PeptideActive-site residuesPositively charged residuesAmino acidsMotifsGenome sequencesCysteine residuesAnnotationIntegral membraneHomologySubunitHighly conservedStructuresParticipate in protein-protein inteEndogenousComplexesMacromoleculesMotifHydrophobic interactionsChainsFunctionalMutationsEscherichiaFolding of aminoSubunitsProperties of proteinsComputationalPhosphataseReceptorViral proteinsNotablyDimersRDNA sequenceMembrane proteinsAbstractTranscriptionSpatialEvolutionaryLeucineConformationalHelicesCDNADynamicsEnzymesPredictHydrophilicIntrinsicallyPredictingTyrosinePolymersMediateKinaseCrucialClassificationCorrelationStructureFunctionBindingAlignmentFoldPPIsGeneratePatternsRegulationInsolubleSoluble proteinImportantZincEvolutionEukaryoticStrainsMolecules
Peptide7
- The salient features of Hombres are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission. (wikipedia.org)
- Tetratrico peptide repeat interactions: to TPR or not to TPR? (embl.de)
- For chains under 40 residues the term peptide is frequently used instead of protein. (phys.org)
- Results: Mutating active site residues Trp-102β and Trp-106β significantly alters FTase peptide selectivity both in vitro and in vivo. (syr.edu)
- Short peptide sequences within viral Gag proteins (encoding the structural proteins of the virus) are required for the separation of the virus from the host cell membrane. (eu.org)
- This pD dependence is due to labile protein deuterons in acidic side-chains and surface peptide groups, which exchange rapidly with water deuterons. (lu.se)
- These opportunities are surveyed here against a background of the immunobiology of allergic sensitization and current state-of-the-art approaches to measurement of peptide/protein reactivity. (cdc.gov)
Active-site residues1
- We selected the Escherichia coli nitro/quinone reductase NfsA for chloramphenicol detoxification by simultaneously randomising eight active-site residues and interrogating ~250,000,000 reconfigured variants. (elifesciences.org)
Positively charged residues2
- Adhesion was largely thanks to the electrostatic interaction between the positively charged residues on the polymers and the negatively charged surfaces. (sortiwa.com)
- The presence of modifiable or positively charged residues before the Tyrosine was also observed in alignments, but their conservation is not strong. (eu.org)
Amino acids13
- The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. (embl.de)
- Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. (embl.de)
- Proteins are organic macromolecules made up of amino acids, which are essential components of cells and sustain life activities. (biomedcentral.com)
- All proteins are polymers of amino acids. (phys.org)
- The polymers, also known as polypeptides, consist of a sequence of 20 different L-α-amino acids, also referred to as residues. (phys.org)
- Proteins are complex biomolecules made of 20 building blocks , amino acids, which are connected sequentially into long non-branching chains, commonly known as polypeptide chains. (kdnuggets.com)
- The most common and established way to engineer a protein is to create its variants with substituted amino acids, also known as mutants. (kdnuggets.com)
- However, since there are 20 standard protein amino acids, a complete mutagenesis of 100-residue long polypeptide would yield 20 100 mutant combinations, should you decide to explore all possible combinations of typical protein amino acids. (kdnuggets.com)
- However, even with the relatively sparse (compared to a number of possible combinations of all protein amino acids in lengthy polypeptide chains) protein databases, Machine Learning can help to unravel complex, non-linear relationships between protein sequences and their structural variability and dynamics. (kdnuggets.com)
- The human TNF cDNA is 1585 base pairs in length and encodes a protein of 233 amino acids. (influenza-x.org)
- The mature protein begins at residue 77, leaving a long leader sequence of 76 amino acids. (influenza-x.org)
- IGF-1 is a 8.28 kDa protein consisting of 69 amino acids. (proteopedia.org)
- Furthermore, using sequence analysis of human genomic DNA, researchers concluded that the amino acids important for catalysis by COX-1 are conserved and are equally important for catalysis by COX-2. (medscape.com)
Motifs12
- The tetratricopeptide repeat (TPR) is a degenerate 34 amino acid sequence identified in a wide variety of proteins, present in tandem arrays of 3-16 motifs, which form scaffolds to mediate protein-protein interactions and often the assembly of multiprotein complexes. (embl.de)
- motifs of Protein Phosphatase 2A PR65/A subunit. (cellsignal.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)
- Most attempts made focus on sequence motifs of protein-protein interactions, binding sites, or sequence conservancy. (biomedcentral.com)
- Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. (biomedcentral.com)
- For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. (biomedcentral.com)
- We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. (biomedcentral.com)
- Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. (biomedcentral.com)
- The resultant motifs are then employed in predicting protein function and functional sites when given a novel sequence (pattern matching). (biomedcentral.com)
- Owing to the stability of their coiled coil structure leucine zipper (LZ) domains of bZIP factors are widely employed as dimerization motifs in protein engineering studies. (neighborshateus.com)
