• Along with the genes for other accessory proteins, the ORF8 gene is located near those encoding the structural proteins, at the 5' end of the coronavirus RNA genome. (wikipedia.org)
  • This protein-sequence information has also been generated by scientists all over the world, mainly through genome sequencing, and is made available through public resources, such as UniProt and Mgnify hosted at EMBL-EBI. (embl.org)
  • Protein structure comparison also helps to improve tools for identifying gene functions in genome databases by defining the essential sequence-structure features of a protein family16. (researchsquare.com)
  • however, as evidenced by genome sequence analysis, the organism lacks common enzymes required for the de novo synthesis of precursors of PGN, which rationalizes its MurNAc auxotrophy. (karger.com)
  • The recent sequencing of the human genome has provided a wealth of information detailing several million genetic variations between individuals. (biomedcentral.com)
  • Recently, genome sequences revealed that in addition to rpoS , an rpoS -like sigma factor was found in V. alginolyticus 12G01. (hindawi.com)
  • Thus locating all RNA-binding proteins (RBPs) in a genome and determining protein-RNA complex structures are key steps for understanding the mechanism of post-transcriptional regulation and for mapping the network of protein-RNA interactions. (buyresearchchemicalss.net)
  • 2009 identified 21 families of these substrate capture proteins, each with a different specificity predicted by genome context analyses. (tcdb.org)
  • Monocyte chemotactic protein 4 (MCP-4), a novel structural and functional analogue of MCP-3 and eotaxin. (rupress.org)
  • To identify such inaccuracies, scoring functions have been developed which analyze different structural features of the protein models in order to derive a quality estimate. (unibas.ch)
  • AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models (2022) Nucleic Acids Res 50: D439-D444. (rcsb.org)
  • Protein structural biology. (embl.org)
  • Since the early 1970s, the structural biology community has archived its experimental structures in the PDB, a freely available global resource that now contains over 180,000 structures. (embl.org)
  • Since several # instances of the same protein may occur (eg, crystallized under different # experimental conditions), the initial set of proteins was filtered so that no # pair of chains superimpose within 2A, have more than 90% of the Calpha superimposable # within 4A, and have more than 90% of sequence identity after structural # superimposition. (cnag.cat)
  • In previous research methods, most of them only used protein amino acid sequence as input information to make predictions, without considering the structural information of PPIs networks graph. (biomedcentral.com)
  • Hence, we suggest a protocol that permits the reliable sequence alignment of distantly related proteins whose structural information is available. (researchsquare.com)
  • The method proposed is clearly suited to work for protein structural members with distant relationships. (researchsquare.com)
  • This structure-based sequence alignment protocol can be employed for a single superfamily or for a large number of structural domain superfamilies in a near-automatic and rapid manner. (researchsquare.com)
  • The availability of accurate structure-based sequence alignments of protein families and superfamilies is crucial to inferring their evolutionary relationships, functional properties4 and to understand the structural variances between the different classes of proteins. (researchsquare.com)
  • A common structural feature of GPCRs is the presence of a highly conserved architecture of seven stretches of transmembrane spanning residues linked by alternate extracellular and intracellular loops. (biomedcentral.com)
  • This review aims to link recent molecular data, often translated into amino acid sequences and predicted three dimensional structural motifs, to known mechanical properties. (bioone.org)
  • multi-dimensional probabilistic matching between sequence profiles generated from PSI-BLAST (15) for query and template sequences and between structural features of a template and those predicted by SPINE X (16-18) for a query sequence. (buyresearchchemicalss.net)
  • Predicted structural features include secondary structure (17) backbone torsion angles (16) and Pranoprofen residue solvent accessibility (18). (buyresearchchemicalss.net)
  • PDB protein sequence positions are represented in blue if residue was experimentally determined, and in gray if not. (rcsb.org)
  • One of the major limitations for using structure-based methods in biomedical research is the limited availability of experimentally determined protein structures. (unibas.ch)
  • This means that for every known sequence in the UniProt data resource there will be either an experimentally determined structure (in the Protein Data Bank, PDB), or a predicted structure in AlphaFold DB, or the structure can be readily modeled using traditional structure-prediction techniques based on models for similar sequences in PDB or AlphaFold DB. (embl.org)
  • Thus, the AlphaFold predictions were consistently very similar to the experimentally determined structures of the proteins included in this round of CASP. (embl.org)
  • The full-length gene, exemplified in SARS-CoV-2, encodes a protein with an immunoglobulin domain of unknown function, possibly involving interactions with the host immune system. (wikipedia.org)
