Correlation protein residues. Medical search. Frequent questions

Interactive analysis includes dendrogram of clustered residues (hierarchical cluster tree), zoomable heatmap, circular diagram of inter-residue relationships, scatterplot of multi-dimensional scaling (MDS), and the mapping of residue clusters to a protein sequence or 3D structure. (cchmc.org)
In GeomNet, the co-evolutionary features extracted from MSA that search from the sequence databases are sent to an improved residual neural network to predict the inter-residue geometric constraints. (sciencegate.app)
In EmaNet, the 1D and 2D features are extracted from the folded model and sent to the deep residual neural network to estimate the inter-residue distance deviation and per-residue lDDT of the model, which will be fed back to GeomNet as dynamic features to correct the geometries prediction and progressively improve model accuracy. (sciencegate.app)

Finally, in spite of the limited sample of residues, we have detected a clear dependence of backbone N-C(alpha)-C angle on residue conformation. (weizmann.ac.il)
Theoretical Studies of Environmental Effects on Protein Conformation. (usu.edu)
Theoretical Studies of Environmental Effects on Protein Conformation: Flexibility of the Peptide Bond S. Scheiner and C. W. Kern J. Am. Chem. (usu.edu)

2011 ) have reviewed the processes by which matrix and membrane proteins are incorporated into the peroxysome. (tcdb.org)
In the budding yeast Saccharomyces cerevisiae , the minimal transport machinery includes the membrane proteins Pex13 and Pex14 and the cargo-protein-binding transport receptor, Pex5. (tcdb.org)
Most peroxisomal membrane proteins do not have PTS1 or PTS2, and insertion requires several peroxins distinct from those required for import of soluble matrix proteins. (tcdb.org)
We could not find a correlation between the content of membrane proteins and the complexity of the organism. (rostlab.org)
In particular, we did not find significantly higher percentages of helical membrane proteins in eukaryotes than in prokaryotes or archae. (rostlab.org)
They have been defined as monotropic integral membrane proteins located primarily in the endoplasmic reticulum (COX-1) and the perinuclear envelope (COX-2). (medscape.com)

Although protein structures have been solved by experiments at an increasing rate, a flood of new sequences have been determined even more rapidly due to the advance of sequencing technologies[ 6 , 7 ]. (biomedcentral.com)
This model, hereafter formation of three-dimensional protein structures. (lu.se)
Although both the hydrophobic aliphatic chain and hydrophilic ζ -amino group of the Lys side chain presumably contribute to the structures and functions of proteins, the dual nature of the Lys residue has not been fully investigated using NMR spectroscopy, due to the lack of appropriate methods to acquire comprehensive information on its long consecutive methylene chain. (copernicus.org)
NetSurfP-2.0 is sequence-based and uses an architecture composed of convolutional and long short-term memory neural networks trained on solved protein structures. (ku.dk)
This structure represents one of the highest resolution protein structures to date and interestingly, it is the only example containing more than one molecule in the asymmetric unit with a resolution better than 1.0 A. The non-crystallographic symmetry has been used as a validation check of the geometrical parameters and it has allowed an estimate for an upper limit of errors associated with this high resolution model. (weizmann.ac.il)
2). Glycomics, the systematic study of all glycan structures in a biological system, relies on effective enzymatic and analytical techniques for correlation of glycan structure with function. (neb.com)
Other commonly used endoglycosidases such as Endoglycosidase H ( NEB #P0702 ) are not suitable for general deglycosylation of N -linked sugars, because it only deglycosylates glycoproteins containing primarily high mannose N -linked structures, as well as leaving one N -acetylglucosamine residue attached to the asparagine. (neb.com)
We demonstrate that the multipoles can be used for the quantitative description of the protein shape and for the comparison of protein structures at various levels of detail. (biomedcentral.com)
Despite this, however, when it comes to quantitatively measure the difference between protein structures, in most cases, the measure of choice remains the root mean square deviation ( rmsd ) between aligned atomic coordinates. (biomedcentral.com)
The axonemal dynein arms (outer (ODA) and inner dynein arms (IDAs)) are multiprotein structures organized by light, intermediate, light intermediate (LIC), and heavy chain proteins. (bvsalud.org)
It has long been suspected that analysis of correlated amino acid substitutions should uncover pairs or clusters of sites that are spatially proximal in mature protein structures. (unimi.it)
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)
Profiles' of protein structures and sequence alignments can detect subtle homologies. (biopred.net)
Computational analysis is increasingly important for inferring the functions and structures of proteins [1] because the speed of DNA sequencing has long since surpassed the rate at which the biological function of sequences can be elucidated experimentally. (biopred.net)
These numbers may or may not suggest that there are 1200-2600 folds in the universe of protein structures. (rostlab.org)

