imidazolium ring of a histidine, and a third residue, usually asparagine or aspartic acid, to orientate and activate the imidazolium ring. (embl.de)
  • In only one family of cysteine peptidases, is the role of the general base assigned to a residue other than a histidine: in peptidases from family C89 (acid ceramidase) an arginine is the general base. (embl.de)
  • Recombinant Mpn HPRT was expressed as an N-terminal fusion protein with a 6 × histidine tag and a tobacco etch virus (TEV) cleavage site at the N-terminus, and was purified to >98% purity by metal affinity chromatography, see more as assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis (data not shown). (bcl-2protein.com)
  • Mutant also exhibited a higher tendency than the w-t protein for aggregation which was examined using fluorescent (Thioflavin-T) and spectroscopic (Congo red) dye binding techniques. (sciencecentral.in)
  • A number of GlxA variants were created in Chapter 3 to elucidate the proteins unique spectroscopic properties. (bl.uk)
  • 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)
  • Purple represents residues in monomer B. Blue is used to highlight areas of interest in select scenes. (proteopedia.org)
  • Every protein actually represents a chain of amino acids, the polypeptide. (cbsetuts.com)
  • The part of disorder in (S)-Mapracorat functioning of several proteins (histones) and transcription (S)-Mapracorat factors, has been already discussed. (pepas.org)
  • The protein kinase activity of these JNK isoforms was measured using the transcription factors ATF2, Elk-1 and members of the Jun family as substrates. (umassmed.edu)