  • Despite a similar overall fold, an insertion in ORF8 likely is responsible for different protein-protein interactions and creates an additional dimerization interface. (wikipedia.org)
  • Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
  • An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
  • The main interest of our group is the development of methods and algorithms for molecular modeling and simulations of three-dimensional protein structures and their interactions. (unibas.ch)
  • Ultimately, the quality of a model determines its usefulness for different biomedical applications such as planning mutagenesis experiments for functional analyses or studying protein-ligand interactions, e.g. in structure based drug design. (unibas.ch)
  • Computational modelling of the interactions between these ligands and both wild type and mutant S1P 4 receptors showed excellent agreement with experimental data, therefore confirming the fundamental role of this residue in ligand recognition by S1P receptors. (biomedcentral.com)
  • Protein-protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to that. (biomedcentral.com)
  • Accurately predicting protein interactions is very important for us to study the properties of cellular systems, improve the understanding of disease and provide a basis for the development of novel therapeutic approaches [ 4 ]. (biomedcentral.com)
  • Bioinformatics analysis of contact maps in PAS domains revealed conserved networks of interactions, where side chain identity is variable, but a cluster of inter-residue interactions is retained. (aps.org)
  • We propose that such conservative interactions is important for efficient protein production. (aps.org)
  • rium properties, completely determined by the interactions within crystal structures of 38 nonhomologous proteins, we find that it the system. (lu.se)
  • For over 40% of the nsSNPs, structure-based methods predicted which of these sequence changes are likely to either disrupt the structure of the protein or interfere with the function or interactions of the protein. (biomedcentral.com)
  • Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. (embl.de)
  • Most methods developed for predicting RNA-binding proteins are based on machine-learning methods that employ information of protein sequences and/or known protein structures (5 6 Meanwhile docking techniques for protein-RNA interactions have been developed by using a scoring/energy function for protein-RNA interaction (7-10). (buyresearchchemicalss.net)
  • The goal of this paper is to define a technique, based on the geometrical and topological structure of protein surfaces, for the detection and the analysis of sites of possible protein-protein and protein-ligand interactions. (scitevents.org)
  • 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)
  • [ 4 ] It is also important to understand that the same polypeptide sequence can produce many different patterns of interresidue or intraresidue interactions. (medscape.com)
  • Comparative or homology modeling, which uses experimentally elucidated structures of related protein family members as templates, is currently the most accurate and reliable approach to model the structure of the protein of interest. (unibas.ch)
  • The SWISS-MODEL expert system developed by our group is a fully automated web-based workbench, which greatly facilitates the process of computing of protein structure homology models. (unibas.ch)
  • Identified recently as part of the non-LEE-encoded (Nle) effector set, this family remained uncharacterised and shared no sequence homology to other proteins including those of known function. (rcsb.org)
  • 2009 ). The designated dysbindin paralogs show very limited sequence homology which raised the question whether DBNDD1 and DBNDD2 are dysbindin-like proteins or proteins that share a less conserved domain with DTNBP1 in the context of otherwise unrelated sequences (Ghiani and Dell'Angelica 2011 ). (springer.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)
  • The sequence conservation of the putative dysbindin domain across all selected species is notable (Fig. 1 shaded region). (springer.com)
  • The hOAT3 cDNA consisted of 2179 base pairs that encoded a 543-amino-acid residue protein with 12 putative transmembrane domains. (aspetjournals.org)
  • Some functionally important residues contributing to the formation of putative binding sites and permeation pathways for the cotransported Na+ ions and I- substrate were identified. (elsevierpure.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)
  • We describe a statistical measure, Mass Distance Fingerprint, for automatic de novo detection of predominant peptide mass distances, i.e., putative protein mod- ifications. (lu.se)
  • Based on the expectation that functionally conserved regions in homologous proteins will display locally higher levels of sequence identity compared with global sequence similarities that pertain to the overall fold, this approach may have wider applications in functional genomics to annotate sequence data. (eurekamag.com)
  • Multiply aligned set of sequences serve as convenient models to depict evolutionary drifts and provide convenient frameworks for mapping allied information such as secondary structures and functionally important residues. (researchsquare.com)