- Leucine zipper domains are made up of two motifs: a basic region that recognizes a specific DNA sequence and a series of leucines spaced 7 residues apart along an α-helix (leucine zipper) that mediate dimerization. (neighborshateus.com)
- LYPxL and PTAP are among the many short linear motifs that were first identified in viral proteins and only later in the regular cellular context. (eu.org)
Genome sequences4
- To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. (nature.com)
- Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. (nature.com)
- Understanding protein sequence-structure relationship is a key to solving many problems of molecular biology, such as annotation of genome sequences, protein structure prediction, protein-protein interaction, and protein evolution, among others. (cam.ac.uk)
- From the 142 confirmed cases, we performed unbiased (Illumina) and SUDV-amplicon-specific (Minion) high-throughput sequencing to obtain 120 SUDV genome-and coding-complete sequences, representing 95.4% (104/109) of SVD-confirmed individuals within a sequence-able range (Ct 30) and 10 genome sequences outside of this range and 6 duplicate genome sequences. (cdc.gov)
Cysteine residues2
- The protease of adenovirus serotype 2 requires cysteine residues for both activation and catalysis. (microbiologyresearch.org)
- Nevertheless, all 4 of them have cysteine residues that are able to make disulfide bond. (proteopedia.org)
Annotation3
- ccPDB: The ccPDB database is designed to provide service to scientific community working in the field of function or structure annotation of proteins. (wikipedia.org)
- To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions) that incorporates several pruning strategies to largely reduce the mining cost. (biomedcentral.com)
- 2016. An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. . (ncbs.res.in)
Integral membrane3
- CXCR1 is a class A, rhodopsin-like G-protein-coupled receptor (GPCR), the largest class of integral membrane proteins responsible for cellular signal transduction and targeted as drug receptors. (rcsb.org)
- This subfamily includes lantibiotic ABC transporter permease subunits EpiE, MutE, SlvE and NisE, which are highly hydrophobic, integral membrane proteins, and part of the bacitracin ABC transport system that confers resistance to the Gram-positive bacteria in which this system operates, specifically to the lantibiotics mutacin, epidermin, nisin and salivaricin, respectively. (nih.gov)
- They have been defined as monotropic integral membrane proteins located primarily in the endoplasmic reticulum (COX-1) and the perinuclear envelope (COX-2). (medscape.com)
Homology2
- Human Tumor Necrosis Factor(TNF) and Lymphotoxin(TNF-beta) are cytotoxic proteins which have similar biological activities and share 30% amino acid homology. (influenza-x.org)
- Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)
Subunit2
- TPR-containing proteins include the anaphase promoting complex (APC) subunits cdc16, cdc23 and cdc27, the NADPH oxidase subunit p67 phox, hsp90-binding immunophilins, transcription factors, the PKR protein kinase inhibitor, and peroxisomal and mitochondrial import proteins. (embl.de)
- The Leucine Zipper and the Basic DNA-Binding Domain (bZIP) This leucine zipper facilitates the dimerization of the protein by interdigitation of two leucine containing helices on different molecules and these residues form the buried subunit interface of the coiled-coil dimer. (neighborshateus.com)
Highly conserved2
- b ) Structure of I-PpoI a homodimeric, 'His-Cys box' homing endonuclease that recognizes and cleaves a highly conserved rDNA sequence. (nature.com)
- These regions are highly conserved amongst mastadenovirus pVI proteins. (microbiologyresearch.org)
Structures14
- The number of available protein structures still lags far behind the number of known protein sequences. (nih.gov)
- 3D Protein Feature View maps protein sequence features (annotations from RCSB PDB and external resources) on 3D protein structures. (rcsb.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)
- Further, a strong direct correlation was observed between the minimum inhibitory concentration values and the distance of the mutated residues in the three-dimensional structures of rpoB and katG to their respective drugs binding sites. (biomedcentral.com)
- In this presentation, first, the strict rule which describe how structure elements - beta-strands come together into super-secondary structures of sandwich-like proteins will be presented. (cam.ac.uk)
- Residues at certain positions constitute the characteristic residue pattern of specific super-secondary structures. (cam.ac.uk)
- We propose a graph-theory approach with significance and power testing to identify modules in protein structures. (biomedcentral.com)
- This modularity gives protein structures enhanced flexibility [ 3 ] and might influence its ability to respond to selection. (biomedcentral.com)
- Unique spatial arrangement of polypeptide chains yields 3D molecular structures, which define protein function and interactions with other biomolecules. (kdnuggets.com)
- It is accepted that complete understanding of protein functions and activity requires knowledge of structures and dynamics. (kdnuggets.com)
- The sequence identity among all species is about 30%, and their structures and functions should be similar in all microbes. (biorxiv.org)
- The functional domains and subdomains are indicated beneath the linearized protein structures. (medscape.com)
