Investigate amino acids in the protein protein residues. Medical search. Frequent questions

This extended linker is larger than the tripeptide found in archetypal vertebrate MTs, but does not conform either with the 40-amino-acid linkers commonly found in plant MT sequences. (portlandpress.com)
The prediction models were trained on influenza protein sequences isolated from both avian and human samples, which were transformed into amino acid physicochemical properties feature vectors. (springer.com)
According to their differential sequences, SPRY proteins were divided into four subtypes (SPRY1, -2, -3 and -4). (spandidos-publications.com)
In this work, we show that substrate recognition of Tsp is mediated by a PDZ domain, a small protein module that promotes protein-protein interactions by binding to internal or C-terminal sequences of their partner proteins. (embl.de)
It should be pointed out that although the two proteins (PPDK and PEPS) share some homology, especially around a central catalytic site, they can be identified using the signature sequences identified by Tjaden and colleagues [10]. (scirp.org)
A comparison of known PPDK and PEPS sequences revealed a high level of conservation of the amino acid sequence surrounding the catalytic histidine located within a central domain of the enzymes that was composed of GGXTS/CHAAI/VI/VA/SR with the regulatory threonine and catalytic histidine (shown in bold) conserved in all species. (scirp.org)
Similarities between the physical structures of avian and mammalian MHC class I glycoproteins have been proposed by comparative alignment of their amino acid sequences. (usda.gov)
Alignment of the BFIV21 sequence with previously published BFIV sequences revealed polymorphisms at position 34 (HLA34), a monomorphic residue in HLA and H-2. (usda.gov)
Traditionally, prediction of the functions of bacterial proteins is carried out for poorly studied molecules or hypothetical proteins predicted based on these genome sequences. (custom-essay.org)
This type of method is called template-based modelling: templates can be found through comparison of amino acid sequences in software BLAST (in particular, BlastP), using text format FASTA. (custom-essay.org)
Correlations between amino-acid residues can be observed in sets of aligned protein sequences, and the analysis of their statistical and evolutionary significance and distribution has been thoroughly investigated. (strath.ac.uk)
In this paper, we present a model based on such covariations in protein sequences in which the pairs of residues that have mutual influence combine to produce a system analogous to a Hopfield neural network. (strath.ac.uk)
However, these signature sequences have not so far been extensively investigated amongst orthologous Bcl-2 family proteins. (sfr-biosciences.fr)
A: An alignment of amino acid sequences of rat preproapelin with human and bovine preproapelin. (phoenixpeptide.com)
B: An alignment of amino acid sequences of human apelin and angiotensin II. (phoenixpeptide.com)
from random sequences of amino acids is addressed. (lu.se)
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)
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)
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)
Some of the visualisations are only for protein sequences while others work also for nucleotide sequences. (lu.se)

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)
When a nitroxide radical's motion becomes more hindered (by steric interactions in the case of spin-labeled proteins), the result will be that the parameters of the CW EPR spectrum will shift towards those of the maximally anisotropic powder spectrum. (utoronto.ca)
The goal of this work is two-fold: first, we have combined mutual information and structural data to describe the amino acid networks within a protein and their interactions. (upf.edu)
As well, interactions between the MscL channel protein and surrounding lipid and the potential relevance of helical kinking in MscL gating pathways were investigated. (caltech.edu)
As could be demonstrated, the oligomerization is based on two independent interactions mediated by different domains of the protein: a known interaction of the N-terminal discoidin domain with the C-terminal portion, termed head-to-tail interaction, and a dimerization of the LisH motif in muskelin that was so far neglected in the literature. (uni-wuerzburg.de)
As part of the analyses, residues that are critical for LisH-dimerization and the head-to-tail binding, respectively, were identified, whose mutation specifically interfered with each of the interactions separately. (uni-wuerzburg.de)
These mutations allowed to investigate the interplay of these interactions during oligomerization. (uni-wuerzburg.de)
when both interactions were disturbed, the protein was present as monomer. (uni-wuerzburg.de)
Moreover, as proteases with different cleavage sites will generate different sets of peptides for the same proteome, combination digestion will yield improved results for various applications, such as identification of proteins, protein-protein interactions and post-translational modifications in various biological systems. (asbmb.org)
Both own phosphorylation status and direct protein-protein interactions are increasingly investigated [ 5 ]. (biomedcentral.com)
These studies aid in understanding how genes determining cell surface proteins can affect interactions between cells and confer viral disease resistance. (usda.gov)
We employ fluorescence spectroscopic and other biophysical methods to study protein-DNA interactions fundamental to such processes as DNA recombination and repair. (wesleyan.edu)
One focus of our research program is dynamic mechanisms of recognition in protein-DNA interactions. (wesleyan.edu)
Our current work uses these fluorescent probes to examine site-specific base dynamics in the context of protein-DNA interactions. (wesleyan.edu)
Considering the widely acknowledged Accordingly, theoretical models of the MG state invariably invoke importance of protein-solvent interactions for stability and fold- a substantial internal hydration20-22. (lu.se)
antiferromagnetic interactions among the residues. (lu.se)
Native or wild-type quaternary protein structure is usually born from a single translated protein sequence with one ordered conformation with downstream protein interactions. (medscape.com)
Protein complexes, which are formed as a result of these interactions, consist of two or more components that associate along specific pathways - protein association pathways. (lu.se)