Intrinsically disordered regions in Pex13 and Pex5 resemble those found in nuclear pore complex proteins. (tcdb.org)
Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. (elifesciences.org)
Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations. (elifesciences.org)
However, a group of proteins called 'intrinsically disordered proteins' are flexible in their shape and lack a stable three-dimensional structure. (elifesciences.org)
analyzed the amino acid sequences of two specific intrinsically disordered proteins from different organisms to reconstruct the versions of the proteins that were likely found in their common ancestors 450-600 million years ago. (elifesciences.org)

corresponding to different fractions of hydrophobic residues. (lu.se)
For sequences with a typical fraction of hydrophobic residues, we impact on how permissive with respect to sequence specificity find that the nonrandomness can be interpreted as anticorrela- the protein folding process is-- only sequences with nonran- tions. (lu.se)
Pairwise comparison of 105 orthologous protein sequences shows a strong bias towards replacement of uncharged polar residues of mesophilic proteins by Lys/Arg, Tyr and some hydrophobic residues in their Nanoarchaeal orthologs. (biomedcentral.com)

Our analysis has been the amino acid sequences in proteins differ from what is carried out using two different methods, which differ substantially expected from random sequences in a statistically significant from what is used in ref. 3, although the starting point is similar. (lu.se)
permissive with respect to sequence specificity the protein folding process is, we have carried out the same analysis for a Section 1: Introduction toy model (7, 8), for which unbiased samples of folding and Hydrophobicity is widely believed to play a central role in the nonfolding sequences can be obtained. (lu.se)
C-terminal PTS1 [(SAC)-(KRH)-(LM)] and N-terminal PTS2 [(RK)-(LIV)-X 5 -(HQ)-(LA)] targeting sequences are recognized by Pex5p and Pex7p, respectively, which may shuttle with the substrate protein to the peroxisomal lumen. (tcdb.org)
Unless the multiple sequence alignment (MSA) for a given protein is provided by the user, alignments are generated on the server side using three iterations of PSI-BLAST with the profile-inclusion threshold of expect (e)-value = 0.001 and the number of aligned sequences 5000. (cchmc.org)
Using a single integrated model, NetSurfP-2.0 predicts solvent accessibility, secondary structure, structural disorder, and backbone dihedral angles for each residue of the input sequences. (ku.dk)
Misleading signal (or problems with the estimation of significance levels) can be caused by phylogenetic correlations between homologous sequences and from correlation due to factors other than spatial proximity (for example, correlation of sites which are not spatially close but which are involved in common functional properties of the protein). (unimi.it)
Established sequence comparison algorithms detect significant similarities between known database sequences and 35-80% of new proteins, depending on the organism. (biopred.net)
Among the conspicuous characteristics featuring its hyperthermophilic adaptation are overrepresentation of purine bases in protein coding sequences, higher GC-content in tRNA/rRNA sequences, distinct synonymous codon usage, enhanced usage of aromatic and positively charged residues, and decreased frequencies of polar uncharged residues, as compared to those in mesophilic organisms. (biomedcentral.com)

In proteins, backbone dihedral angles and side chain rotamers are commonly used as parameters, and in RNA the base pairing pattern may be used. (wikipedia.org)
We propose a novel protein single-model QA method which is built on a new representation that converts raw atom information into a series of carbon-alpha (Cα) atoms with side-chain information, defined by their dihedral angles and bond lengths to the prior residue. (sciencegate.app)

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)
Effective encoding of residue contact information is crucial for protein structure prediction since it has a unique role to capture long-range residue interactions compared to other commonly used scoring terms. (biomedcentral.com)
The residue contact information can be incorporated in structure prediction in several different ways: It can be incorporated as statistical potentials or it can be also used as constraints in ab initio structure prediction. (biomedcentral.com)
To seek the most effective definition of residue contacts for template-based protein structure prediction, we evaluated 45 different contact definitions, varying bases of contacts and distance cutoffs, in terms of their ability to identify proteins of the same fold. (biomedcentral.com)
A proper encoding of residue contact information is crucial for structure prediction because in principle, a full distance map or a residue contact map has sufficient information for reconstructing the tertiary structure of a protein[ 25 ]. (biomedcentral.com)
Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. (nature.com)
The experimental pKa values for the L30e protein in the folded state were used as a benchmark to test the robustness of pKa prediction by various computational methods such as H++, MCCE, MEAD, pKD, PropKa, and UHBD. (rcsb.org)
Two main factors affect the utility of potential prediction tools: their accuracy must enable extraction of reliable structural information on the proteins of interest, and their runtime must be low to keep pace with sequencing data being generated at a constantly increasing speed. (ku.dk)
How to use model quality assessment to further improve the accuracy of protein structure prediction, especially not reliant on the existing templates, is helpful for unraveling the folding mechanism. (sciencegate.app)
Here, we investigate whether model quality assessment can be introduced into structure prediction to form a closed-loop feedback, and iteratively improve the accuracy of de novo protein structure prediction. (sciencegate.app)
Results: In this study, we propose a de novo protein structure prediction method called RocketX. (sciencegate.app)
AbstractQuality Assessment (QA) plays an important role in protein structure prediction. (sciencegate.app)
Our experiment points out new directions for QA problem and our method could be widely used for protein structure prediction problem. (sciencegate.app)
The NMR-assisted modeling challenge in CASP13 provided a blind test to explore the capabilities and limitations of current modeling techniques in leveraging NMR data which had high sparsity, ambiguity and error rate for protein structure prediction. (sciencegate.app)
However, relatively high levels of false-positive predictions typically render such methods, in isolation, of little use in the ab initio prediction of protein structure. (unimi.it)
Using protein engineering, we created Fab mutants with defined biophysical properties and tested them in biochemical PK prediction assays and for in vivo clearance. (pegsummiteurope.com)
During the past year, applications of these powerful new HMM-based profiles have begun to appear in the fields of protein-structure prediction and large-scale genome-sequence analysis. (biopred.net)
In this review, I will explain what HMMs are, describe their strengths and limitations, and highlight how HMM-based profiles are beginning to be used in protein structure prediction and large-scale genome sequence analysis. (biopred.net)