- Protein structures are invaluable for biochemical studies and for mechanical or molecular mechanics calculations have become the understanding of how proteins work. (lu.se)
- The most common strong alternative and complement to experimental methods to methods to obtain protein structures are X-ray crystallography obtain insight in biochemical processes. (lu.se)
Participate in protein-protein inte2
- This makes it important to predict which residues participate in protein-protein interactions using only sequence information. (nih.gov)
- The p.Asn173His mutation affects a residue in the forkhead domain that is 100% conserved among vertebrate orthologs and is predicted to participate in protein-protein interactions. (molvis.org)
Endogenous3
- Disfunction in the PPIs will affect people's health and cause diseases, research shows that many diseases are the result of abnormal PPIs involving endogenous proteins, proteins from pathogens or both [ 3 ]. (biomedcentral.com)
- Here, we set to clarify this complex matter and question of whether aggregation is an important constraint in protein evolution that can be the discriminant between beneficial and detrimental situations by considering two cases: we studied molecular evolution of proteins in an endogenous vs. exogenous host. (frontiersin.org)
- Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)
Complexes2
- Computational tools to study RNA-protein complexes. (ncbs.res.in)
- In one study of a large set of protein-ligand complexes, we tried to improve the free energies of binding by using MD simulations with QM-derived charges, which sometimes led to improved results, but not always. (lu.se)
Macromolecules1
- Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, oxygen, and sulphur. (phys.org)
Motif12
- Multiple-TPR motif proteins would fold into a right-handed super-helical structure with a continuous helical groove suitable for the recognition of target proteins, hence defining a novel mechanism for protein recognition. (embl.de)
- The TPR snap helix: a novel protein repeat motif from mitosis to transcription. (embl.de)
- Motif finding algorithms have been widely used in this field for finding sequence signatures when given a set of related sequences (pattern mining). (biomedcentral.com)
- The Leucine Zipper Motif Mediates Both DNA Binding and Protein Dimerization. (neighborshateus.com)
- The LYPxL motif binds to the V-domain of eukaryotic Alix protein. (eu.org)
- Mammalian host protein Syntenin has the LYPxL motif. (eu.org)
- The yeast YPxL motif binds to a hydrophobic groove in the central V-domain of yeast proteins Bro1 and Rim20 (Alix_V domain-containing proteins), which are implicated in vacuolar transport and the pH response respectively. (eu.org)
- As in the standard LYPxL motif, the binding is stabilized by both hydrophobic interactions as well as by a few important hydrogen bonds. (eu.org)
- In the motif of the yeast taxonomic grouping, the hydrophobic residue preceding the Tyrosine seems not to be strongly conserved. (eu.org)
- The fourth position of the motif is most commonly represented by either leucine or isoleucine, but sequence alignments indicate other hydrophobic residues are also allowed. (eu.org)
- The LYPxL motif interacts with the cellular protein Alix (ALG2-interacting protein-1, or AIP1), which is associated with the Endosomal Sorting Complex Required for Transport (ESCRT). (eu.org)
- The link between the LYPxL motif and ESCRT was then established by identifying the ESCRT-associated protein Alix as a binding partner of LYPxL ( Strack,2003 ). (eu.org)
Hydrophobic interactions1
- The helices are held together by hydrophobic interactions between leucine residues, which are located on one side of each helix. (neighborshateus.com)
Chains1
- The two protein chains forming the dimer are color-coded. (elifesciences.org)
Functional10
- A number of residues are necessary to perform a particular biochemical function, and around 40-50 residues appears to be the lower limit for a functional domain size. (phys.org)
- Protein sizes range from this lower limit to several thousand residues in multi-functional or structural proteins. (phys.org)
- Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance. (biomedcentral.com)
- 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)
- To fix ideas, functional relations containing only few biophysical parameters of this assumption can never be fully guarantied and which role zocor online purchase different parts performing a simple fully-connected neural network for predicting drug-target interaction. (stpancraschurch.org)
- Our inferred dynamic modules in the protein NPC1 are also shown to match functional components of the protein related to the NPC1 disease. (biomedcentral.com)
- We were able to describe functional/structural sub-domain architecture related to key residues for starch cleavage, calcium, and chloride binding sites in the α -amylase, and sterol opening-defining modules and disease-related residues in the NPC1. (biomedcentral.com)
- The protein-based mining mode of WildSpan is developed for discovering functional regions of a single protein by referring to a set of related sequences (e.g. its homologues). (biomedcentral.com)
- The mining results conducted in this study reveal that WildSpan is efficient and effective in discovering functional signatures of proteins directly from sequences. (biomedcentral.com)
- Bioinformatics analysis of mutations sheds light on the evolution of Dengue NS1 protein with implications in the identification of potential functional and druggable sites. (ncbs.res.in)