A gene was identified (1229 bp) with a putative open reading frame (204 bp) encoding a 67-amino-acid protein exhibiting several characteristic features of MT proteins, including 16 cysteine residues (24%) and only one aromatic residue. (portlandpress.com)
Although the protein sequence showed high identity with plant and invertebrate MTs, it contained a unique 'linker ' region (14 amino acid residues) between the two putative metal-binding domains which contained no cysteine residues. (portlandpress.com)
Using site-directed mutagenesis we have shown that both PPDK and PEPS in which the serine and cysteine residues, respectively, were substituted with an alanine the enzymes could be regulated indicating that the serine and cysteine residues, respectively, are not essential for regulation. (scirp.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)
The observed conformational changes illustrate a general mechanism by which proteins can tolerate mutations. (rcsb.org)
Furthermore, the structural fate of amino acid mutations, which impair the functionality of RemA, could be investigated. (uni-marburg.de)
In addition, knowledge of protein structure may prompt potential partners for protein interaction and thus encourage researchers to develop or improve new enzymes or antibodies, or, for example, to explain the phenotype of the mutations performed or to help determine the location of the mutations in order to change specific phenotypes. (custom-essay.org)
Mutations encoding basic (Arg), non-polar (Leu and Pro) and uncharged polar (Asn, Gln and Tyr) amino acids at M39 were introduced into a DENV-2 genomic-length cDNA clone and their effects on virus replication were examined. (microbiologyresearch.org)
Selected mutations were introduced into a prM-E gene cassette and expressed transiently in COS cells to investigate whether the mutations impaired prM/E association or secretion. (microbiologyresearch.org)
Western blot analysis of the ETHE1 protein indicated that some of the missense mutations are associated with the presence of the protein, suggesting that the corresponding wild type amino acid residues have a catalytic function. (bmj.com)
Many mechanisms of protein function contribute to amyloidogenesis, including "nonphysiologic proteolysis, defective or absent physiologic proteolysis, mutations involving changes in thermodynamic or kinetic properties, and pathways that are yet to be defined. (medscape.com)
Peu de renseignements sont disponibles sur les mutations des virus saisonniers de la grippe A(H1N1)pdm09 et H3N2 en Jordanie. (who.int)
Les mutations individuelles sont décrites en détail. (who.int)

An S-peptide Fucus MT fusion protein expressed in Escherichia coli exhibited a relative molecular mass of ∼ 14 kDa. (portlandpress.com)
Photoaffinity labeling with a fluorescent nonpolar peptide caused the covalent attachment of the peptide to a single site on the Tsp protein. (embl.de)
The isolated PDZ domain (amino acids 206-334) is capable of folding into a well-behaved structure and binds to a nonpolar peptide with a dissociation constant (K(D)) of 1.9 microM, similar to that of the intact Tsp protein. (embl.de)
Site-directed mutagenesis of a surface residue at the peptide binding site of the PDZ domain, valine 229, to Glu or Gln resulted in an increase in the K(M) value but had no effect on the k(cat) value. (embl.de)
Studies with HLA-A2 have shown that changes in residue 34 do not affect viral peptide presentation. (usda.gov)
Thus, the principle of protein or peptide haptenation could be used in in vitro assays to predict the sensitization potential of a new chemical entity. (cdc.gov)
Upon signal peptide removal, the resulting 55-residue isoform, proapelin/apelin-55, can be further processed to 36-, 17-, or 13-residue isoforms with length-dependent pharmacological properties. (phoenixpeptide.com)
Inferences about hydration have usually been indirect (where the ous structural and dynamic information about the internal peptide chain is not, there is solvent) or have relied on uncertain (buried) and external (surface) hydration of globular proteins in premises. (lu.se)
Disulphide bonds forming loops of amino acids of the peptide backbone have a major impact on internal dynamics that can be interpreted with a reduced set of Zimm modes. (lu.se)
Each serotype of BoNT hydrolyzes their protein substrates at different peptide bonds. (cdc.gov)