Mutation on these residues can lead to new strains of coronavirus with different degrees of infectivity and virulence. (biorxiv.org)
Here, a systematic approach to investigate the effect of an active-site-residue mutation on a model enzyme, human carbonic anhydrase II (CA II), is described. (iucr.org)
At neutral pH, where these residues are uncharged, we find no evidence of buried water molecules near the mutation site. (lu.se)
Exhaustive mutation scanning by fluorescence-assisted mismatch analysis discloses new genotype-phenotype correlations in angiodema. (lu.se)
The patient has a mutation on exon 15, A504T, which changed an asparagine residue to a valine residue. (medscape.com)

PNGase F digestion deaminates the asparagine residue to aspartic acid, leaving the oligosaccharide intact for further analysis. (neb.com)

We believe that with the Access SARS-CoV-2 assay, clinicians get high medical value as it detects antibodies against the SARS-CoV-2 spike protein that may be more likely to confer immunity. (beckmancoulter.com)

The measurement of interproton nuclear Overhauser enhancements (NOEs) and dihedral angle restraints of aromatic amino acids is a critical step towards determining the structure of a protein. (ubc.ca)
Shown here is a strategy for assigning the H-1,C-13, and N-15 signals from the aromatic side chains of histidine, tryptophan, tyrosine, and phenylalanine using a suite of homo- and hetero-nuclear scalar and NOE correlation experiments, as well as selective deuterium isotope labelling. (ubc.ca)
In addition, a comparison of NOE information obtained from homonuclear NOE spectroscopy (NOESY) and C-13-edited NOESY - heteronuclear single quantum correlation experiments indicates that high-resolution homonuclear two-dimensional NOESY spectra of selectively deuterated proteins are invaluable for obtaining distance restraints to the aromatic residues. (ubc.ca)
E.A. Orabi and A.M. English ( 2018 ) Modeling protein S-aromatic motifs reveals their structural and redox flexibility, J. Phys Chem. (concordia.ca)
E.A. Orabi and A.M. English ( 2016 ) Sulfur-Aromatic Interactions: Modeling Cysteine and Methionine Binding toTyrosinate and Histidinium Ions to Assess Their Influence on Protein Electron Transfer , Isr. (concordia.ca)

Among various structure-based terms, residue-residue contact potentials[ 21 - 23 ] are unique in that they capture long-range interactions in a protein structure[ 24 ]. (biomedcentral.com)
Here, we used time-resolved high-throughput proteomic analyses to identify and quantify the phosphorylation events and protein-protein interactions encoding T cell ligand discrimination in antigen-experienced T cells. (nature.com)
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)
antiferromagnetic interactions among the residues. (lu.se)
Analysis of protein-solvent interactions has revealed the occurrence of an extensive cluster of water molecules, predominantly arranged in pentagonal fused rings and surrounding hydrophobic moiety of side-chains. (weizmann.ac.il)
At multiple time points during evolution, new or modified proteins - and consequently new potential interactions between proteins - have emerged. (elifesciences.org)
The findings shed light on fundamental principles of how new protein-protein interactions emerge and evolve on a molecular level. (elifesciences.org)
A next step for the future will be to investigate how other protein-protein interactions have evolved and to identify general underlying patterns. (elifesciences.org)
A deeper knowledge of how this molecular evolution happened will broaden our understanding of present day protein-protein interactions and might aid the design of drugs that can mimick proteins. (elifesciences.org)
Glycosylation defines the adhesive properties of glycoconjugates and it is largely through glycan-protein interactions that cell- cell and cell-pathogen contacts occur, a fact that highlights the importance of glycobiology. (neb.com)
Most attempts made focus on sequence motifs of protein-protein interactions, binding sites, or sequence conservancy. (biomedcentral.com)
All or other nearby charged groups, the pKa shift of a buried pH-dependent properties of proteins are ultimately governed residue is dominated by the large electrostatic self-energy by the electrostatic interactions of ionizable side chains. (lu.se)
2004). The effect of electrostatic interactions is usually polarization effects in the protein are subsumed in an quantified in terms of the shift, DpKa, of the pKa value of an apparent dielectric constant, eP. (lu.se)
[ 5 ] Its structure is characterized by a marked periodicity in leucine residues, which enables it to be involved in protein-protein interactions. (medscape.com)