Mutations8
- Recent structural determination of GPCRs has advanced by modifying the receptors with stabilizing mutations, insertion of the protein T4 lysozyme and truncations of their amino acid sequences, as well as addition of stabilizing antibodies and small molecules that facilitate crystallization in cubic phase monoolein mixtures. (rcsb.org)
- Specifically, aggregation was found to be associated with increased cell fitness in the case of TDP-43 mutations, as it protects the host from aberrant interactions. (frontiersin.org)
- By contrast, in the case of TEM-1 beta-lactamase mutations, aggregation is linked to a decreased cell fitness due to inactivation of protein function. (frontiersin.org)
- Any situation, such as mutations or anomalous expression, could result in disruption of these beneficial interactions with consequent aggregation and depletion of normal function. (frontiersin.org)
- In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods. (biomedcentral.com)
- A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. (biomedcentral.com)
- Mutations in one module favor growth over maintenance through a partial loss of an interaction associated with faster elongation. (bvsalud.org)
- Moreover, I have intentionally left out a fundamentally important fact - mutations may significantly affect protein dynamics, and thus its function). (kdnuggets.com)
Escherichia2
- We applied GLASS to a dataset of 60,472 Escherichia coli strains and used this to reexamine the longstanding debate about the role of essentiality versus expression level in the rate of protein evolution. (bvsalud.org)
- Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors. (ncbs.res.in)
Folding of amino1
- Then the main sequence regularities (a specific set of residues at particular positions), which dictate the folding of amino acid sequence will be described. (cam.ac.uk)
Subunits1
- Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a microfilament. (phys.org)
Properties of proteins2
- In our paper, we use GCNs to learn the position information of proteins in the PPIs networks graph, which can reflect the properties of proteins to some extent. (biomedcentral.com)
- The biggest value of Machine Learning methods in prediction of biophysical properties of proteins is their ability to " equate " loosely related protein features to measurable experimental data. (kdnuggets.com)
Computational4
- In this study, computational models for 11 influenza proteins have been constructed using the machine learning algorithm random forest for prediction of host tropism. (springer.com)
- 172 Computational analysis and prediction of proteins that undergo domain swapping. (ncbs.res.in)
- Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening. (ncbs.res.in)
- We mostly used molecular mechanics (MM) in order to model the protein-ligand interactions, which is more approximate than quantum-mechanical (QM) methods, but necessary to reduce the computational cost when doing calculations on protein-ligand systems, which often contain tens of thousand of atoms. (lu.se)
Phosphatase3
- The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. (embl.de)
- Here, we report the crystal structure of the TPR domain of a protein phosphatase, PP5. (embl.de)
- For phosphatase treatment, total proteins were isolated from pollen grains (Fig 6A). (stpancraschurch.org)
Receptor7
- The receptor is in liquid crystalline phospholipid bilayers, without modification of its amino acid sequence and under physiological conditions. (rcsb.org)
- Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). (nature.com)
- Protein docking of amino acid sequences of IBD Virus and chicken MHC II molecules indicated a possible receptor - ligand type relationship. (eajournals.org)
- IGF-1 then acts as a ligand and can interact with Insulin Receptor protein and Insulin-like Growth Factor Binding Protein . (proteopedia.org)
- Insulin-like Growth Factor 1 Receptor ( IGF-1R ) is a transmembrane protein receptor. (proteopedia.org)
- At the cellular level, the actions of glucocorticoids are mediated by a 94-kd protein, the glucocorticoid receptor (GR). The human (h) GR belongs to the steroid/thyroid/retinoic acid superfamily of nuclear receptors and functions as a ligand-dependent transcription factor that regulates the expression of glucocorticoid-responsive genes positively or negatively. (medscape.com)
- The AF-1 plays an important role in the interaction of the receptor with molecules necessary for the initiation of transcription, such as coactivators, chromatin modulators, and basal transcription factors, including RNA polymerase II, TATA-binding protein (TBP), and a host of TBP-associated proteins (TAFIIs). (medscape.com)
Viral proteins2
- Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. (nature.com)
- Temperature sensitivity of processing of viral proteins. (microbiologyresearch.org)
Notably1
- Notably, the result of sequences pi and the LFP, e. (stpancraschurch.org)
Dimers3
- Nonpolar and ionic interactions in histone-like nucleoid-structuring (H-NS) site1 and site2 dimers. (elifesciences.org)
- How are dimers of leucine zipper proteins dimerize? (neighborshateus.com)
- Dimers of leucine zipper proteins recognize short, inverted, repeat sequences. (neighborshateus.com)
RDNA sequence1
Membrane proteins2
- Alix is associated with the ESCRT system, which is involved in endosomal sorting of membrane proteins. (eu.org)