Diana Samodova and a team at the University of Copenhagen characterized another protease, ProAlanase, isolated from the fungus Aspergillus niger , that cleaves primarily on the C-terminal side of proline and alanine amino acid residues of proteins. (asbmb.org)
Aliphatic index The aliphatic index of a protein is a measure of the relative volume occupied by aliphatic side chain of the following amino acids: alanine, valine, leucine and isoleucine. (qiagenbioinformatics.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)
One crucial determinant of host tropism is hemagglutinin (HA) receptor specificity, in particular, preference of specific species of sialic acid on host cells. (springer.com)
Until early 1990s, renal organic anion transport was thought to be carried out by a few carrier proteins that showed wide substrate specificity. (aspetjournals.org)
Trypsin has been used predominantly due to its high specificity (it cleaves exclusively after the amino acids arginine and lysine), widespread availability and ease of use. (asbmb.org)
PTEN is a protean protein with a dual-specificity cytosolic lipid and tyrosine phosphatase activity. (biomedcentral.com)
Its substrate specificity suggests that Tsp may contain a substrate recognition domain, which selectively binds to the nonpolar C-termini of substrate proteins, separate from its catalytic site. (embl.de)
We also demonstrated that altering the intermediate amino acid did not alter the specificity of the regulatory proteins for their protein substrates. (scirp.org)
Sensitivity and specificity are key characteristics for diagnostic tools, and a high sensitivity is important Ribonucleic acid (RNA) extraction was conducted on a when the test is used to identify emerging infectious 140l aliquot of each sample using the QIAamp Viral diseases. (who.int)

The hOAT3 cDNA consisted of 2179 base pairs that encoded a 543-amino-acid residue protein with 12 putative transmembrane domains. (aspetjournals.org)
Systematic deletion mutagenesis of Tsp localized the binding site to amino acids 206-307, a region that completely encompasses the putative PDZ domain (217-301). (embl.de)
By using sequence alignment of herpesviruses homologs, we identified conserved amino acids in the putative pUL105 ATP binding site and in the putative pUL70 zinc finger pattern. (frontiersin.org)
The primase pUL70 contains several conserved motifs or regions, including a region (residues 881-920) that corresponds to a putative zinc-finger pattern shown to play essential role in HSV-1 ( Biswas and Weller, 1999 ). (frontiersin.org)

The Enterobacteriaceae, which are quite common in the human gut, can create curli, which are functional amyloid proteins. (wikipedia.org)
When expressing membrane proteins, researchers must assume from the start that the protein will be difficult to express in functional form. (neb.com)
As a solution NEB offers a tunable T7 expression strain for the production of membrane proteins and other difficult targets so that the level of functional protein may be optimized. (neb.com)
Functional analysis employing site directed mutagenesis identified BF amino acid residues forming serologic epitopes as well as residues important in antigen presentation to ALV induced cytotoxic T lymphocytes. (usda.gov)
Modelling by template has a vast practical potential because if the structure of at least one protein from which functional family is known, then it is possible to try to build models for almost every protein in this family. (custom-essay.org)
This model suggests that an explanation for observed characters of proteins such as the diminution of function by substitutions distant from the active site, the existence of protein folds (superfolds) that can perform several functions based on one architecture, and structural and functional resilience to destabilizing substitutions might derive from their inherent network-like structure. (strath.ac.uk)
Functional prediction analyses suggested that ArsR M is a difunctional protein with transcriptional regulation and methyltransferase activities. (biomedcentral.com)
While deletion of the N-terminal extension had no significant functional impact in HeLa cells, our results suggest that the human Bcl2l10 protein evolved a calcium-binding motif in its alpha 5-alpha 6 interhelical region by acquiring critical negatively charged residues. (sfr-biosciences.fr)
AbstractMotivationMolecular-level classification of protein-protein interfaces can greatly assist in functional characterization and rational drug design. (edu.in)
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 tests used for protein C testing can include enzyme-linked immunosorbent assay (ELISA), chromogenic assays, and the activated partial thromboplastin time (aPTT)-based functional protein C assay. (medscape.com)
An ELISA measures protein C immunological levels with very high sensitivity but cannot detect functional defects. (medscape.com)
Chromogenic assays can detect low levels of protein C with high sensitivity and can detect most functional defects. (medscape.com)
The aPTT-based functional protein C assay may yield misleadingly low protein C levels in the presence of (1) a factor V Leiden mutation and some other causes of activated protein C resistance, (2) elevated plasma factor VIII levels, or (3) hyperlipidemia. (medscape.com)

Unexpectedly, all ten amino acid substitutions marginally reduce protein thermostability. (rcsb.org)

Maps are used to visualise physicochemical properties of amino acids in the alignment positions. (lu.se)

E 1 SO 4 transport activity surpassed GSH-stimulated levels in the presence of tripeptides in which Cys was substituted with the hydrophobic amino acids Leu, Phe, and homo-Phe. (aspetjournals.org)
These findings shed new light on hydrophobic stabilization of proteins. (lu.se)
Whereas the N state has been character- taken to imply that hundreds of water molecules penetrate the MG ized at high resolution, many aspects of the D and MG states are protein (except for a relatively small hydrophobic core)5,7,8,17-19. (lu.se)
corresponding to different fractions of hydrophobic residues. (lu.se)

Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
Three fluorinated metformin derivatives (MTF1, MTF2 and MTF3) were synthesized and investigated for their human bloodstream - human serum albumin (HSA) interaction studies by multi-spectroscopic techniques (circular dichroism, steady state, time-resolved and synchronous fluorescence), combined with molecular docking and quantum chemical calculation. (amrita.edu)
This information enabled to map the amino acids contributing to binding, which showed that the binding site of the head-to-tail interaction coincides with the generic ligand binding site of the discoidin domain. (uni-wuerzburg.de)
In accordance with the strong conservation of these residues among the alpha subunits of the GABA(A) receptor, it could be shown that an interaction with muskelin in vitro is also possible for the alpha2 and alpha5 subunits. (uni-wuerzburg.de)
By means of biochemical methods, crucial residues of RemA responsible for DNA interaction could be functionally investigated. (uni-marburg.de)
However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. (embl.de)
We have also used this methodology to investigate the amino acid residues involved in the Msh4-Msh5 binding interaction. (wesleyan.edu)
To evaluate the structural features of GSH required for interaction with the protein, we investigated the ability of a series of GSH analogs to enhance GSH stimulatable transport of [ 3 H]estrone 3-sulfate (E 1 SO 4 ). (aspetjournals.org)

To investigate the relation between protein stability and the predicted stabilities of individual secondary structural elements, residue Pro86 in an alpha-helix in phage T4 lysozyme was replaced by ten different amino acids. (rcsb.org)
One of these structural changes altered the protein so that it could no longer function for viral resistance. (usda.gov)
The other structural change allowed normal viral resistance to occur but affected the shape of the protein on the surface of cells. (usda.gov)
Insertions or deletions (indels) of amino acids residues have been recognized as an important source of genetic and structural divergence between paralogous Bcl-2 family members. (sfr-biosciences.fr)
Choosing the right templates in the immunoglobulin superfamily (IgSF) is challenging because its members share low sequence identity and display a wide range of alternative binding sites despite structural homology.ResultsWe present a new approach to predict protein interfaces. (edu.in)
The current view of protein folding and stability is largely based on SAXS and DLS data13-16 and the extensive exposure of hydropho- a generic structural classification into native (N), compact dena- bic residues suggested by the finding that the heat capacity of the tured or molten globule (MG), and unfolded or denatured (D) MG state is midway between that of the N and D states7 have been conformational states1-10. (lu.se)
A general property of disordered proteins is their structural expansion that results in a high macromolecular flexibility. (lu.se)

For the binding site on the GABA(A) receptor, it was confirmed that the thirteen most C-terminal residues of the intracellular domain are critical for the binding of muskelin. (uni-wuerzburg.de)
Incubation with lipoic acid, sesamin and episesamin/sesamin for 48h had significant effect on all analysed genes involved in lipid uptake, β-oxidation, elongation and desaturation, some effects were detected on the expression of peroxisome prolifertor-activated receptor (PPARs). (nel.edu)
However, RNA-sequencing showed that the LPS-induced pathways related to Toll-like receptor signaling, chemokine signaling, and NOD-like receptor signaling, and JAK-STAT/MAPK signaling pathways were upregulated in adduct-treated cells relative to parent phenolic acids, while neurodegenerative disorder-related pathways and metabolic pathways were downregulated. (bvsalud.org)
The IL-21 receptor (IL-21R) is closely related to the IL-2 receptor beta chain and is capable of transducing signals through its dimerization with the common cytokine receptor gamma chain (gamma(c)), the protein whose expression is defective in humans with X-linked severe combined immunodeficiency. (nih.gov)
Apelin peptides are cognate ligands for the apelin receptor, a G-protein-coupled receptor (GPCR). (phoenixpeptide.com)
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)
TCDD for every step of the mechanism described for 2,3,7,8-TCDD carcinogenesis in humans including receptor binding, gene expression, protein activity changes, cellular replication, oxidative stress, promotion in initiation-promotion studies and complete carcinogenesis in laboratory animals. (who.int)

Total nucleic acids from nasal swabs were isolated by using the MagnaPure 96 total nucleic acid isolation kit (Roche, Mannheim, Germany), and samples were tested for MERS-CoV by using 2 TaqMan assays: 1 for the envelope (upE) and 1 for the nucleocapsid gene (N), as described previously ( 9 , 13 ). (cdc.gov)
Antibodies recognize specific configurations (epitopes, or antigenic determinants) on the surfaces of antigens (eg, proteins, polysaccharides, nucleic acids). (msdmanuals.com)

And finally, many proteins from higher organisms require complex disulfide bonds for stability and proper folding. (neb.com)
This insensitivity of stability to the amino acid at position 86 is not simply explained by statistical and thermodynamic criteria for helical propensity. (rcsb.org)
Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. (elifesciences.org)
The proteins were expressed having a three -HA tag that would distinguish them in the mTORC1 Activator Storage & Stability endogenous TAO. (ezh2inhibitor.com)
First, the number of possible spatial configurations of proteins is incredibly vast, and secondly, the physical foundations of protein structuring and its stability have not been thoroughly investigated. (custom-essay.org)
The hydration of nonnative states is central to protein folding and stability but has been probed mainly by indirect methods. (lu.se)

