Biological proteins protein residues. Medical search. Frequent questions

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)
The SPRY2 protein contains 315 human amino acid residues (35 kDa), with the C-terminal residues 178-282 being rich in cysteine. (spandidos-publications.com)
Nevertheless, all 4 of them have cysteine residues that are able to make disulfide bond. (proteopedia.org)
Reversible cysteine modifications allow for potential redox regulation of proteins. (hindawi.com)
Our method allows for the identification of the proteins, identification of redox-sensitive cysteines within proteins, and quantification of the redox status of individual cysteine-containing peptides. (hindawi.com)
Cysteine is the most important redox-responsive amino acid within proteins largely due to the wide range of oxidation states that sulfur can occupy-so called, "sulfur switches" [ 4 ]. (hindawi.com)
In proteins where cysteine is not within the active site, activity can be modulated by changing conformation or by influencing its regulatory role, for example, iron sulfur complexes (ISCs) in aconitase possess cysteines required for its activity [ 7 ]. (hindawi.com)
Allosterically regulated proteins that require an activator are sometimes based on a thiol exchange interaction involving cysteines, for example, pyruvate kinase uses fructose bisphosphate (FBPs) as a heterotrophic activator and it contains a cysteine in its FBP binding site [ 8 ]. (hindawi.com)
Thus, reversible cysteine modifications can influence protein activity and the relative quantification of the status of the thiol can potentially provide valuable insights into protein activity where the protein exists in a range of redox states. (hindawi.com)
All IGFBP superfamily members are cysteine-rich proteins with conserved cysteine residues, which are clustered in the amino- and carboxy-terminal thirds of the molecule. (rndsystems.com)

A polyclonal antibody targeting the dimethyl-Lysine 9 of Histone 3 was tested against various H3 peptides and shown to bind to all peptides containing the dimethyl-Lysine 9, no matter the surrounding residues. (eurogentec.com)
Conventional methods involve the reaction of polymers which have one reactive end with the reactive residues of proteins/peptides. (chemistryviews.org)

To determine if the anti-PTM antibody does recognize the protein member in a specific assay, it is advised to perform a western blotting experiment, and refer to the size of the target protein member to assess its phosphorylation state. (eurogentec.com)
Phosphorylation of serine residues within Histone H3 is a highly dynamic process that associates with acetylation and methylation to create combinatorial patterns which are read by specific detector proteins (A. Sawicka & C. Seiser (2012) Biochimie 94, 2193-2201). (eurogentec.com)
Post-transitional modifications of IGFBP, including glycosylation, phosphorylation and proteolysis, have been shown to modify the affinities of the binding proteins to IGF. (rndsystems.com)
For example, phosphorylation mainly occurs on a subset of three types of amino acids, including serine (S), threonine (T) and tyrosine (Y). Methylation is predominantly found on lysine (K) and arginine (R) residues. (deepdyve.com)
Protein phosphorylation is the most common post-translation modification of proteins and regulates many biological processes. (lu.se)
Three sequential phosphorylation events on specific residues of p27, regulate the activity of these complexes and ultimately control cell cycle proliferation or arrest. (lu.se)

The system uses both global and local information (i.e., features from the entire protein such as secondary structure composition, protein length, and fraction of surface residues, and features from a local window of sequence-consecutive residues). (rostlab.org)