- The ESCRT system is involved in the selective trafficking of membrane proteins to the lysosome by incorporating the membrane proteins into multivesicular bodies (MVBs). (eu.org)
Abstract2
- abstract = "Background: FTase recognizes and modifies many proteins with C-terminal CA1A2X sequences. (syr.edu)
- abstract = "We have studied the thermodynamically significant low-energy conformations of 200 random 24-residue model proteins on a square lattice with the Rosenbluth and Rosenbluth (1955) chain growth algorithm combined with multilink additions and Boltzmann weighting. (princeton.edu)
Transcription7
- The recently discovered TPR gene family encodes a diverse group of proteins that function in mitosis, transcription, splicing, protein import and neurogenesis. (embl.de)
- The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
- The basic leucine zipper (bZIP) transcription factors are sequence-specific DNA-binding proteins that regulate transcription. (neighborshateus.com)
- Basic-region leucine zipper (bZIP) proteins are one of the largest transcription factor families that regulate a wide range of cellular functions. (neighborshateus.com)
- The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
- Among the established custom DNA binding domains, Cas9 is most easily scaled to facilitate genome-scale perturbations 3 , 4 due to its simplicity of programming relative to zinc finger proteins and transcription activator-like effectors (TALEs). (cdc.gov)
- Cas9 nuclease can be converted into an RNA-guided DNA binding protein (dCas9) via inactivation of its two catalytic domains 12 , 13 and then fused to transcription activation domains. (cdc.gov)
Spatial2
- The spatial arrangement of alpha-helices in the PP5-TPR domain is similar to those within 14-3-3 proteins. (embl.de)
- To be able to perform their biological function, proteins fold into one, or more, specific spatial conformations, driven by a number of noncovalent interactions such as hydrogen bonding, ionic interactions, Van Der Waals forces and hydrophobic packing. (phys.org)
Evolutionary5
- Given the double valence of protein aggregation that can result either in the formation of toxic assemblies or physiologically required organelles, it has long been debated what could determine whether aggregation is beneficial or detrimental from an evolutionary perspective. (frontiersin.org)
- Inferring protein-protein interacting sites using residue conservation and evolutionary information. (paperexplained.cn)
- We also analyzed the evolutionary modularity of a data set of α -amylase catalytic domain homologs, and the dynamic modularity of the Niemann-Pick C1 (NPC1) protein N-terminal domain. (biomedcentral.com)
- We still use a similar thought relating protein evolution, since domains are accepted as the protein evolutionary modules, and its modular reuse has been demonstrated in all domains of life [ 2 ]. (biomedcentral.com)
- 2020. Distinct Evolutionary Origins of Intron Retention Splicing Events in Antiporter Transcripts Relate to Sequence Specific Distinctions in Species. . (ncbs.res.in)
Leucine2
- The leucine zipper is formed by amphipathic interaction between two ZIP domains. (neighborshateus.com)
- Like valine, leucine is hydrophobic and generally buried in folded proteins. (neighborshateus.com)
Conformational2
- Results from comparative analysis of residue conservation, conformational mobility, and coevolutionary patterns for uracil-DNA glycosylase. (bahargroup.org)
- The CusB protein is part of the CusCBA periplasmic Cu(I) efflux system in Gram-negative bacteria, and it was recently reported to play a key role in the functioning of the whole CusCBA system, in which conformational changes as well as the assembly/disassembly process control the opening of the transporter. (biorxiv.org)
Helices1
- Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. (embl.de)
CDNA1
- However, it is difficult to capture the complexity of transcript isoform variance using these libraries, and large cDNA sequences are often difficult to clone into size-limited viral expression vectors. (cdc.gov)
Dynamics8
- Dynamics of p38 MAP kinase inferred from a structural ensemble using PCA is compared to intrinsic dynamics of the protein modeled using ANM. (bahargroup.org)
- Workflow for comparative analysis of sequence evolution and structural dynamics is shown. (bahargroup.org)
- Comparative analysis of dynamics of drug target proteins and model systems from experiments (PCA) and theory (ANM). (bahargroup.org)
- Moreover, iron interactions with N-terminally acetylated α S, the physiologically relevant form of the human protein, will be addressed to shed light on the current understanding of protein dynamics and the physiological environment in the disease state. (hindawi.com)
- Protein structure, function and dynamics predictions through Machine Learning methodology are not an exception. (kdnuggets.com)
- Thus predictions using complex numerical models that underlie Machine Learning methodology, can be further tweaked and refined by providing independent experimental proxies of protein structure and dynamics. (kdnuggets.com)
- For metal- powerful methods to obtain and compare reaction and activation loproteins, a third method to obtain local information about the energies for suggested enzyme mechanisms and they can also provide atomic details about the protein dynamics. (lu.se)
- Additionally, we compared how MD and grand-canonical Monte Carlo (GCMC) can be used to assess dynamics and thermodynamics of protein-ligand binding for both buried and solvent-exposed binding sites. (lu.se)
Enzymes3