An increase in the aliphatic index increases the thermostability of globular proteins. (qiagenbioinformatics.com)

PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. (embl.de)
All 20 amino acids consist of combinations of only five different atoms. (qiagenbioinformatics.com)
But this sequence can even consist of 101 amino acids, between which there will be, respectively, 100 bonds. (vpchothuegoldenking.com)
All types of amyloid consist of one major fibrillar protein that defines the type of amyloid. (medscape.com)
[ 5 ] Only 10% of amyloidosis deposits consist of components such as glycosaminoglycans (GAGs), apolipoprotein-E (apoE), and serum amyloid P-component (SAP), while nearly 90% of the deposits consist of amyloid fibrils that are formed by the aggregation of misfolded proteins. (medscape.com)

The covalent binding of acrolein (107028) with human serum albumin was investigated. (cdc.gov)

It is necessary to carry out pairwise alignment, which allows revealing conservative residues in the whole family or separate subfamilies of proteins. (custom-essay.org)
Visualises polarity of residues in MSA alignment positions. (lu.se)
There are four plots to indicate similarity in the alignment positions plus two plots, those fro hydropathy and polarity, to show trends in amino acid propensities. (lu.se)

The possible mechanism to explain the biophysics of this compass sense involves electron transfers within the photoreceptive protein cryptochrome. (nature.com)
A self-assisted mechanism with the leucyl amino group and Asp80 as proton acceptors is the most likely. (nih.gov)
The use of a separate substrate recognition domain such as a PDZ domain may be a general mechanism for achieving selective protein degradation. (embl.de)
Both are regulated by a phosphorylation-dephosphorylation mechanism involving a bifunctional serine/ threonine kinase and a pyrophosphorylase (PPDK regulatory protein, PDRP, and PEPS regulatory protein, PSRP, respectively). (scirp.org)
In plants the regulatory mechanism involves phosphorylation of a threonine residue that is separated by a single amino acid from the histidine residue that forms a phosphorylated intermediate during catalysis. (scirp.org)
Although details of the regulatory mechanism were elucidated in the middle 1980s the maize PPDK regulatory protein was not cloned until 2006 [9]. (scirp.org)
Until recently, the protein folding mechanism remained unknown, until the team of DeepMind, the Google division that creates neural networks, decided to use artificial intelligence to solve this problem. (vpchothuegoldenking.com)
We investigated the mechanism of neutralization of VEEV infection by the broadly cross-reactive E1-specific MAb 1A4B-6. (cdc.gov)
The key step in the reaction mechanism of multicopper oxidases (MCOs)--the cleavage of the O-O bond in O2--has been investigated using combined quantum mechanical and molecular mechanical (QM/MM) methods. (lu.se)

Apelin is found in 13-55 residue isoforms in vivo, all of which share the C-terminal portion of the preproapelin precursor. (phoenixpeptide.com)

Analyses of the albumin treated with acrolein for amino acids revealed a disappearance of lysine and histidine residues with concomitant appearance of four new peaks. (cdc.gov)
The results indicated that although lysine and histidine residues were modified, such modification did not alter the functions or biological properties of albumin, such as binding to palmitic-acid or bromcresol-green. (cdc.gov)
Using antibodies, we demonstrated that the regulation of both Listeria monocytogenes PPDK and Escherichia coli PEP synthetase involves the phosphorylation of a threonine residue located close to the catalytic histidine residue. (scirp.org)
The amino acid located between the regulatory threonine and the catalytic histidine is highly conserved being serine in PPDK and cysteine in PEPS. (scirp.org)

Finally, codepletion of Rad51, an important homologous recombination repair protein, abrogates the DNA damage after SET8 depletion. (rupress.org)
The most accurate protein interface predictions rely on finding homologous proteins with known interfaces since most interfaces are conserved within the same protein family. (edu.in)

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)
Biochemical analysis corroborated that the LisH motif in muskelin serves as a dimerization element, and, moreover, showed that the C-terminal domain of the protein substantially stabilizes this dimerization. (uni-wuerzburg.de)

Alternatives to trypsin will be beneficial in cases where digestion by trypsin is not ideal, such as when the content of arginine and lysine in the protein is low. (asbmb.org)