  • To inform each other and human, model organism studies require a complete map of functionally-equivalent genes and processes across species, in order to facilitate mapping of biological and experimental findings across species, but such maps are extremely difficult to obtain experimentally. (biorxiv.org)
  • Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. (nature.com)
  • Prediction of the 3D structure of a protein from its amino acid sequence remains a fundamental scientific problem, and it is considered as one of the grand challenges in computational biology. (unibas.ch)
  • Methods for structure modeling and prediction have made substantial progress over the last decades, but still fall short in accuracy compared to high-resolution experimental structures. (unibas.ch)
  • Assessing the quality of a blind prediction in comparison to experimental reference structures allows benchmarking the state-of-the-art in structure prediction and identifying areas which need further development. (unibas.ch)
  • The Critical Assessment of Structure Prediction ( CASP ) experiment has for the last 25 years assessed the progress in the field of protein structure modeling. (unibas.ch)
  • The " Continuous Automated Model EvaluatiOn" (CAMEO) project aims to complement CASP and provide a fully automated blind assessment for prediction servers only based on weekly pre-released sequences of the Protein Data Bank PDB. (unibas.ch)
  • Here, using atomistic molecular dynamics simulation, we study the correlations between the RBD dynamics with physically distant residues in the spike protein, and provide a deeper understanding of their role in the infection, including the prediction of important mutations and of distant allosteric binding sites for therapeutics. (biorxiv.org)
  • Combining amino acid sequence information and position information makes a stronger representation for protein, which improves the accuracy of PPIs prediction. (biomedcentral.com)
  • Profiles generated using structure-based sequence alignments of distantly related proteins at the family or superfamily level could be utilized to predict the fold of hypothetical sequences through profile-sequence search method is another success in the structure prediction area. (researchsquare.com)
  • Prediction of protein coding region (GeneMark analysis). (or.jp)
  • In the present report we have compared and contrasted structure- and sequence-based methods of prediction to over 5500 genes carrying nearly 24,000 nsSNPs, by employing an automatic comparative modelling procedure to build models for the genes. (biomedcentral.com)
  • For binding affinity prediction we extracted a knowledge-based energy function DRNA from protein-RNA complex structures (19) based on a distance-scaled finite ideal-gas reference (DFIRE) state (20). (buyresearchchemicalss.net)
  • It has an immunoglobulin-like domain with distant similarity to the ORF7a protein. (wikipedia.org)
  • We performed a Basic Local Alignment Search Tool (BLAST) analysis to identify regions of local similarity between the human DBNDD1 and protein sequences from other species (Fig. 1 ). (springer.com)
  • It was subsequently realised that proteins (or domains) with similar amino-acid sequences have similar overall 3D structures, and that the degree of this similarity (measured by the root-mean-square distance, or RMSD, between corresponding atoms in the two models) is correlated with the degree of sequence similarity. (embl.org)
  • Members of the S1P receptor family display higher sequence similarity to each other (approximately 40% identity) than to members of the LPA receptor family (approximately 30% identity). (biomedcentral.com)
  • The diversity among GPCRs primarily stem from the presence of characteristic N-terminal extracellular domains and C-terminal intracellular domains and to a relatively lesser extent from the connecting loops which share limited sequence similarity. (biomedcentral.com)
  • The new 1D-3D Group Alignment Viewer supports exploration of multiple sequence alignments (MSA) at sequence and structure levels for PDB experimental structures and Computed Structure Models (CSMs). (rcsb.org)
  • RCSB.org clusters protein entities (PDB experimental structures and CSMs) by sequence identity threshold and UniProt accession. (rcsb.org)
  • Template-based protein modeling techniques exploit the evolutionary relationship between a target protein and templates with known experimental structures, based on the observation that evolutionarily related sequences generally have similar 3D structures. (unibas.ch)
  • QMEANBrane further extends the approach to membrane protein structures, which play crucial roles in many biological processes and are important drug targets. (unibas.ch)
  • Experimental structures and CSMs are clearly identified throughout the website: a dark-blue flask icon is used for PDB structures and a cyan computer icon for CSMs. (rcsb.org)
  • "Group" summary pages and search results simplify exploration of PDB structures with similar sequence identity/UniProt ID or were deposited as part of the same study. (rcsb.org)
  • Structure Summary Pages offer details of experimental PDB structures (e.g., 4HHB ) and CSMs (e.g. (rcsb.org)
  • Analogous to the validation slider for experimental structures, all CSMs report global and local confidence levels as pLDDT scores . (rcsb.org)
  • View experimental PDB structures and CSMs in Mol* from Structure Summary Pages (e.g. (rcsb.org)