Infection of human cells by the novel coronavirus (SARS-Cov-2) involves the attachment of the receptor binding domain (RBD) of the spike protein to the peripheral membrane ACE2 receptors. (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)
We applied time-independent component analysis (tICA) and protein connectivity network model, on all-atom molecular dynamics trajectories, to identify key non-RBD residues, playing crucial role in the conformational transition facilitating spike-receptor binding and infection of human cell. (biorxiv.org)
1 , 2 Largely expressed on the surface of SARS-CoV-2, the spike (S) protein plays a crucial role in binding to the host angiotensin-converting enzyme 2 (ACE2) through the receptor-binding domain (RBD) and facilitating viral entry, 3 , 4 which is therefore considered as one of the most preferred targets against SARS-CoV-2. (biorxiv.org)
The cloning of cDNA and genomic DNA encoding the PTH/parathyroid hormone-related protein (PTHrP) receptor. (massgeneral.org)
KDEL receptor (KDELR) is a key protein that recycles escaped endoplasmic reticulum (ER) resident proteins from the Golgi apparatus back to the ER and maintains a dynamic balance between these two organelles in the early secretory pathway. (bvsalud.org)
Cyclic AMP-dependent protein kinase A (PKA) is a ubiquitous enzymatic complex that is involved in a broad spectrum of intracellular receptor signaling. (bvsalud.org)
Eph receptors and their ligands, Ephrin proteins (Eph receptor interacting proteins), play a key role in many pathological states (abnormally elevated RTK activity is a feature of most human cancers), and therefore Eph receptors can be used as potential drug targets [ 9 , 10 ]. (aging-us.com)
After initial binding to heparan sulfate proteoglycan (HSPG) on the cell surface, the virus binds to its primary receptor called sodium-taurocholate co-transporting polypeptide (NTCP) through the large surface protein (LHBsAg) preS1 domain and enters the cytoplasm with the help of the epidermal growth factor receptor (EGFR) [5, 6]. (ghuhlo.top)
In the case of SARS-CoV-2, the spike proteins bind angiotensin-converting enzyme 2 (ACE2 receptor) on human cells with high affinity. (beckmancoulter.com)
Though the coronavirus uses many different proteins to replicate and invade cells, the spike protein is the major surface protein that it uses to bind to a receptor. (beckmancoulter.com)
After the spike protein binds to the human cell receptor, the viral membrane fuses with the human cell membrane, allowing the genome of the virus to enter human cells and begin infection. (beckmancoulter.com)
The coronavirus spike protein mediates entry into host cells by attaching to a receptor on respiratory cells called angiotensin-converting enzyme 2, or ACE2, 11 the existence of antibodies against it may suggest neutralization of SARS-CoV-2 infection. (beckmancoulter.com)
Research also shows that the S protein undergoes dramatic conformational changes to expose the RBD and key residues for receptor binding to enter the host cell. (beckmancoulter.com)
The Access SARS-CoV-2 IgG assay is designed to detect antibodies to the RBD (receptor-binding domain) of the spike protein, which may be important for immunity. (beckmancoulter.com)

In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. (nature.com)
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)
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)
Yan and his coworkers 11 trained a Naïve Bayes classifier by using only sequence information, such as the identities of the target residue and its sequence neighboring residues. (nature.com)
Wang and his coworkers 12 investigated the discriminative power of three sequence features from protein sequence, including the side chain pKa value, the hydrophobicity index and the molecular mass of an amino acid. (nature.com)
The full-length sequence of DAPK1 has 1,430 residues ( Farag and Roh, 2019 ), which consists of the catalytic domain (CD), the autoregulatory domain (ARD), eight ankyrin repeats, two P-loop motifs, the cytoskeletal binding domain, the death domain, and the serine-rich C-terminal tail. (frontiersin.org)
In this way, the analysis is more sensitive to teins in the SWISS-PROT data base, convincingly show that long-range correlations along the sequence. (lu.se)
We showed that the residue-residue correlations and the resultant long-range cooperativity depend on the ferritin shell packing, which, in turn, depends on protein sequence composition. (ku.edu)
Glycosylation refers to a sequence of events that take place in the Golgi body and the endoplasmic reticulum of the cells of the expression system (predominantly mammalian) that lead to post-translational addition and processing of carbohydrate or glycan moieties to the protein backbone (usually serine- or threonineâ linked glycosylation for O-linked glycans and asparagineâ linked glycosylation for N-linked glycans) (6). (chromatographyonline.com)
The ability to predict local structural features of a protein from the primary sequence is of paramount importance for unraveling its function in absence of experimental structural information. (ku.dk)
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)
To the best of our knowledge, there is no method that can predict the binding site of SAM in a given protein sequence. (edu.in)
Result: This manuscript describes a method SAMbinder, developed for predicting SAM interacting residue in a protein from its primary sequence. (edu.in)
All models were trained, tested, and evaluated on 145 SAM binding protein chains where no two chains have more than 40\% sequence similarity. (edu.in)
We prove that, when the biologically relevant portions of the proteins are retained, it can robustly discriminate between the various families in the set in a way not possible through sequence or conventional structural representations alone. (biomedcentral.com)
Accordingly, methods based on different mathematical principles such as information theory, correlation coefficients and maximum likelihood have been developed to identify co-evolving amino acids from multiple sequence alignments. (unimi.it)
An increase of a single percentage point may mean learning something useful about an additional 700 human proteins by the time elucidation of the sequence of the human genome nears completion round about the year 2002. (biopred.net)
Pairwise sequence comparison methods such as BLAST and FASTA generally assume that all amino acid positions are equally important even though a great deal of position-specific information is usually available for a protein or protein family of interest. (biopred.net)
Multiple alignments of protein sequence families indicate residues that are more conserved than others, and the points at which insertions and deletions are more frequent. (biopred.net)
A 'profile' (defined as a consensus primary structure model consisting of position-specific residue scores and insertion or deletion penalties) is an intuitive step beyond the pairwise sequence alignment methods. (biopred.net)
One is faced with a number of difficult problems: what are the best ways to set the position-specific residue scores, to score gaps and insertions, and to combine structural and multiple sequence information? (biopred.net)
The effect of sequence variations within the coding region of the C1 inhibitor gene on disease expression and protein function in families with hereditary angio-oedema. (lu.se)