She was the first to improve the sequence coverage of ancient proteins by combining different techniques such as peptide mass fingerprinting and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Understanding how ancient proteins are formed and incorporated into archaeological materials are essential in sampling, evaluating contamination and planning analyses. (wikipedia.org)
a - d , f ) A simple way to gain insight into function is to use ribbon representation colored by sequence features: for example, domains ( a ), SNPs ( b ), exons ( c ), protein binding sites ( d ) and sequence conservation ( f ). ( e ) An effective way to show overall shape is with nonphotorealistic rendering using flat colors and outlines. (nature.com)
The third difference is the very high proportion of proline residues in the sequence accounting for about one-third of the sequence. (springer.com)
The idea behind the latest work 1 , 2 is simple - model the transition state for a reaction, stabilize it by surrounding it with carefully placed chemical groups, graft the resulting active site into an existing protein and then alter the amino-acid sequence of the protein to accommodate the changes. (nature.com)
The design process involved modifying the amino-acid sequence of a naturally occurring protein. (nature.com)
Protein flexibility and rigidity predicted from sequence. (rostlab.org)
We used this analysis to develop a neural network-based method that predicts flexible-rigid residues from amino acid sequence. (rostlab.org)
The most important local feature was the evolutionary exchange profile reflecting sequence conservation in a family of related proteins. (rostlab.org)
The only requirement for this method is that the protein or peptide must have a defined peptide sequence at its C-terminus, which is easily achieved by recombinant expression or by solid-phase synthesis. (chemistryviews.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)
For billions of years, the process of evolution has optimized the sequence of amino acids that make up naturally occurring proteins to suit the needs of the organisms that make them. (acm.org)
This question is a combinatorial optimization problem, because the output of a protein design computation is a sequence of amino acids. (acm.org)
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)

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)
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)
Structural biology is rapidly accumulating a wealth of detailed information about protein function, binding sites, RNA, large assemblies and molecular motions. (nature.com)
Molecular biologists view RNA structures and complexes with proteins to gain insight into RNA signal and message processing. (nature.com)
The proposal will apply an interdisciplinary approach in an international environment to maximize its chances of success: the biological role of reading domains will be evaluated with molecular biology (histone and chromatin pulldowns, ChIP-seq, confocal microscopy), biochemistry (Peptide arrays, mass spectrometry, methyltransferase activity assays) and biophysics techniques (fluorescence anisotropy, circular dichroism spectroscopy) as well as crystallography (solving the structure of reading domains). (europa.eu)
The tertiary structure of proteins provides crucial information for understanding molecular mechanisms of biological functions. (biomedcentral.com)
Disclaimer note: The observed molecular weight of the protein may vary from the listed predicted molecular weight due to post translational modifications, post translation cleavages, relative charges, and other experimental factors. (novusbio.com)
Structural flexibility has been associated with various biological processes such as molecular recognition and catalytic activity. (rostlab.org)
Exemplified by MED12, hypermethylation of these proteins by CARM1 served as a molecular beacon for recruiting coactivator protein, tudor domain-containing 3 (TDRD3), to ensure the full activation of estrogen/ERa target genes. (nih.gov)
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)
Together these proteins form a molecular switch that can be turned on and off. (elifesciences.org)
One of the key molecular events in skin sensitization is protein haptenation, i.e. the chemical modification of self-skin protein(s) thus forming macromolecular immunogens. (cdc.gov)
The basis of hapten- molecular mechanisms of the sensitization pro- protein binding work is the hypothesis that upon cess will result in novel opportunities for the skin absorption, only protein-reactive chemicals development of alternative methods for assessing (or those that can be metabolically or chemically skin sensitization hazard and relative potency of converted to protein-reactive species) are able to chemicals. (cdc.gov)
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)

It is found in proteins involved in several biological processes as diverse as signal transduction pathways, cytoskeleton organization, membrane traffic or organelle assembly. (eu.org)
This review describes recent advances in the role of human HMGB proteins and other proteins interacting with them, in cancerous processes related to oxidative stress, with special reference to ovarian and prostate cancer. (hindawi.com)
Bisected N -glycans represent a unique class of protein N -glycans that play critical roles in many biological processes. (rsc.org)
While protein arginine methyltransferases (PRMTs) and PRMT-catalyzed protein methylation have been well-known to be involved in a myriad of biological processes, their roles in carcinogenesis, particularly in estrogen receptor alpha (ERa)-positive breast cancers, remain incompletely understood. (nih.gov)
In this regard, comprehensive studies of the impact of amino acid variation on protein PTMs will be helpful for further understanding of how genetic polymorphisms are involved in regulating biological and pathological processes and providing instructive information for drug development of various related diseases. (deepdyve.com)