  • In November 2020, more than 60 years after the first protein structures were determined experimentally, AlphaFold was recognised as the best-performing method for predicting 3D protein structure by the assessors of the 14th round of the biennial CASP experiment. (embl.org)
  • AlphaFold builds on this huge body of experimental information and generates its predictions by analysing the relationship between these known protein structures and huge amounts of protein-sequence data. (embl.org)
  • When DeepMind decided to predict the structures of a huge number of proteins and started to think about how to disseminate the 3D models freely and openly, an obvious partner to collaborate with was the European Bioinformatics Institute, EMBL-EBI, the European home of many biological data resources used by the AlphaFold team, including PDBe and UniProt. (embl.org)
  • however, the low sequence identity between hNIS and relevant secondary transporters with available experimental structures makes the choice of a template and the generation of 3D models nontrivial. (elsevierpure.com)
  • Since protein structures have a much higher degree of conservation than the sequences2, comparison of protein structures may reveal distant evolutionary relationships that would not be detected from sequence information alone3,4. (researchsquare.com)
  • Rapid structure-based sequence alignments employ a comparison of the orientations of the secondary structures (Murthy20, SSAP7,21, and SEA22 programs) or hexapeptide fragments (DALI5,6) to recognize accurate alignments of protein domains that belong to the same superfamilies. (researchsquare.com)
  • Protein design aims to rationally design proteins that fold into particular target structures capable of performing new desired functions. (gorkalasso.com)
  • 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)
  • proteins and protein-RNA complex structures. (buyresearchchemicalss.net)
  • It is difficult to locate RBPs and determine their protein-RNA complex structures experimentally due to high flexibility of RNA structures and the difficulty associated with crystallization of complex structures. (buyresearchchemicalss.net)
  • Despite this difficulty there is a steady increase in the number of protein-RNA complex structures deposited in the protein data bank from 45 in 2001 Pranoprofen to 180 in 2011 (non-redundant at 90% sequence identity or less) (1). (buyresearchchemicalss.net)
  • Experimental discovery of new RBPs and determination of protein-RNA complex structures however is costly and inefficient. (buyresearchchemicalss.net)
  • There is a need for the development of highly accurate bioinformatics tools for predicting RNA binding function and protein-RNA complex structures. (buyresearchchemicalss.net)
  • More specifically SPOT-Seq-RNA employs a template library of non-redundant protein-RNA complex structures and attempts to match the query sequence to the protein structures in protein-RNA complexes by the fold recognition technique SPARKS X (12). (buyresearchchemicalss.net)
  • Significant matches will be employed to predict the complex structures between a target sequence and template RNA as well as the binding affinity of the complex. (buyresearchchemicalss.net)
  • The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
  • Until early 1990s, renal organic anion transport was thought to be carried out by a few carrier proteins that showed wide substrate specificity. (aspetjournals.org)
  • Experimental characterisation confirmed that replacement of glutamic acid with glutamine in S1P 1 changed ligand specificity from S1P to LPA, and the reciprocal mutation in LPA 1 resulted in recognition of both LPA and S1P [ 7 ]. (biomedcentral.com)
  • X-ray crystallography, protein modeling, mutagenesis and DNA binding assays reveal that LFY specificity can be defined using only three residues. (gorkalasso.com)
  • Specificity assays show that related ligands bind less tightly to the designed protein. (gorkalasso.com)
  • The dysbindin (dystrobrevin-binding protein) protein family is a group of evolutionarily related proteins of moderate size (Mw 13-45 kDa) in higher Eukaryotes. (springer.com)
  • Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
  • The very premise of using model organisms to inform human biology relies on the fact that many biological processes, and the underlying genomic elements that encode them, are frequently conserved across large evolutionary distances, especially for protein-coding genes. (biorxiv.org)
  • Further analysis revealed conserved residues that affect protein stability and in vivo protein production, indicating that both effects drive evolutionary conservation in PYP, but through two largely distinct sets of residues. (aps.org)
  • tackle this question using the LEAFY (LFY) gene of plants as the evolutionary model {1}, carrying out a wide range of experimental and computational analyses. (gorkalasso.com)
  • For any given set of species, gene families are created by first identifying all the genes in all species and then clustering them based on their sequence similarities. (biorxiv.org)
  • This is evident at the subfamily level comparisons since Ciona GPCR sequences are significantly analogous to vertebrate GPCR subfamilies even while exhibiting Ciona specific genes. (biomedcentral.com)
  • The reports on base sequences of spider silk protein genes have gained importance as the mechanical properties of silk fibers have been revealed. (bioone.org)
  • The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