- Enzymes are a type of protein that facilitate chemical reactions. (elifesciences.org)
- Frequently, researchers are aiming at improving catalytic performance of protein enzymes, or adding completely new types of chemical activities to known proteins. (kdnuggets.com)
- In drug discovery, it is of utmost importance to accurately calculate the free energies of binding ligands to various protein targets, such as enzymes and receptors. (lu.se)
Predict8
- To further evaluate the advantages and disadvantages of the model, the one-core and crossover network are conducted to predict PPIs, and the data show that the model correctly predicts the interaction pairs in the network. (biomedcentral.com)
- In this paper, AAC, CT and AC methods are used to encode the sequence, and SDNN-PPI method is proposed to predict PPIs based on self-attention deep learning neural network. (biomedcentral.com)
- It can also correctly predict the protein interaction of cell and tumor information contained in one-core network and crossover network.The SDNN-PPI proposed in this paper not only explores the mechanism of protein-protein interaction, but also provides new ideas for drug design and disease prevention. (biomedcentral.com)
- 20 ] proposed auto covariance (AC) to extract information from protein sequences and used support vector machine model to predict PPIs in the Saccharomyces cerevisiae dataset with 88.09% accuracy. (biomedcentral.com)
- 22 ] utilized four categories of protein sequence information (AC, CT, LD, MAC) to encode proteins as feature vectors focusing on dimensionality reduction and proposed a new hierarchical PCA-EELM (principal component analysis-integrated extreme learning machine) model to predict protein interactions. (biomedcentral.com)
- In addition, features from all 11 proteins were used to construct a combined model to predict host tropism of influenza virus strains. (springer.com)
- These signatures can then be used to predict function or functionally important residues of a novel protein. (biomedcentral.com)
- DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity. (ncbs.res.in)
Hydrophilic2
- We use a model proposed by Dill (1985) that represents the protein as a connected sequence of hydrophobia and hydrophilic beads on the lattice with nearest-neighbor interactions between the constituent beads. (princeton.edu)
- Two interaction sets were investigated - attraction between just the hydrophobia beads and attraction between hydrophobia residues and also between hydrophilic residues. (princeton.edu)
Intrinsically2
- In salivaricin D-producing strain Streptococcus salivarius 5M6c, self-immunity against the intrinsically trypsin-resistant salivaricin is mediated via ABC transporter proteins SlvF, SlvE and SlvG, while in Lactococcus lactis, self-immunity against nisin is mediated by the ABC transporter NisFEG. (nih.gov)
- The major constituent of LBs is aggregated α -synuclein ( α S), an intrinsically unfolded protein predominantly localized in the presynaptic regions of dopaminergic neurons. (hindawi.com)
Predicting4
- Most proteins perform their functions by interacting with other proteins, so predicting PPIs accurately is crucial for understanding cell physiology. (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)
- Further, protein structural modelling could provide a means of predicting the impact of polymorphisms on drug efficacy in the absence of phenotypic data. (biomedcentral.com)
- Understanding and predicting host tropism of influenza proteins lay an important foundation for future work in constructing computation models capable of directly predicting interspecies transmission of influenza viruses. (springer.com)
Tyrosine3
Polymers4
- It has been challenging, however, to introduce such sequences in synthetic polymers due to difficulties in controlling monomer sequences. (sortiwa.com)
- Gong and her colleagues discovered that the synthetic polymers with adjacent cationic-aromatic sequences could easily be manufactured using a highly scalable, cost-effective method called "cation-p complex-aided free-radical polymerization. (sortiwa.com)
- The researchers found that the two residue types in polymers bonded together to form a hydrogel that stuck well to negatively-charged solid surfaces in saltwater - the adhesive strength approached approximately 60 kPa. (sortiwa.com)
- But, interestingly, polymers made from these cationic -aromatic monomers without adjacent sequences weren't nearly as adherent, indicating that adjacent aromatic residue enhances electrostatic interaction in high ionic strength environments. (sortiwa.com)
Mediate1
- These sequences are called late assembly (L-) domains and mediate the interaction with components of ESCRT. (eu.org)
Kinase2
Crucial2
- The intracellular loops of GPCRs are crucial for G-protein interactions, and activation of CXCR1 involves both amino-terminal residues and extracellular loops. (rcsb.org)
- More knowledge of the underlying mechanism is needed to attain a full understanding of CusB functioning, which is associated with targeting specific and crucial residues in CusB. (biorxiv.org)
Classification2
- We applied support vector machines to sequences in order to generate a classification of all protein residues into those that are part of a protein interface and those that are not. (nih.gov)
- The family-based mining mode of WildSpan is developed for extracting sequence signatures for a group of related proteins (e.g. a protein family) for protein function classification. (biomedcentral.com)
Correlation2