Insulin-like Growth Factor ( IGF-1 ) is a member of the insulin protein family. (proteopedia.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)
The superfamily of insulin-like growth factor (IGF) binding proteins include the six high-affinity IGF binding proteins (IGFBP) and at least four additional low-affinity binding proteins referred to as IGFBP related proteins (IGFBP-rP). (rndsystems.com)
ALS (Acid Labile Subunit) is a liver-derived protein that exists in a ternary complex with Insulin-like Growth Factor (IGF)-binding Protein-3 (IGFBP-3) or IGFBP-5, and either IGF-I or IGF-II. (rndsystems.com)

An example of enzymes that bind a single substrate and release multiple products are proteases , which cleave one protein substrate into two polypeptide products. (wikipedia.org)
But enzymes have evolved to accelerate only biological reactions, under the narrow set of conditions that are compatible with life. (nature.com)
Catalytically inactive proteins have been converted into modestly catalytic ones for two different reactions, but the observed enhancements of rate 6 , 7 were only about a millionth of those produced by naturally occurring enzymes. (nature.com)
Proteins are present in all living organisms and are the building materials of many essential biological compounds such as enzymes, hormones, and antibodies. (thepaleodiet.com)
The third study established that residues in active sites of enzymes are predicted by our method to have unexpectedly low B-values. (rostlab.org)
The proteins are modified post-translationally by enzymes, such as kinases, methylases and acetylases. (eurogentec.com)
Most PTMs are catalyzed by highly specific protein modifying enzymes, which have some specific recognition motif. (deepdyve.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)

He also pioneered the use of antibodies for the study of ancient proteins in the 1970s and 1980s, utilising different immunological techniques such as Ouchterlony double immunodiffusion (interactions of antibodies and antigens in a gel). (wikipedia.org)
Dental calculi are defined as calcified biofilms, created and mediated by interactions between calcium phosphate ions and a wide range of oral microbial, human, and food proteins during episodic biomineralisation. (wikipedia.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)
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)
Interactions with other proteins or molecules are another feature of cysteines that can affect protein activity. (hindawi.com)
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)
posttranslational modifications, amino acid variations, computational mutation analysis, protein PTM predictor, network biology Introduction Protein PTMs are biochemical alterations of amino acids that change the physicochemical properties of target proteins, leading to structural changes and therefore regulating protein-protein interactions and cellular signal transduction in developmental and cancer pathways [1]. (deepdyve.com)
The HP model has favorable interactions between adjacent, not directly bound hydrophobic residues. (lu.se)
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)

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)
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)
Wnts bind to the cell surface Frizzled family receptors in conjunction with low-density lipoprotein receptor-related protein family receptors (LRP5 or 6) resulting in the stabilization of intracellular beta -catenin levels (2). (novusbio.com)
While most membranous and disease related proteins are regulated by miRNAs, the G-protein coupled receptor (GPCR) family is an exception, being mostly unregulated by miRNAs. (frontiersin.org)
Global mapping of CARM1 substrates revealed that CARM1 methylates a large cohort of proteins with diverse biological functions, including regulation of intracellular estrogen receptor signaling, chromatin organization, chromatin remodeling and others. (nih.gov)
These toxins inhibit the release of neurotransmitters at the neuromuscular junction by cleaving soluble NSF attachment protein receptor (SNARE) complex proteins in nerve cells, which prevents the fusion of neurotransmitter containing vesicles to cell membranes 2 . (cdc.gov)

E.A. Orabi and A.M. English ( 2018 ) Modeling protein S-aromatic motifs reveals their structural and redox flexibility, J. Phys Chem. (concordia.ca)
The protein HMGB1 behaves as a redox sensor and its structural changes, which are conditioned by the oxidative environment, are associated with different functions of the protein. (hindawi.com)
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)
Protein sizes range from this lower limit to several thousand residues in multi-functional or structural proteins. (phys.org)
Thus, our work could open up for a novel and detailed understanding of the structural and dynamical changes involved in a much larger set of proteins. (lu.se)

Scientifically speaking, protein is a macronutrient that consists of amino acid residues joined by peptide bonds. (thepaleodiet.com)
Each serotype of BoNT hydrolyzes their protein substrates at different peptide bonds. (cdc.gov)