  • Acquisitions of OspC genes that are novel for the region confer to recipients unique identities to host immune systems and, presumably, selective advantage when immunity to existing types is widespread among hosts. (cdc.gov)
  • The mRNA and protein expression of the 26 genes was associated with sensitivity or resistance to 18 NCCN-recommended drugs for treating breast cancer. (cdc.gov)
  • Accurate sequence alignments of distantly related proteins are crucial for the better understanding of proteins at their family/superfamily level. (researchsquare.com)
  • PAS domains form a diverse superfamily of signaling proteins defined by a weak but characteristic pattern of sequence conservation. (aps.org)
  • Within the RNaseA superfamily there is a group of highly cationic proteins secreted by innate immune cells with anti-infective and immune-regulatory properties. (frontiersin.org)
  • When evidence suggests that homologous membrane transport proteins of the ABC2 type couple transport to ATP hydrolysis using a homologue of the ABC-type ATPases, we list these proteins in the ABC superfamily. (tcdb.org)
  • Those which bind phosphorylated tyrosine residues may recruit multi-phosphorylated substrates for the adjacent active domains and are more conserved, while the other class have accumulated several variable amino acid substitutions and have a complete loss of tyrosine binding capability. (embl.de)
  • However, unlike typical ABC transporters (E.I. Sun & M.H. Saier, unpublished results), they use small integral membrane proteins that are postulated to capture specific substrates. (tcdb.org)
  • Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
  • Engineered mutations to the 10E8 paratope at light-chain solvent-exposed residues that add positive charge or hydrophobic sidechains proved to increase antibody association to anionic phospholipid vesicles in vitro and also boosted neutralization potency 27 . (elifesciences.org)
  • Early stage computational and experimental studies on potential therapeutics have concentrated on the receptor binding domain, although this region is prone to mutations with the possibility of giving rise to widespread drug resistance. (biorxiv.org)
  • Significant research effort for drug design against COVID-19 is focused on the receptor binding domain of the spike protein, although this region is prone to mutations causing resistance against therapeutics. (biorxiv.org)
  • These residues can not only be targeted by broad spectrum antibodies and drugs, mutations in them can generate new strains of coronavirus resulting in future epidemic. (biorxiv.org)
  • 6 Significantly, the sites in S protein have been demonstrated to be vulnerable to acquire mutations. (biorxiv.org)
  • However, we observed that mutations at these residues often substantially reduce the degree of protein production. (aps.org)
  • 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)
  • The cysteine residue responsible for dimerization of the SARS-CoV-2 protein is not conserved in the SARS-CoV sequence. (wikipedia.org)
  • structure to be out of phase with relative alkylation rates of engineered cysteine residues in the TM binding site of the alpha(2A)-adrenergic receptor. (eurekamag.com)
  • Mutation on these residues can lead to new strains of coronavirus with different degrees of infectivity and virulence. (biorxiv.org)
  • Majority of both experimental 11 - 14 and computational 15 - 17 efforts for inhibitor design are focused on the receptor binding domain (RBD) despite the fact that this region is highly mutation prone. (biorxiv.org)
  • We tested whether mutation of this "ligand selectivity" residue to glutamine could confer LPA-responsiveness to the related S1P receptor, S1P 4 . (biomedcentral.com)
  • Mutation of this residue to glutamine confers LPA responsiveness with preference for short-chain species. (biomedcentral.com)
  • Our paper emphasizes the relevance of Extreme Learning Machine (ELM) in Bioinformatics applications by addressing the problem of predicting the disulfide connectivity from protein sequences. (scitevents.org)
  • ORF8 is a gene that encodes a viral accessory protein, Betacoronavirus NS8 protein, in coronaviruses of the subgenus Sarbecovirus. (wikipedia.org)
  • ORF8 in SARS-CoV-2 encodes a protein of 121 amino acid residues with an N-terminal signal sequence. (wikipedia.org)
  • The full-length ORF8 in SARS-CoV encodes a protein of 122 residues. (wikipedia.org)
  • The gcsap open reading frame encodes a protein with a 78 residue prepro-sequence typical of other fungal secreted aspartic proteinases. (microbiologyresearch.org)
  • The neuraminidase (NA) gene encodes the other surface protein of the virus. (cdc.gov)
  • The consensus model developed in this work is compared to available biophysical and biochemical experimental data for a number of different LeuT-fold proteins. (elsevierpure.com)
  • Biochemical assays revealed that the BioM, N, and Y proteins form stable complexes in membranes of the heterologous host. (tcdb.org)
  • 5 , 7 - 9 More specifically, a study analyzing 10,022 SARS-CoV-2 genomes from 68 countries revealed 2969 different missense variants, with 427 variants in the S protein. (biorxiv.org)
  • In view of the fact that sequencing of genomes is usually considered straightforward, patent offices around the world in many cases consider the identification of a new protein as obvious and non-patentable. (uhthoff.com.mx)