- Prediction of protein-protein interactions based on protein-protein correlation using least squares regression. (paperexplained.cn)
- To our knowledge, there is no other method attempting to identify sub-domain architecture from the correlation among residues. (biomedcentral.com)
Structure14
- In Antigen DB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. (wikipedia.org)
- We combine structure-based protein engineering and molecular genetics to restrict the activity of the potentially toxic endonuclease to spermatogenesis. (nature.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)
- Folding a protein sequence into its minimum-energy structure represents such a problem. (lu.se)
- Protein folding, going from sequence to structure by mini- a quadratic Hamiltonian requires additional spin variables and mizing an energy function, represents a difficult optimization implementing interactions such as self-avoidance becomes problem. (lu.se)
- repeats vary more in length, amino acid sequence and 3D-structure. (cellsignal.com)
- In order to understand the functions of proteins at a molecular level, it is often necessary to determine the three dimensional structure of proteins. (phys.org)
- This is the topic of the scientific field of structural biology, that employs techniques such as X-ray crystallography or NMR spectroscopy, to determine the structure of proteins. (phys.org)
- 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 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)
- The pattern can be viewed as an amino acid 'tag' that brands a sequence as having a particular super-secondary structure. (cam.ac.uk)
- In the protein world, the phenotype is the structure and the phenotypic variance is given by slight variations in protein structure shape. (biomedcentral.com)
- Although the very basic forces that govern protein 3D structure formation are known and understood, the exact nature of polypeptide folding remains elusive and has been studied extensively for the past 50 years. (kdnuggets.com)
- The sequence, structure, and habitat of selected histone-like nucleoid-structuring (H-NS) orthologs. (elifesciences.org)
Function6
- PPIs play an important role in cellular systems of organisms, most proteins perform their functions by interacting with other proteins, so information about the PPIs can help us better understand the function of proteins [ 1 ]. (biomedcentral.com)
- Loss of solubility and aggregation can lead to the partial or complete abrogation of protein function. (frontiersin.org)
- The majority of proteins function as monodispersed ordered species dissolved in intra- or extra-cellular aqueous fluids. (frontiersin.org)
- You can make a quick protein representation in interactive sessions using showProtein() function. (bahargroup.org)
- We targeted two methionine residues (M227 and M241) that are essential for the proper function of CusB. (biorxiv.org)
- On the nature of a glassy state of matter in a hydrated protein: Relation to protein function. (expasy.org)
Binding10
- containing proteins include the Ran-GTP binding importin and exportin cargo transport proteins. (cellsignal.com)
- In one data set, mutants of a protein involved in RNA biogenesis and processing, human TAR DNA binding protein 43 (TDP-43), were expressed in S. cerevisiae . (frontiersin.org)
- Coevolution of NEF-binding residues analzyed using mutual information is displayed for the Hsp70 ATPase domain. (bahargroup.org)
- IGF binding proteins ( IGFBPs ) weight 24 to 45 kDa. (proteopedia.org)
- Once IGF1 is bound to Insulin-like Growth Binding Protein (IGFBP), IGF-1 cannot be linked to IGF1R any longer. (proteopedia.org)
- IGFBP-3 , the most abundant protein, accounts for 80% of all IGF binding. (proteopedia.org)
- IGF-1 docks IGFBP with a series of polar and non-polar interactions all along its binding site. (proteopedia.org)
- It leans against three hydrophobic residues on the Alix surface, with the binding centered on a conserved phenylalanine in ALIX ( Baietti,2012 ). (eu.org)
- Collation and analyses of DNA-binding protein domain families from sequence and structural databanks. (ncbs.res.in)
- The human GR is a modular protein composed of distinct regions illustrated in panel B in the image below, as follows: (1) The amino-terminal A/B region, also called immunogenic or N-terminal domain (NTD) and (2) the C, D, and E regions, which correspond to the DNA-binding domain, the hinge region, and the ligand-binding domain, respectively. (medscape.com)
Alignment2
- The site2 sequence alignment indicates in red the residue sites that potentially form salt bridges in H-NS ST , and in green the residues that form nonpolar contacts in H-NS ST . For additional details, see Figure S1. (elifesciences.org)
- The discovered W-patterns are used to characterize the protein sequence and the results are compared with the conserved positions identified by multiple sequence alignment (MSA). (biomedcentral.com)
Fold3
- With a distributed encoding onto the lattice, it differs from earlier attempts to fold lattice proteins on quantum annealers, which were based upon chain growth techniques. (lu.se)
- In order to verify the generalization ability of SDNN-PPI, a 5-fold cross-validation on the intraspecific interactions dataset of Saccharomyces cerevisiae (core subset) and human is used to measure our model in which the accuracy reaches 95.48% and 98.94% respectively. (biomedcentral.com)
- However, a logical consequence of replacing a major part of a protein with a completely new amino acid sequence will likely be new fold, hence new functionality. (kdnuggets.com)