Changes in the redox state of cells affect proteins, lipids, and nucleic acids in different ways. (hindawi.com)

Acrylamide and its metabolite glycidamide, also considered a toxicant, are reactive compounds and readily form adducts with biological macromolecules, including proteins. (cdc.gov)
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)

The chemical structure of proteins is very systematic 5 -they consist of a chain of atoms known as the backbone , which consists of three-atom (nitrogen-carbon-carbon) repeats known as residues , each of which features a sidechain of atoms emanating from the first carbon. (acm.org)

Protein methylation at lysine residues modulates chromatin structure, affects gene expression and mammalian development. (europa.eu)
Lysine methylation marks manifest their biological effect via so-called 'readers' (or reading domains) which recognize and bind the methylation mark and directly alter the chromatin structure or act as a scaffold for other proteins, which induce biological responses. (europa.eu)
KMET-READ plans to investigate the biological role of these reading domains in essential histone lysine methyltransferases - PHDs in MLL2 and MLL3 and CDs in SUV39H1 and SUV39H2. (europa.eu)
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)

Therefore, the various concentration of the insulin proteins regulates the cell activity in different context, for instance in excess of glucose or lack of Growth Hormone. (proteopedia.org)
The V-ATPase complex regulates non-canonical Atg8-family protein lipidation through ATG16L1 recruitment. (babraham.ac.uk)

So we ask: Can we use computation to design non-naturally occurring proteins that suit our biomedical and industrial needs? (acm.org)
Due to the vast diversity of naturally occurring proteins, it is possible-and very useful-to begin a protein design computation with a naturally occurring protein and then to modify it to achieve the desired function. (acm.org)

E.A. Orabi and A.M. English ( 2018 ) A Simple Additive Potential Model for Simulating Hydrogen Peroxide in Chemical and Biological Systems , J. Chem. (concordia.ca)
For instance, the SwissVariant database (http://swissvar.expasy.org/) contained 76 613 variants in 20 244 human proteins on 10 January 2018. (deepdyve.com)

IGFBPs modulate the biological activities of IGF proteins. (rndsystems.com)

To increase the utilization of current computational resources, we 﫿rst provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. (deepdyve.com)
Kinact: a computational approach for predicting activating missense mutations in protein kinases. (lu.se)

The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains. (eu.org)
Repeat arrays of these proteins have been demonstrated or predicted to form almost identical tertiary structures: a right-handed super helix that wraps around the DNA double strand with the base specifying residue of each repeat positioned in the major groove next to its cognate target base. (uni-muenchen.de)
The code that describes the relationship between the base specifying residues and their cognate bases is often referred to as the TALE code. (uni-muenchen.de)

Association of p62, a multifunctional SH2- and SH3-domain-binding protein, with src family tyrosine kinases, Grb2, and phospholipase C gamma-1. (eu.org)
for example, kinases such as MAP kinases, JAK, PI3K and many others, when activated upon a specific stimulus in a specific cellular context, will not phosphorylate one target only, but usually a subset of different protein targets which will collectively lead to the expected stimulation. (eurogentec.com)
If these residues are inaccessible to kinases, how do they get phosphorylated then? (lu.se)
Somatic variations in protein kinases with experimental evidence demonstrating their functional role. (lu.se)
Kin-Driver: a database of driver mutations in protein kinases. (lu.se)
Nonsynonymous coding SNVs in protein kinases. (lu.se)
wKinMut: an integrated tool for the analysis and interpretation of mutations in human protein kinases. (lu.se)

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)
Residue contacts defined by Cβ−Cβ distance of 7.0 Å work best overall among tested to identify proteins of the same fold. (biomedcentral.com)
One of the goals of this work was to identify proteins in human urine modified by acrylamide exposure using SELDI-TOF-MS and four types of ProteinChip array (Bio-Rad Laboratories, Hercules, CA) to determine which array would be most useful for the planned analysis of urine from occupationally exposed workers. (cdc.gov)

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)
Redox proteomics has taken advantage of the thiol specificity of ICAT reagents not only to identify targets of ROS but also to quantify oxidative thiol modifications in individual proteins. (hindawi.com)