Scores for each metric are organized in symmetrical matrices with the main diagonal presenting plain or weighted frequencies, as defined above, of each individual residue for MI-and χ2-based metrics, and the individual Shannon entropies using 20 states (20 amino acids) for S-based metric. (cchmc.org)
One typical algorithm is H2r, which characterizes each individual residue position k by the conn(k)-value, which is the number of significantly correlated pairs it belongs to. (uni-regensburg.de)

In this study, we detect the allosteric networks in Pseudomonas aeruginosa bacterioferritin (BfrB), bacterial ferritin (FtnA), and bullfrog M and L ferritins (Ftns) by a network-weaving algorithm (NWA) that passes threads of an allosteric network through highly correlated residues using hierarchical clustering. (ku.edu)

This group of polysaccharides has a backbone of alternating 3-linked β- d -galactose and 4-linked α- d -galactose residues (Tuvikene et al. (springer.com)
For structural analysis of asparagine-linked carbohydrates, sugars are released from the protein backbone by enzymes such as PNGase F ( NEB #P0704 ). (neb.com)
The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding and was applied to give a new insight to protein dynamics. (typeset.io)

In particular, the conformational entropy of the amino acid side chains in a protein is thought to be a major contributor to the energetic stabilization of the denatured state and thus a barrier to protein folding. (wikipedia.org)
ments of the amino acids along the protein chains. (lu.se)
To under- denoted the AB model, consists of chains of two kinds of stand the statistical distribution of hydrophobicity along proteins ``amino acids'' interacting with Lennard-Jones potentials. (lu.se)
The two protein chains forming the dimer are color-coded. (elifesciences.org)
PNGase F hydrolyzes nearly all types of N-glycan chains from glycopeptides/ proteins. (neb.com)
These species include waters of hydration, other peptide units, and the side chains of amino acid residues. (usu.edu)
Interaction of a peptide unit with the electrically charged side chains of several residues is also predicted to result in a significantly more rigid peptide. (usu.edu)
The ionizable amino acid side chains of proteins are usually located at the surface. (lu.se)
Most ionizable side chains reside at the protein surface, parent physical significance. (lu.se)

The technique had high potential for determining the structural and magnetic resonance properties and the reactivity of the radicals of proteins, nucleic acids and their building blocks. (europa.eu)
It is believed that the functional space of all proteins can be spanned by combining a rather small number of structural units, termed folds. (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)
To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. (typeset.io)
Three-dimensional (3D) structural information allows structural environments to be taken into account when scoring aligned residues, and allows insertions and deletions to be expected more frequently in surface loops than in core secondary structure elements. (biopred.net)
the regions with structural homology covered 20%-30% of all residues. (rostlab.org)
https://cen.acs.org/analytical-chemistry/structural-biology/Structure-novel-coronavirus-spike-protein/98/i8. (beckmancoulter.com)

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)
The analysis of a large in silico testbed demonstrated that specificity and precision were higher for H2rs than for H2r and two other methods of correlation analysis. (uni-regensburg.de)
Auto Core Fragment in silico Screening (ACFIS) server was used for deconstruction-reconstruction of Ciclopirox in complex with HBV core protein. (ghuhlo.top)
Mohebbi A, Ghorbanzadeh T, Naderifar S, Khalaj F, Askari FS, Sammak AS (2023) A fragment-based drug discovery developed on ciclopirox for inhibition of Hepatitis B virus core protein: An in silico study. (ghuhlo.top)

The concept is most commonly applied to biological macromolecules such as proteins and RNA, but also be used for polysaccharides and other molecules. (wikipedia.org)

The addition of a precursor 13-residue oligosaccharide moiety GlcNAc2Man8Gluc3 to the nascent polypeptide chain occurs in the endoplasmic reticulum, following which the assembly folds and acquires its secondary, tertiary, and quaternary structure. (chromatographyonline.com)

The results described here demonstrate how a granular description of the protein structure can be achieved using multipolar coefficients. (biomedcentral.com)

For anticoagulation potency, the formation of the SP/protease protein complex and the associated non-specific polar interaction between the negatively and positively charged groups in the polysaccharide and protein is responsible for anticoagulant activity. (springer.com)
Hydrophobic contact residues are shown as sphere models and polar contact residues as stick models. (elifesciences.org)
Because of the complex possible paths thorough the many buried polar residues and lack of high-resolution crystal structure, the path for protons through the E-channel is elusive. (cuny.edu)