  • However, such alignments of distantly related proteins are often hard to obtain by automatic multiple sequence alignment programs. (researchsquare.com)
  • Despite the availability of several structure-based sequence alignment procedures (DALI5,6, SSAP7, CE8, 3DCOFFEE9, MUSTANG10 etc.) in the public domain, we have observed, from our large-scale construction of aligned protein domain superfamilies13-15 that a huge amount of manual intervention is required for the choice of initial equivalences, in dealing with distantly related multiple members. (researchsquare.com)
  • Both of the integral membrane protein constituents of these systems may be distantly related, and in this respect they resemble typical ABC porters. (tcdb.org)
  • Two of these residues are found to determine the half-sequence identity, while the remaining residue influences the dimerization mode and the requirement for a spacer between half-sites. (gorkalasso.com)
  • For this reason the full-length gene and its protein are sometimes called ORF8ab. (wikipedia.org)
  • It is similar in structure to the ORF7a protein, suggesting it may have originated through gene duplication. (wikipedia.org)
  • We, thus, analyze sequences recognized by MucR in the rem gene promoter, showing that this protein recognizes AT-rich sequences and does not require a consensus sequence to bind DNA. (bvsalud.org)
  • Human dysbindin domain-containing protein 1 (DBNDD1) is encoded by the gene DBNDD1 at chromosome locus 16q24.3. (springer.com)
  • The hOAT3 protein was shown to be localized in the basolateral membrane of renal proximal tubules and the hOAT3 gene was determined to be located on the human chromosome 11q12-q13.3 by fluorescent in situ hybridization analysis. (aspetjournals.org)
  • Some of these responses reflect activation of G protein-coupled receptors of the endothelial differentiation gene (Edg) family. (biomedcentral.com)
  • The N-terminal sequence, 23 residues long, was used to design a gene-specific primer. (microbiologyresearch.org)
  • Southern nalyses at medium and high stringency indicated that G. cingulata possesses ne gene for the secreted aspartic proteinase, and Northern blots indicated that gene expression was induced by exogenous protein and repressed by ammonium salts. (microbiologyresearch.org)
  • In this experiment, we observed cytokine gene expression changes in Gallus gallus embryo after challenge with Delta SARS-CoV-2 RBD spike protein antigen, from a concentration of 10 µg/mL to a series of highly diluted forms in ethanol, along with controls. (openaccesspub.org)
  • One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. (cdc.gov)
  • By acquisition of the complete part or a large part of a novel ospC gene, an otherwise adapted strain would assume a new serotypic identity, thereby being comparatively fitter in an area with a high prevalence of immunity to existing OspC types. (cdc.gov)
  • By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. (cdc.gov)
  • BioMNY-mediated biotin uptake was severely impaired by replacement of the Walker A lysine residue of BioM, demonstrating dependency of high-affinity transport on a functional ATPase. (tcdb.org)
  • The constituent proteins are normally synthesised in specialised glands where the epithelial cells are responsible for the biosynthesis. (bioone.org)
  • Consequently, a lot of effort is put into identifying the constituent proteins using mass spectrometric methods. (lu.se)
  • The SARS-CoV-2 ORF8 protein is highly immunogenic and high levels of antibodies to the protein have been found in patients with or recovered from COVID-19. (wikipedia.org)
  • The modeling platform developed here uncovers insights into lipid participation in antibodies' recognition of membrane proteins and highlights antibody features to prioritize in vaccine design. (elifesciences.org)
  • Conversely, broad spectrum therapeutics like drugs and monoclonal antibodies can be generated targeting these key distant regions of the spike protein. (biorxiv.org)
  • Large scale screening of therapeutic molecules and antibodies are underway aiming to target the spike protein and consequently prevent infection. (biorxiv.org)
  • 18 The human immune system started generating antibodies specific to residues outside RBD even at the earlier stage of the pandemic. (biorxiv.org)
  • The S protein generates neutralizing -antibodies, protective immunity, and T-cell responses. (openaccesspub.org)
  • The HA is also the primary target of neutralizing antibodies elicited by infection or vaccination, and the HA of virus from this specimen is very closely related (99% identity) to the A/Astrakhan/3212/2020-like pre-pandemic candidate vaccine viruses (e.g. (cdc.gov)
  • The SARS-CoV-2 spike protein is a significant type 1 trans-membrane protein with two subunits, S1 and S2. (openaccesspub.org)
  • Sigma factors are a class of proteins constituting essential dissociable subunits that confer sequence-specific DNA binding properties to RNA polymerase (RNAP). (hindawi.com)
  • The numbers on the left and right sides of a black line in the graphical overview indicate the lengths (in amino acid residues) of the non-homologous N-terminal and C-terminal portions flanking the homologous region (indicated by the black line), respectively. (or.jp)
  • There is an urgent need for computational tools that can rapidly and reliably identify DNA-binding sites in DNA-binding proteins. (nature.com)