PPIs7
- Combining amino acid sequence information and position information makes a stronger representation for protein, which improves the accuracy of PPIs prediction. (biomedcentral.com)
- 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)
- Protein-protein interactions (PPIs) dominate intracellular molecules to perform a series of tasks such as transcriptional regulation, information transduction, and drug signalling. (biomedcentral.com)
- The method adopts amino acid composition (AAC), conjoint triad (CT), and auto covariance (AC) to extract global and local features of protein sequences, and leverages self-attention to enhance DNN feature extraction to more effectively accomplish the prediction of PPIs. (biomedcentral.com)
- Especially in PPIs, there are abundant amino acid sequence information data, which is sufficient to establish PPIs prediction calculation model [ 11 ]. (biomedcentral.com)
- The basic steps of PPIs prediction based on protein sequence consist of two parts: protein coding method and machine learning model. (biomedcentral.com)
- 21 ] proposed local descriptors (LD) to represent protein sequences and successfully predicted potential PPIs on Saccharomyces cerevisiae (core subset) dataset by implementing K-neighbor model. (biomedcentral.com)
Generate2
- Here we generate a synthetic sex distortion system by exploiting the specificity of the homing endonuclease I-PpoI, which is able to selectively cleave ribosomal gene sequences of the malaria vector Anopheles gambiae that are located exclusively on the mosquito's X chromosome. (nature.com)
- In representation phase, the methods generate a vectorized representation for each protein using its attribute information. (biomedcentral.com)
Patterns5
- Scutella have distinctive cell patterns that are formed by a sequence of hyphal branching and septation. (ubc.ca)
- It has been attributed to specific patterns in protein sequence , and it has an immediate consequence for protein stability , susceptibility to enzymatic digestion inside living cells, protein-protein interactions and in turn a decisive role in many debilitating human pathologies . (kdnuggets.com)
- WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. (biomedcentral.com)
- We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. (biomedcentral.com)
- It is demonstrated in this study that the W-patterns discovered by WildSpan provides useful information in characterizing protein sequences. (biomedcentral.com)
Regulation3
- Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. (embl.de)
- TNF-alpha is produced by monocytes, which can stimulate endothelial cells to produce the multilineage growth factor granulocyte-macrophage colony-stimulating factor and extend the role of this immunoregulatory protein to the regulation of hematopoiesis in vitro. (influenza-x.org)
- The role of adenovirus structural proteins in the regulation of adenovirus infection. (microbiologyresearch.org)
Insoluble1
- 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)
Soluble protein1
- TNF is a soluble protein that causes damage to tumor cells but has no effect on normal cells. (influenza-x.org)
Important6
- Features important for intracellular G-protein activation and signal transduction are revealed. (rcsb.org)
- Thus, understanding the relationship between protein evolution and aggregation is an important goal. (frontiersin.org)
- Assessing protein modularity is important to understand protein evolution. (biomedcentral.com)
- This indicates that even with this simple model, important characteristics of the low-energy states of the model proteins are sensitive to the details of the interaction set used. (princeton.edu)
- The functionally important residues of proteins are generally conserved during evolution [ 3 ]. (biomedcentral.com)
- The Mubende variant exhibited 96% amino acid similarity with historic SUDV sequences from the 1970s and a high degree of conservation throughout the outbreak, which was important for ongoing diagnostics and highly promising for future therapy development. (cdc.gov)
Zinc1
- C) Enlargement of part of the DBD showing the amino acid sequence (single letter codes) of the 2 zinc fingers and the dimerization loop (in bold). (medscape.com)
Evolution3
- Therefore, NfsA provides an opportunity to study the evolution of proteins and how bacteria adapt to antibiotics. (elifesciences.org)
- Here, we analysed two deep mutational scanning experiments to investigate the role of protein aggregation in molecular evolution. (frontiersin.org)
- Combining both interaction losses simultaneously improved maintenance and growth, challenging the idea that growth-maintenance tradeoff resorts only from limited resources, and revealing how compensatory evolution operates within RNAP. (bvsalud.org)
Eukaryotic1
- H untington, E longation Factor 3, PR65/ A , T OR) is found in the four diverse eukaryotic proteins for which the domain is named. (cellsignal.com)
Strains2
- When used together as a host tropism prediction system, zoonotic strains could potentially be identified based on different protein prediction results. (springer.com)
- The Mubende variant glycoprotein amino acid sequences exhibited 99.7% similarity altogether and a maximum of 96.1% glycoprotein similarity compared to historical SUDV strains from 1976. (cdc.gov)
Molecules1
- In the cell, most tasks are performed by big molecules called proteins, which behave like molecular machines. (elifesciences.org)