Conversely, broad spectrum therapeutics like drugs and monoclonal antibodies can be generated targeting these key distant regions of the spike protein. (biorxiv.org)
These residues can not only be targeted by broad spectrum antibodies and drugs, mutations in them can generate new strains of coronavirus resulting in future epidemic. (biorxiv.org)
Large scale screening of therapeutic molecules and antibodies are underway aiming to target the spike protein and consequently prevent infection. (biorxiv.org)
18 The human immune system started generating antibodies specific to residues outside RBD even at the earlier stage of the pandemic. (biorxiv.org)

The mass of the predicted mature protein of Bothrops protease A, a trypsin-like serine peptidase, is 25.4 kDa. (springer.com)

Notably, the first two post-translational modifications, which are required for the initial activation of these complexes, occur on solvent inaccessible (i.e., buried) tyrosine residues. (lu.se)

For instance, the Type I protein arginine methyltransferases are known to methylate a number of proteins that contain an arginine glycine glycine (RGG)-motif [6]. (deepdyve.com)

p27 is a protein that binds to and prevents the activation of different G1 and S phase cyclin-CDK complexes. (lu.se)
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)

More generally, bioinformatics analyses have shown that ~15% of all phosphorylated residues are buried in the non-phosphorylated state, suggesting that transient exposure might be a general mechanism involved in protein regulation. (lu.se)

Expression and purification of the mitochondrial transmembrane protein FAM210A in Escherichia coli. (rochester.edu)
BioServUKDescription:SARS Coronavirus Membrane Protein (Matrix) (E.coli) 500ugStorage conditions: -80˚C. Avoid repeated. (proteomecommons.org)

Surface-enhanced laser desorption time-of-flight mass spectroscopy (SELDI-TOF-MS) is a bioanalytical technique used for the rapid examination of intact protein or protein mixtures to exploit the biochemical or biophysical characteristics of intact molecules to separate a complex protein mixture or isolate specific protein classes. (cdc.gov)
HMGB1 is an abundant protein, 10 6 molecules per cell [ 7 ], which has been postulated as a redox sensor [ 8 ]. (hindawi.com)
Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a microfilament. (phys.org)
Proteins are a class of large molecules that are involved in the vast majority of biological functions, from cell replication to photosynthesis to cognition. (acm.org)
At neutral pH, where these residues are uncharged, we find no evidence of buried water molecules near the mutation site. (lu.se)

Indeed, it has been demonstrated that cysteines are characterized by the most extreme conservation pattern, being highly conserved in functional positions of proteins but poorly conserved otherwise [ 5 ]. (hindawi.com)
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)

Despite extensive research, bone scaffolding is still a challenge, and the role of non-collagenous proteins (a wide range of proteoglycans and other proteins) remains poorly understood. (wikipedia.org)
This often limits control of the site and the grafting ratio, and can result in heterogeneous conjugates with poorly controlled stoichiometry and unacceptably low biological activity. (chemistryviews.org)

Reading domains include Plant homeodomains (PHD) and Chromodomains (CD) found in many chromatin proteins. (europa.eu)

Like modern proteomics, the study of ancient proteins has also been enabled by technological advances. (wikipedia.org)

Human IGFBP-6 cDNA encodes a 240 amino acid (aa) residue precursor protein with a putative 24 aa residue signal peptide that is processed to generate the 216 aa residue mature protein that is O-glycosylated. (rndsystems.com)
7] analyzed amino acid variations of 15 different PTMs and indicated that about 4.5% of amino acid variations may affect protein function through disruption of PTMs, and the mutation of 238 PTMs sites in human proteins was causative of disease. (deepdyve.com)
For example, the amino acid glutamine is involved when the Listeria GEF and one of the human GEFs activate the protein, whereas a different amino acid-aspartate-is involved when one of the other human GEFs is responsible for the activation. (elifesciences.org)
create a human Rab protein that cannot be activated by the GEF from the bacteria that cause Listeria, but can still be activated by its normal human GEF. (elifesciences.org)
Recombinant human IL-15 is a 12.9 kDa protein consisting of 114 amino acid residues. (prosci-inc.com)
KinMutBase is a comprehensive knowledge base for human diseaserelated variations in protein kinase domains. (lu.se)