  • This method significantly increases the accuracy of the local per-residue quality estimates at a relatively small computational cost, as demonstrated by the results of the community wide CAMEO and CASP XIII experiments. (unibas.ch)
  • Baker and colleagues describe a novel computational method to design ligand-binding proteins, which is combined with directed-evolution experiments. (gorkalasso.com)
  • Evidence from statistical cluster analyses of a multiple sequence alignment of G protein-coupled receptor seven-helix folds supports the existence of structurally conserved transmembrane (TM) ligand binding sites in the opioid/opioid receptor-like (ORL1) and amine receptor families. (eurekamag.com)
  • A binding site is defined as all the protein residues with at least one # atom within 5A of any of the ligand atoms. (cnag.cat)
  • In the present study, the role of this residue in determining ligand selectivity for the S1P 4 receptor was examined. (biomedcentral.com)
  • As a result, the designed protein is able to bind the target ligand with picomolar affinity. (gorkalasso.com)
  • Unlike ORF7a, ORF8 lacks a transmembrane helix and is therefore not a transmembrane protein, though it has been suggested it might have a membrane-anchored form. (wikipedia.org)
  • 2023 ). (1) the BioMNY complex with ATPase (BioM) and transmembrane protein (BioN). (tcdb.org)
  • Some transporters have a conserved transmembrane protein and two nucleotide binding proteins similar to those of ABC transporters. (tcdb.org)
  • It would be an advantage if the functional effects of an nsSNP on protein structure and function could be predicted, both for the final identification process of a causal variant in a disease-associated chromosome region, and in further functional analyses of the nsSNP and its disease-associated protein. (biomedcentral.com)
  • Comparative genomic and experimental analyses ( Rodionov et al . (tcdb.org)
  • A confidence score called "predicted local distance difference test" (pLDDT) is computed for each amino acid residue to estimate how well the method has converged (i.e., how well the predicted structure agrees with multiple sequence alignment data and PDB structure information). (rcsb.org)
  • The Herzyk and Hubbard template is found to be in better accord with experimental studies of amine, opioid and rhodopsin receptors owing to the reduced physical separation of the extracellular parts of TM helices V and VI and differences in the rotational orientation of the N-terminal of helix V that reveal side chain accessibilities in the Baldwin et al. (eurekamag.com)
  • Tissue inhibitors of metalloproteases (TIMPs) are a multifunctional family of proteins that orchestrate extracellular matrix turnover, tissue remodelling and other cellular processes. (biomedcentral.com)
  • In addition, we sequenced 99 ospC flanking sequences from different lineages and compared the complete cp26 sequences of 11 strains as well as the cp26 bbb02 loci of 56 samples. (cdc.gov)
  • We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. (cdc.gov)
  • They are typically trained from a set of input features, which can be generally divided into three categories: protein sequence information, protein structure information and a combination of the two categories. (nature.com)
  • 2KKX: Solution Structure of C-terminal domain of reduced NleG2-3 (residues 90-191) from Pathogenic E. coli O157:H7. (rcsb.org)
  • The dysbindin domain-containing protein 1 (DBNDD1) is a conserved protein among higher eukaryotes whose structure and function are poorly investigated so far. (springer.com)
  • Our chemical-shift based secondary structure analysis reveals the human DBNDD1 as an intrinsically disordered protein. (springer.com)
  • AlphaFold is an Artificial Intelligence (AI) system developed by DeepMind that predicts a protein's three-dimensional (3D) structure from its amino-acid sequence. (embl.org)
  • The initial release of the resource provides structure predictions for most of the proteins in the human proteome as well as for the proteomes of 20 other species of significant biological or medical interest. (embl.org)
  • As a result, AlphaFold is able to produce accurate structure predictions even for amino-acid sequences that it has never encountered before. (embl.org)
  • This protocol employs two stages of structure-based sequence alignments in order to obtain reliable alignments. (researchsquare.com)
  • Three dimensional structure is highly conserved in protein evolution1. (researchsquare.com)
  • We have earlier shown that the large-scale alignments of several protein domain superfamilies are possible by resorting to structure-based sequence alignment methods13-15. (researchsquare.com)
  • Protein families, and more recently also protein superfamilies, are characterized by a shared three-dimensional structure and patterns of conservation of amino acid sequence. (aps.org)
  • Obtaining a comprehensive understanding of the factors that drive the conservation of residues at specific positions in a protein is an important challenge in understanding protein structure, function, and evolution. (aps.org)
  • Yet, the local yield a set of mean atomic positions r 0 density, averaged over volume elements of 0.1-1 nm3, varies k r k that define the ``ground-state'' protein structure, or, if resolution permits, a small substantially within a protein (14, 17, 18). (lu.se)
  • In the United States, it was easier to obtain patent protection for proteins defined by their structure. (uhthoff.com.mx)