A complex proton transfer path from the N- to the P-side is found consisting of six clusters of highly inter-connected hydrogen-bonded residues. (cuny.edu)
A weighted Pearson correlation analysis shows coupling between residue protonation states in RCs and the E-channel of Complex I. The inter-cluster correlation analysis in the E-channel shows there is not much correlation between the clusters. (cuny.edu)

Ca 2+ /CaM binds to the death-associated protein kinase 1 (DAPK1) to regulate intracellular signaling pathways. (frontiersin.org)
We then test the parameterization on a benchmark set of the protein kinase-like superfamily. (biomedcentral.com)
AKAP12 expression levels also affected the expression of stemness markers associated with STAT3, potentially via regulating the expression of protein kinase C. CONCLUSION: This study suggests Colorectal CSCs overexpress AKAP12 and maintain stem cell characteristics through the AKAP12/PKC/STAT3 pathway. (bvsalud.org)
Studies have shown that this retrograde transport pathway is partly regulated by two KDELR-interacting proteins, acyl-CoA-binding domain-containing 3 (ACBD3), and cyclic AMP-dependent protein kinase A (PKA). (bvsalud.org)
The activity of PKA depends on A-kinase anchoring proteins (AKAPs) that attach to PKAs close to their substrates to control signaling. (bvsalud.org)
Inhibiting Focal Adhesion Kinase (FAK), Protein Kinase B (PKB) and Extracellular Regulated Rotein Kinases (ERK) affects cell motility and survival. (aging-us.com)
Inflammatory cytokines and growth factors via RSK AKT and Protein Kinase A (PKA) induce phosphorylation of EphA2 Ser897. (aging-us.com)
Its activation is tightly controlled by numerous other signaling proteins including protein kinase C (PKC), Sab/SH3BP, and caveolin-1. (medscape.com)

We defined quantitative signatures of ligand affinity based on protein phosphorylation and protein-protein interaction (PPI) stoichiometry for critical molecular events associated with TCR signaling. (nature.com)
While the phosphorylation of tyrosine residues in the immunoreceptor tyrosine-based activation motifs (ITAMs) of Cd3 and the inducible interaction between Cd3 and Zap70 remained largely unaffected, the abundance of activated Zap70 dropped with decreasing peptide affinity. (nature.com)
Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
A cooperative and competitive interaction between multiple enzymes, cell lines, and cell culture conditions causes processing of the oligosaccharide structure during which some of the already attached moieties like mannose are trimmed to yield a fiveâ residue core (Man3GlcNAc2), to which N-acetylglucosamine (GlcNAc), fucose, galactose, and N-acetylneuraminic acid (sialic acid or Neu5Ac) residues get added in a probabilistic fashion. (chromatographyonline.com)
Proteomics, the systematic study of proteins in biological systems, has expanded the knowledge of protein expression, modification, interaction and function. (neb.com)

When results of fold recognition were examined for individual proteins, we found that the effective contact definition depends on the fold of the proteins. (biomedcentral.com)

The conformational entropy associated with a particular structure or state, such as an alpha-helix, a folded or an unfolded protein structure, is then dependent on the probability of the occupancy of that structure. (wikipedia.org)
The entropy of heterogeneous random coil or denatured proteins is significantly higher than that of the tertiary structure of its folded native state. (wikipedia.org)
The tertiary structure of proteins provides crucial information for understanding molecular mechanisms of biological functions. (biomedcentral.com)
2. investigation of structure, i.e. surface accessibility and confinement, and dynamic processes, i.e. intermolecular electron and proton transfer, in native and ill defined partly folded and denatured states of proteins as promising new applications. (europa.eu)
The tool is part of the POLYVIEW-2D protein structure visualization server and available from the resulting pages of POLYVIEW-2D. (cchmc.org)
Methods of correlation analysis allow for the identification of pairs of residue positions, whose occupancy is mutually dependent due to constraints imposed by protein structure or function. (uni-regensburg.de)
We determined A by deducing substitution frequencies from contacting residue pairs observed in the homologs of 35 809 proteins, whose structure is known. (uni-regensburg.de)
We observe a correlation of 80% between predictions and experimental data for solvent accessibility, and a precision of 85% on secondary structure 3-class predictions. (ku.dk)
AbstractComputational methods that produce accurate protein structure models from limited experimental data, e.g. from nuclear magnetic resonance (NMR) spectroscopy, hold great potential for biomedical research. (sciencegate.app)
The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis. (weizmann.ac.il)
This correlation can be fruitfully used as a valuable tool in protein structure validation. (weizmann.ac.il)
The specific order of amino acids in a protein determines its shape and structure, which in turn controls what the protein can do. (elifesciences.org)
That the structure determines the function of proteins is a central paradigm in biology. (biomedcentral.com)
The functions of a protein are determined by its three dimensional structure. (biomedcentral.com)
In the protein world, the phenotype is the structure and the phenotypic variance is given by slight variations in protein structure shape. (biomedcentral.com)
Emerin is a 34-kd protein that belongs to a family of nuclear proteins that bind a variety DNA regulatory molecules and to molecules thought to be important in maintaining nuclear membrane structure. (medscape.com)
2 Howes L. Structure of novel coronavirus spike protein solved in just weeks. (beckmancoulter.com)
https://www.livescience.com/coronavirus-spike-protein-structure.html. (beckmancoulter.com)