Ion channels are integral membrane proteins found in all cells that mediate the selective passage of specific ions or molecules across a cell membrane. (caltech.edu)
This is mediated by the secretion of extracellular proteins and other biological molecules. (uni-marburg.de)
For -lactalbu- min, only water molecules conserved in the human and baboon structures are shown (the structure of the bovine protein has not been reported). (lu.se)
GAGs are long, linear polysaccharide molecules composed of repeating dimers, each of which contains a hexuronic acid (or galactose in the case of keratan sulfate) and an amino sugar. (medscape.com)
The large proteoglycan molecules made up of protein cores, and GAG branches are secreted by cells and constitute a significant fraction of the extracellular matrix of connective tissue. (medscape.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)
Identification of reaction products by LC-MS/MS showed that Michael addition occurred in all reactions with amino acids tested. (bvsalud.org)
In addition, the effectiveness of antitoxin treatment may vary depending on circulating toxin levels, so that rapid identification and quantification of BoNT proteins in clinical specimens and food is desirable for optimization of treatment. (cdc.gov)

Here, we characterized oxidative modification of tryptophan (Trp) residues in the PSII core, and hypothesize that the oxidation of N-terminal Trp is one of the key oxidations in the PSII repair, likely enhancing D1's accessibility to FtsH. (elifesciences.org)
The work supports a role for chemical modification in the recognition and subsequent degradation of a key protein subunit of PSII by a bacterial-type protease, suggesting that tryptophan oxidation of components of the photosynthetic apparatus after high light stress plays a critical role in initiating the PSII repair system. (elifesciences.org)

In this study, the precise epitopes in GAD-65 of three different mouse monoclonal antibodies (MoAbs) (N-terminal MoAb within amino acid residues 4-17. (nottingham.ac.uk)
The precise epitopes in IA-2 of two different MoAbs (76B and 76F) were also investigated. (nottingham.ac.uk)

If a membrane protein expresses at a high level, almost certainly some of this protein will be found in the insoluble fraction. (neb.com)
The hOAT3 protein was shown to be localized in the basolateral membrane of renal proximal tubules and the hOAT3 gene was determined to be located on the human chromosome 11q12-q13.3 by fluorescent in situ hybridization analysis. (aspetjournals.org)
Part 3: Membrane protein biogenesis is regulated by a structurally unique, co-translational state of FtsY. (uni-marburg.de)
Membrane proteins are translated by ribosomes and predominantly inserted into the membrane by the SecYEG-translocon. (uni-marburg.de)
These results are an important step towards the conceptual understanding of membrane protein biogenesis and -targeting. (uni-marburg.de)
PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. (embl.de)
We also investigated the problem of what impact this truncation has on membrane integration from the protein. (ezh2inhibitor.com)
In all situations, we discovered that the mutated protein was identified inside the membrane fraction right after alkali extraction of isolated mitochondria (see Fig. S1 inside the supplemental material), suggesting that deletion in the N terminus of TAO has no impact on integration from the protein into the mitochondrial membrane in the intact cell. (ezh2inhibitor.com)
The mature flavivirus particle comprises a nucleocapsid core surrounded by a lipid bilayer containing the membrane (M) (derived from the precursor prM) and envelope (E) proteins. (microbiologyresearch.org)

To reveal amino acid followers, -helix and -sheet location, as a rule, computer programming methods are used. (custom-essay.org)
On the other hand, if it is not possible to find a template for modelling protein structure, then physical and chemical methods are used. (custom-essay.org)
In affected indivi- chemicals possessing the ability to react with duals, it has a serious impact on their quality of proteins, and hence these methods do not esti- life. (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)

These two Prdx6's have only 8% difference in their primary sequence (with 19 amino acids) with no apparent modification at any of the key conserved residues. (jascoinc.com)
Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. (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)

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)
In this work, we have investigated the aminoacetylation step catalyzed by leucyl-tRNA synthase, using ab initio quantum chemical/molecular mechanical hybrid potentials in conjunction with reaction-path-location algorithms and molecular dynamics free energy simulations. (nih.gov)
In a recent paper in the journal Molecular & Cellular Proteomics , Tirsa L.E. van Westering and researchers at the University of Oxford used mass spectrometry to identify differential protein expression in muscles at three different ages (representing the different stages of DMD pathology) from two strains of mice with genetically altered DMD and one strain of unaltered mice (control). (asbmb.org)
To investigate the occurrence, development and transfer process of MM, a novel molecular targeted therapy was established to provide a reliable basis for research. (spandidos-publications.com)
Molecular weight The molecular weight is the mass of a protein or molecule. (qiagenbioinformatics.com)
A calculation of the molecular weight of a protein does not usually include additional post-translational modifications. (qiagenbioinformatics.com)
To clarify the molecular basis of IL-21 actions, we investigated the role of tyrosine residues in the IL-21R cytoplasmic domain. (nih.gov)