  • Here we describe SPOT-Seq-RNA a template-based technique that combines predictions of protein-RNA complex structure and binding affinity (11). (buyresearchchemicalss.net)
  • The study of the 3D structure of proteins supports the investigation of their functions and represents an initial step towards protein based drug design. (scitevents.org)
  • Their amino acid sequences suggest that they are mainly cytosolic or nuclear proteins partly associating with membranes (Talbot et al. (springer.com)
  • Proteins of the MucR/Ros family play a crucial role in bacterial infection or symbiosis with eukaryotic hosts. (bvsalud.org)
  • The alanine substitutions of UBE2D2 residues Arg5 and Lys63, critical for activation of eukaryotic E3 ligases, also significantly decreased both NleG binding and autoubiquitination activity. (rcsb.org)
  • and MANE (Matched Annotation from NCBI and EMBL-EBI)) and 1,106 core eukaryotic protein complexes produced by RoseTTAFold and AlphaFold2 from the ModelArchive. (rcsb.org)
  • Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
  • This suggests that the 75-residue form with the characteristic NH2 terminus of an MCP is the biologically relevant species. (rupress.org)
  • In recent years, high-throughput biological techniques and large-scale experimental approaches for PPIs identification have achieved tremendous development, lots of PPIs data from different organisms has been discovered by researchers [ 2 ]. (biomedcentral.com)
  • proteins could carry out their biological functions. (lu.se)
  • Simulations estimating protein-membrane interaction strength for PGZL1 variants along an inferred maturation pathway show bilayer affinity is evolved and correlates with neutralization potency. (elifesciences.org)
  • We therefore decided to investigate whether replacement of this residue (E 3.29(122) ) with glutamine conferred LPA-responsiveness to the S1P 4 receptor and hence determine the role of this residue in this lower-affinity S1P receptor. (biomedcentral.com)
  • However, and despite important recent advances in the field, efforts have had limited success in designing proteins with high affinity and selectivity for small ligands. (gorkalasso.com)
  • The nucleotide sequence reported in this article has been submitted to the GenBank/EBI Data bank with accession number AB042505 . (aspetjournals.org)
  • A proportion of these will alter protein sequences, the most common of which is the non-synonymous single nucleotide polymorphism (nsSNP). (biomedcentral.com)
  • The proteins are subsequently secreted into the glandular lumen where they are stored until extrusion. (bioone.org)
  • Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. (cdc.gov)
  • Silks are composed principally of proteins with a predominance of alanine, serine and glycine and silk proteins are able to undergo irreversible transformations from soluble protein to insoluble fibres. (bioone.org)
  • Thus, while evolution indicates that these residues are critical, the mechanistic reason for their conservation remains unresolved. (aps.org)
  • 2022 ) predicts human DBNDD1 - with a short stretch of helical propensity between residues L77 and S95 - entirely as an IDP. (springer.com)
  • Subsequent cloning and sequencing of gcsap fragments obtained from PCR with genomic DNA revealed a 73 bp intron beginning at nt 728. (microbiologyresearch.org)
  • The contribution of tumor and stromal cells to PTX3 production in TNBC was assessed by analyzing single cell RNA sequencing data and RNAscope performed on TNBC tumor samples. (bvsalud.org)
  • RESULTS: In silico and experimental data indicate that PTX3 is mainly produced by tumor cells in TNBC and that its expression levels correlate with tumor stage. (bvsalud.org)
  • But the coverage of PPIs data is still very low and there is lots of noisy data in the PPIs dataset, since experimental methods inevitably produce false-positive results [ 5 ]. (biomedcentral.com)
  • The alignments of protein sequences are required for the organization and assimilation of vast amounts of data. (researchsquare.com)
  • The analysis of sensor space data can be used to determine systematic differences of neural activity between experimental conditions in target AEF components. (jak1inhibitor.com)
  • Our experimental data on photoactive yellow protein argue against a role in allosteric switching or protein stability. (aps.org)
  • crystal contacts also agrees with experimental data. (lu.se)
  • The modeling was based on templates from the LeuT-fold protein family and was done with emphasis on the refinement of the substrate-ion binding pocket. (elsevierpure.com)
  • This metric predicts the regions of sequence where the model is likely to be of high quality and the regions where the model is probably less reliable. (embl.org)
  • A third output from AlphaFold predicts the uncertainty in the relative position, orientation and thus distance between pairs of residues. (embl.org)
  • Sphingosine-1-phosphate and lysophosphatidic acid (LPA) are ligands for two related families of G protein-coupled receptors, the S1P and LPA receptors, respectively. (biomedcentral.com)
  • The S1P receptors contain a conserved glutamic acid residue present within the third TM that corresponds to glutamine in the LPA receptors. (biomedcentral.com)
  • G protein-coupled receptors (GPCRs) constitute a large family of integral transmembrane receptor proteins that play a central role in signal transduction in eukaryotes. (biomedcentral.com)