2023 ). Imaging fluorescence cross-correlation spectroscopy showed that cargo import correlates with transient focusing of GFP-Pex13 and GFP-Pex14 on the peroxisome membrane. (tcdb.org)
We present new methods to measure the cross correlation term coming from the interference between the dipolar (NH) and the nitrogen-15 chemical shift anisotropy relaxation mechanisms. (univ-lorraine.fr)
The interest to include the cross correlation parameters in order to determine simultaneously the chemical exchange and the chemical shift anisotropy is also exposed. (univ-lorraine.fr)

B ) Table showing observed molecular weight and calculated molecular weight for monomeric protein of H-NS 1-57. (elifesciences.org)
Application of principal component analysis in protein unfolding: an all-atom molecular dynamics simulation study. (typeset.io)
We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide-ubiquitin and melittin. (typeset.io)
Equilibrium molecular dynamics simulations, in which proteins spontaneously and repeatedly fold and unfold, have recently been used to help elucidate the mechanistic principles that underlie the folding of fast-folding proteins. (typeset.io)

Electrostatic contribution of ionizable groups to the protein stability can be estimated from the differences between the pKa values in the folded and unfolded states of a protein. (rcsb.org)
The pKa values in both the folded and unfolded states obtained at 298 and 333 K were similar, suggesting that electrostatic contribution of ionizable groups to the protein stability were insensitive to temperature changes. (rcsb.org)
Such buried ionizable groups destabilize the protein and may trigger conformational changes in response to pH variations. (lu.se)

Considering substitution frequencies for residue pairs by means of the von Neumann entropy and a p-value improved the success rate in identifying important residue positions. (uni-regensburg.de)

No significant correlation was observed between predictors. (ghuhlo.top)
There was a significant correlation between pre-operative cystic fluid CEA level and the intensity of luminal CEA staining. (gastrores.org)

6 Significantly, the sites in S protein have been demonstrated to be vulnerable to acquire mutations. (biorxiv.org)
Sets of pairs of sites whose behaviour is identified by these methods as correlated are often significantly enriched in pairs of spatially proximal residues. (unimi.it)
To assess this, a study performed a pseudovirus particle-based neutralization assay and found that there was a significantly positive correlation in the neutralizing antibody titers between pseudovirus and SARS-CoV-2. (beckmancoulter.com)

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)

The NPC1 protein is involved in the intracellular lipid metabolism coordinating sterol trafficking. (biomedcentral.com)
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)

Background The identification of functionally important residue positions is an important task of computational biology. (uni-regensburg.de)

functional proteins. (lu.se)
PROT data base (6) of functional proteins, this method yields model containing only two amino acid types, hydrophobic and clear evidence for nonrandomness. (lu.se)

The traits potentially attributable to the symbiotic/parasitic life-style of the organism include the presence of apparently weak translational selection in synonymous codon usage and a marked heterogeneity in membrane-associated proteins, which may be important for N. equitans to interact with the host and hence, may help the organism to adapt to the strictly host-associated life style. (biomedcentral.com)

A large pore is formed by transmembrane proteins. (tcdb.org)
We predicted that approximately 15%-30% of all proteins contained transmembrane helices. (rostlab.org)
However, we found more proteins with seven transmembrane helices in eukaryotes and more with six and 12 transmembrane helices in prokaryotes. (rostlab.org)

M.S. Shadrina, A.M. English and G.H. Peslherbe ( 2016 ) Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O 2 Migration and Escape in Myoglobin as a Case Study , J. Chem. (concordia.ca)

The server computes pairwise coevolution scores using three metrics: Mutual Information, Chi-square Statistic, and Pearson correlation. (cchmc.org)
Coevolution scores are computed from the MSA using three different covariance metrics: mutual information ( MI , Eq. 1), chi-square statistic ( χ 2 , Eq. 2), and Pearson correlation ( r , Eq. 3). (cchmc.org)

PNGase F cleaves between the innermost GlcNAc and asparagine residues of high mannose, hybrid and complex oligosaccharides from N -linked glycoproteins (5), as shown in Figure 2. (neb.com)

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)
Microbiological and gene expression data correlated in four instances, existing knowledge of the substrate specificity of NorC resulted in correlation in two others, and a transcriptional/translational disconnect is possible for the remaining two. (manchester.ac.uk)

Lower fold recognition accuracy was observed when inaccurate threading alignments were used to identify common residue contacts between protein pairs. (biomedcentral.com)

In addition to improved accuracy, the processing time has been optimized to allow predicting more than 1000 proteins in less than 2 hours, and complete proteomes in less than 1 day. (ku.dk)