In contrast, a site directed substitution in residue 34 dramatically alters ALV antigen presentation by the BFIV21 class I glycoprotein. (usda.gov)
We found that substitution of the γ-Glu residue with Gly, β-Asp, and α-Glu resulted in complete loss of transport stimulation. (aspetjournals.org)

human monoclonal antibody (b96.11 huAb) and polyclonal antibodies (SMS patients' sera) were investigated. (nottingham.ac.uk)
Upon induction with doxycycline, the proteins were detected inside the whole-cell lysate by Western blotting using either anti-TAO or an anti-HA monoclonal antibody (Fig. 3). (ezh2inhibitor.com)
To support our subcellular fractionation data, we performed immunolocalization in the ectopically expressed proteins in intact T. brucei cells, utilizing a monoclonal antibody against HA. (ezh2inhibitor.com)
Additionally, utilizing a monoclonal antibody against TAO, we observed a equivalent colocalization with the endogenous protein with stained mitochondrion (Fig. four). (ezh2inhibitor.com)
To investigate nuclear lamin phosphorylation, we generated a monoclonal antibody (C7B8D) against Ser-28-phosphorylated GFLB3. (elsevierpure.com)

Cleavage sites are serotype-specific, with the exception of BoNT/F5, which cleaves between amino acids 54 L and 55 E, four amino acids different from the standard BoNT/F cleavage site of 58 Q and 59 K 13 . (cdc.gov)

Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. (nature.com)
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)
From the prediction models constructed, all achieved high prediction performance, indicating clear distinctions in both avian and human proteins. (springer.com)
When used together as a host tropism prediction system, zoonotic strains could potentially be identified based on different protein prediction results. (springer.com)
Protein prediction is an incredibly important goal since it allows to simplify biotechnological research in the process of designing new drugs or enzymes. (custom-essay.org)
Taking into account multi-variant protein functions, the task of accurate and analytical prediction is one of the most important directions of modern bioinformatics. (custom-essay.org)
Prediction of protein structure and functions is a complex task for two reasons. (custom-essay.org)

One of the most critical tasks of modern bioinformatics is to predict and foretell the structure and, consequently, the functions of bacterial proteins. (custom-essay.org)
This essay on Predicting Bacterial Proteins' Structure and Function was written by a student just like you. (custom-essay.org)
Botulinum neurotoxins (BoNTs) are bacterial proteins that cause the life-threatening disease botulism 1 . (cdc.gov)

The first one provides length variation at the N-terminus (before the BH4 domain) and the second one is located between the predicted alpha 5-alpha 6 pore-forming helices, providing an unprecedented case in the superfamily of helix-bundled pore-forming proteins. (sfr-biosciences.fr)
Next, based on the similarity of residue level conservation scores derived from the evolutionary profiles, a query protein is hierarchically clustered with all available template proteins in its superfamily with known interface definitions. (edu.in)

This model may also provide a basis for mapping the relationship between structure, function and evolutionary history of a protein family, and thus be a powerful tool for rational engineering. (strath.ac.uk)

Their ability to exist as biofilm structures has been alluded to but not extensively investigated. (biomedcentral.com)

This is when paramagnetic (or "spin") centres are covalently linked to proteins at specific amino acid residues. (utoronto.ca)
Quinones, produced by the oxidation of phenolic compounds, covalently bind to nucleophilic groups on amino acids or proteins. (bvsalud.org)

As a main result, we found that clusters of co-evolving residues related to the catalytic site of an enzyme have distinguishable topological properties in the network. (upf.edu)

In my presentation, I will summarize recent QENS and NSE results on the dynamics of the intrinsically disordered myelin basic protein (MBP) and the chemically denatured bovine serum albumin (BSA) (1,2,3). (lu.se)

An alpha-synuclein fragment, known as the non-amyloid beta (non-abeta) component (NAC) of Alzheimer's disease amyloid, originally found in an amyloid-enriched fraction, was shown to be a fragment of its precursor protein, NACP. (wikipedia.org)
Alpha-synuclein is a synuclein protein of unknown function primarily found in neural tissue, making up as much as one percent of all proteins in the cytosol of brain cells. (wikipedia.org)
Also effects on the fatty acid composition were found. (nel.edu)
PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. (embl.de)
Subcellular fractionation analysis clearly showed that while the FLTAO, 10TAO, and 20TAO mutants have been accumulated exclusively in the mitochondrial fraction, some of the expressed 30TAO and 40TAO was found inside the cytosolic fraction in procyclic parasites (Fig. 3B to F). As controls, we employed VDAC, a mitochondrial protein, and TbPP5, a cytosolic protein, to validate the quality on the subcellular fractionation. (ezh2inhibitor.com)
Caffeic acid (CA) and chlorogenic acid (CGA) are commonly found phenolic acids in plant-derived foods and beverages. (bvsalud.org)
If leucine is found N-terminally in mammalian proteins the estimated half-life is 5.5 hours. (qiagenbioinformatics.com)
Interestingly, immunity-associated GTPase family M (IRGM), the most targeted protein, was found to interact with the autophagy-associated proteins ATG5, ATG10, MAP1CL3C and SH3GLB1. (sfr-biosciences.fr)
Moreover we found that the expression of IRGM-interacting MeV-C, HCV-NS3 or HIV-NEF proteins per se is sufficient to induce autophagy, through an IRGM dependent pathway. (sfr-biosciences.fr)
Activated protein C is found at levels approximately 2000 times lower than this. (medscape.com)