We found that overall the residue contact pattern can distinguish protein folds best when contacts are defined for residue pairs whose Cβ atoms are at 7.0 Å or closer to each other. (biomedcentral.com)
For capturing contacts between neighboring β strands, considering the distance between Cα atoms is better than the Cβ−based distance because the side-chain of interacting residues on β strands sometimes point to opposite directions. (biomedcentral.com)

5 , 7 - 9 More specifically, a study analyzing 10,022 SARS-CoV-2 genomes from 68 countries revealed 2969 different missense variants, with 427 variants in the S protein. (biorxiv.org)
Pathogenic and neutral variants for 82 proteins used to compare generic and protein specific predictors. (lu.se)

Mutation on these residues can lead to new strains of coronavirus with different degrees of infectivity and virulence. (biorxiv.org)
The development of better methods for mutation analysis-related protein PTMs will help to facilitate the development of personalized precision medicine. (deepdyve.com)

Therefore, when raising an anti-PTM antibody to one protein from a family, the risk is high that this antibody will also cross-react to other family members in the same sample. (eurogentec.com)
antibody, raised against a peptide harboring this PTM only, may not work in a biological sample. (eurogentec.com)
Indeed, modified residues close to one PTM may prevent the PTM-specific antibody to bind its epitope. (eurogentec.com)
Dilute the Capture Antibody to the working concentration in PBS without carrier protein. (rndsystems.com)

Ashutosh Chilkoti and colleagues, Duke University, Durham, NC, USA, developed a high-yield synthesis of site-specific protein/peptide-polymer therapeutics by using a modular approach involving recombinant expression, enzymatic attachment of an azido group to the protein/peptide, and polymer coupling by a copper-free click reaction (pictured). (chemistryviews.org)

IGF binding proteins ( IGFBPs ) weight 24 to 45 kDa. (proteopedia.org)
Some IGFBPs may also have intrinsic bioactivity that is independent of their ability to bind IGF proteins. (rndsystems.com)

RipTALs are effector proteins delivered during bacterial wilt disease caused by R. solanacearum strains. (uni-muenchen.de)
In the case of the RipTALs this work should begin to unravel the role these proteins play in bacterial wilt disease, as a means to fight this devastating pathogen. (uni-muenchen.de)
In addition the TALEs and RipTALs may simply represent one face of the TALE-likes, a protein family mediating as yet unknown biological roles as bacterial DNA binding proteins. (uni-muenchen.de)
Botulinum neurotoxins (BoNTs) are bacterial proteins that cause the life-threatening disease botulism 1 . (cdc.gov)

Improvements in mass spectrometry has led to the development of a number of techniques to quantify the relative protein abundance within a given sample. (hindawi.com)

B-values derived from experimental data are widely used to measure residue flexibility. (rostlab.org)

The Rab subfamily of proteins is part of the large Ras superfamily, and all members of this superfamily are activated and inactivated in a similar way, with the binding and unbinding of GDP and GTP taking place at a structure called the G-domain. (elifesciences.org)

This makes it applicable to a large subset of protein/peptide drugs and to diverse water-soluble polymers. (chemistryviews.org)

At least four phylogenetically distinct groups of bacteria encode repeat proteins with the common ability to bind specific DNA sequences with a unique but conserved code. (uni-muenchen.de)

This is especially important in reference to redox proteins that contain thiol switches susceptible to activation or inactivation. (hindawi.com)
Cysteines often form part of active sites, allowing for the protein to be switched on or off depending on redox state. (hindawi.com)

Scar/WAVE-1, a Wiskott-Aldrich syndrome protein, assembles an actin-associated multi-kinase scaffold. (eu.org)

As an additional benefit, it can help to reduce the risk of biological contamination, where food residues on surfaces could potentially provide nutrients for spoilage or pathogenic bacteria to thrive. (neogen.com)
With the Clean-Trace® Surface Protein Plus Test Swab, monitoring for contamination on surfaces and in hard to reach areas is simple with results in 10 minutes. (neogen.com)