This is consistent with reports that the slow phosphorylation of tyrosine residues of the Lat adaptor associates with recruitment and activation of the phospholipase Plcγ1, thereby constituting an important kinetic bottleneck for ligand discrimination 11 . (nature.com)

for example, empirical methods to estimate the loss of conformational entropy in a particular side chain on incorporation into a folded protein can roughly predict the effects of particular point mutations in a protein. (wikipedia.org)
The limited conformational range of proline residues lowers the conformational entropy of the denatured state and thus stabilizes the native states. (wikipedia.org)
Configuration entropy Folding funnel Loop entropy Molten globule Protein folding Doig AJ, Sternberg MJE. (wikipedia.org)
1995). Side-chain conformational entropy in protein folding. (wikipedia.org)
Zhang J, Liu JS (2006) On Side-Chain Conformational Entropy of Proteins. (wikipedia.org)
1993). Empirical scale of side-chain conformational entropy in protein folding. (wikipedia.org)
At the end it will write out the total entropy, or decomposed on a residue or atom-wise basis. (lu.se)

Side-chain conformational entropies can be defined as Boltzmann sampling over all possible rotameric states: S = − R ∑ i p i ln ⁡ p i {\displaystyle S=-R\sum _{i}p_{i}\ln p_{i}} where R is the gas constant and pi is the probability of a residue being in rotamer i. (wikipedia.org)
To estimate correlation, entropies can also be calculated by employing the maximum information spanning tree algorithm [1] (MIST), with the pdb2entropy program, developed by Fogolari et al. (lu.se)
Entropies were calculated to the tenth nearest neighbor to account for high-order correlations, whereas entropies calculated to the first nearest neighbor were considered correlation-free. (lu.se)

The ancestral proteins were then 'resurrected' by recreating them in test tubes and their characteristics and properties analyzed with experimental and computational biophysical methods. (elifesciences.org)

Our model, based on time-independent component analysis (tICA) and protein graph connectivity network, was able to identify multiple residues, exhibiting long-distance coupling with the RBD opening dynamics. (biorxiv.org)
CoeViz is a web-based tool for analysis and visualization of coevolution of protein residues. (cchmc.org)
F.N. Baker and A. Porollo (2016) CoeViz: a web-based tool for coevolution analysis of protein residues . (cchmc.org)
The extent to which the conclusions drawn from the analysis of such proteins, which fold on the microsecond timescale, apply to the millisecond or slower folding of naturally occurring proteins is, however, unclear. (typeset.io)

There was linear correlation between hyperfine coupling constants and polarisation amplitude for the geminate reaction products yielding the sign and value of hyperfine coupling constants (HFCC) while the position and coupling in NMR spectrum provided assignment of individual nuclear spins in the molecule. (europa.eu)
After uncoating, the virus takes its genome into the nucleus through the nuclear transfer signal on its nucleocapsid proteins. (ghuhlo.top)

Eukaryotes contain two protein translational systems, one in the cytoplasm and one in the mitochondria. (nih.gov)
As a first attempt to address this outstanding issue, we examine here the folding of ubiquitin, a 76-residue-long protein found in all eukaryotes that is known experimentally to fold on a millisecond timescale. (typeset.io)
We found twice as many coiled-coil proteins in eukaryotes (10%) as in prokaryotes and archaes (4%-5%), and we predicted approximately 15%-25% of all proteins to be secreted by most eukaryotes and prokaryotes. (rostlab.org)
A classification by cellular function verified that eukaryotes have a higher proportion of proteins for communication with the environment. (rostlab.org)

2011) addresses two of these aspects, the translocation of soluble proteins into the peroxisomal matrix and the biogenesis of the peroxisomal membrane. (tcdb.org)

The feasibility of our approach is demonstrated for the Δ+ PHS/V66K variant of staphylococcal nuclease (SNase), which contains 21 Lys residues, including the engineered Lys-66 with an unusually low p K a of ∼ 5.6. (copernicus.org)
To examine the role of water penetration, we have measured the 17O and 2H magnetic relaxation dis- persions (MRD) for the V66E and V66K mutants of staphylococcal nuclease, where glutamic acid and lysine residues are buried in predominantly apolar environments. (lu.se)

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)
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)

Using this pKa-shift approach, we experimentally measured the electrostatic contribution of all aspartate and glutamate residues to the stability of a thermophilic ribosomal protein L30e from Thermococcus celer. (rcsb.org)

Anatomy10

Organisms11

Chemicals and Drugs109

Analytical, Diagnostic and Therapeutic Techniques and Equipment46

Phenomena and Processes78

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science10

Health Care4

Inter-residue3

Conformation3

Membrane proteins6

Structures16

Intrinsically disordered5

Hydrophobic residues3

Sequences8

Dihedral angles2

Prediction18

Mutation5

Asparagine residue1

SARS-CoV-2 Spike Protein1

Aromatic5

Interactions15

Receptor15

Sequence22

Individual residue2

Hierarchical1

Backbone3

Chains9

Structural7

Silico4

Macromolecules1

Endoplasmic reticulum1

Coefficients1

Polar3

Clusters2

Kinase8

Interaction5

Depends1

Structure18

Cross correlation3

Molecular4

Ionizable groups3

Frequencies1

Significant correlation2

Significantly3

Evolutionary2

NPC12

Computational biology1

Functional2

Organism1

Transmembrane3

Simulations1

Pearson2

GlcNAc1

Specificity2

Alignments1

10001

Phosphorylation1

Entropy7

Entropies3

Biophysical methods1

Analysis4

Nuclear2

Eukaryotes4

Translocation1

Staphylococcal nuclease2

Mutations2

Experimentally1