Ligand orientation depends on the position of the positive residue in the target peptide. (eu.org)
We also ran QM/MM simulations on casein-kinase 2 (CK2), where the ligand and a few surrounding residues were treated at the QM level, and the rest of the system at the MM level. (lu.se)
This entropy largely stems from the fluctuation of the protein and ligand. (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)

Ancient proteins are complex mixtures and the term palaeoproteomics is used to characterise the study of proteomes in the past. (wikipedia.org)

In this review, we focus on key biological questions where visualizing three-dimensional structures can provide insight and describe available methods and tools. (nature.com)
Today's situation is very different: the rate at which structures are solved has greatly increased, with over 60,000 high-resolution protein structures now available in the consolidated Worldwide Protein Data Bank (wwPDB) 1 . (nature.com)
For example, many biochemists regularly view protein structures to gain insight into protein function ( Fig. 1 ). (nature.com)
i ) Superposition is commonly used to compare two or more related structures-for example, two distinct states of the same protein, or, as shown here, two separate proteins with similar structure (PDB 1QCF and 1FMK ) 98 . (nature.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)

Real‑time quantitative polymerase chain reaction (PCR) and western blot analyses were used to detect SPRY2 expression and miR‑21 protein expression levels. (spandidos-publications.com)

Once IGF1 is bound to Insulin-like Growth Binding Protein (IGFBP), IGF-1 cannot be linked to IGF1R any longer. (proteopedia.org)
A Rab protein is always bound to another molecule, which determines whether it is inactive or active. (elifesciences.org)

Microfilaments, microtubules, and intermediate filaments serve as the cytoskeleton of the cell and form a complex network by interacting with cytoskeleton-associated proteins. (doria.fi)

According to their differential sequences, SPRY proteins were divided into four subtypes (SPRY1, -2, -3 and -4). (spandidos-publications.com)

Cysteines are one of the most rarely used amino acids, but when conserved in proteins they often play critical roles in structure, function, or regulation. (hindawi.com)

Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)
We conclude that protein function is informative across species in predicting post-transcriptional miRNA regulation in living cells. (frontiersin.org)

Both acrylamide and glycidamide react with hemoglobin (HGB), specifically at the N-(2 carbamoylethyl) valine residue of the ß-peptide subunit. (cdc.gov)

According to the 'histone code' hypothesis, combinatorial modifications dictate a biological readout. (eurogentec.com)
Within an individual protein there may be a number of cysteines which could allow for multiple thiol modifications. (hindawi.com)

Elabscience Category Type: Polyclonal Synonyms: 2019-nCoV E protein, 2019-nCoV sM protein, Envelope small membrane protein. (proteomecommons.org)

Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues. (rochester.edu)

Anatomy11

Organisms11

Chemicals and Drugs87

Analytical, Diagnostic and Therapeutic Techniques and Equipment50

Phenomena and Processes87

Disciplines and Occupations6

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture1

Information Science13

Health Care7

Cysteine10

Peptides2

Phosphorylation6

Surface residues1

Sequence14

Molecular14

Processes5

Insulin-like G5

Enzymes8

Interactions10

Receptor7

Structural5

Peptide bonds2

Nucleic acids1

Macromolecules2

Structure of proteins1

Lysine4

Regulates2

Naturally occurrin2

20182

Modulate1

Computational2

Cognate3

Kinases7

Identify proteins3

Individual proteins2

Antibodies4

Serine1

Tyrosine1

Arginine methyltransferases1

Complexes2

Bioinformatics1

Coli2

Molecules5

Functional2

Poorly2

Chromatin1

Proteomics1

Human6

Atoms2

Variants2

Mutation2

Antibody4

Involving recombinant1

IGFBPs2

Bacterial4

Mass spectrometry1

Experimental1

Superfamily1

Subset1

Ability to bind1

Redox2

Scaffold1

Contamination2

Ligand4

Mixtures1

Structures5

Analyses1

Bound2

Cytoskeleton1

Sequences1

Play critical roles1

Regulation2

Subunit1

Modifications2

Synonyms1

Oxidation1