Polyhistidine, serving as a model compound, was treated with acrolein and subjected to amino acid analyses. (cdc.gov)
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)
There is little information on their evolution in Jordan so this study investigated the genetic and antigenic variability of A(H1N1)pdm09 and H3N2 viruses in Jordan by performing phylogenetic and genetic analyses of the HA and NA genes of A(H1N1)pdm09 and H3N2 viruses between 2011 and 2013. (who.int)
Afin de remédier à ce problème et d'étudier les variations génétiques et antigéniques des virus A(H1N1)pdm09 et H3N2, nous avons procédé à des analyses génétiques et phylogénétiques des gènes de l'hémagglutinine (HA) et de la neuraminidase (NA) de ces virus, sur la période 2011-2013 en Jordanie. (who.int)

Expression of cloned envelope protein genes from the flavivirus tick-borne encephalitis virus in mammalian cells and random mutagenesis by PCR. (microbiologyresearch.org)
Mutagenesis of the NS2B-NS3-mediated cleavage site in the flavivirus capsid protein demonstrates a requirement for coordinated processing. (microbiologyresearch.org)
Site directed mutagenesis experiments showed that reducing the positive charge of this surface-exposed region of the E protein DII correlated with improved Ae. (cdc.gov)

1) Continuous wave (CW) EPR spectroscopy can measure the absorption and relaxation properties of spin labels on spin-labeled proteins, thereby yielding information about the mobility, solvent accessibility, polarity, etc. of the labeled site. (utoronto.ca)
1-chloromethyl-1-fluorosilacyclopentane (1-ClM-1-FSiCP) was synthesized for the first time and investigated by means of vibrational spectroscopy and theoretical calculations. (researchgate.net)
Neutron Spin-Echo spectroscopy (NSE) on the other hand, offers the highest energy resolution in the field of neutron spectroscopy and allows the study of slow collective motions in proteins up to several hundred nanoseconds and in the nanometer length-scale. (lu.se)

Effects of bioactive compounds on expression of genes involved in lipid metabolism and fatty acid composition were investigated in Atlantic salmon (Salmo salar L.) primary hepatocytes. (nel.edu)
Features such as isoelectric point or amino acid composition can reveal important information of a novel protein. (qiagenbioinformatics.com)
The amino acid composition is important when calculating the extinction coefficient. (qiagenbioinformatics.com)
Atomic composition Amino acids are indeed very simple compounds. (qiagenbioinformatics.com)

To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. (elifesciences.org)
In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. (elifesciences.org)
We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. (elifesciences.org)
In photosynthetic organisms, maintenance of photosynthetic light reaction is manifested by so called Photosystem II (PSII) repair system, where the reaction center protein D1 is targeted to photo-oxidative damage and rapidly degraded by the processive protease FtsH. (elifesciences.org)

And then Mehmet Berkman will highlight the SHuffle line of E. coli strains for producing proteins with complex disulphide bonds. (neb.com)

These included proteins associated with the extracellular matrix and muscle function, many of which had not been reported in previous studies. (asbmb.org)
The protein RemA is central to this process, as it activates the secretion of these extracellular components. (uni-marburg.de)

This cellular compartmentalization of PTEN was investigated in lung neuroendocrine tumors (lung NET). (biomedcentral.com)

The polymer complex consists of ISCA1 protein monomers with internally bound iron sulphur clusters and simultaneously binds ten cryptochromes. (nature.com)
Thus this paper describes, for the first time, an MT gene identified from macroalgae which is induced by copper exposure and whose encoded protein product binds cadmium and copper. (portlandpress.com)

Nucleotide-binding proteins often play an extremely important role as regulators of genomic function. (wesleyan.edu)

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)
In this study we have chosen to investigate pyrite and its surrounding minerals in order to identify the different mineral phases as well as the chemical variations from micro- to nano-scale. (horiba.com)
In a study from 2011, the protein muskelin was described as a central coordinator of the retrograde transport of GABA(A) receptors in neurons. (uni-wuerzburg.de)
To establish a basis for understanding the mode of operation of muskelin, the aim of this thesis was an in-depth In a study from 2011, the protein muskelin was described as a central coordinator of the retrograde transport of GABA(A) receptors in neurons. (uni-wuerzburg.de)
Therefore, this leaves a gap for an up-to-date study to investigate the possibilities of developing an efficient forest industry cluster in Angola. (helsinki.fi)
This study suggests that veneer peeling and sawn timber production could be selected for the primary wood production, carpentry and furniture for the secondary processing and wood residues to produce sustainable energy. (helsinki.fi)
This study highlights the importance of investigating alternative proteases for proteomic experiments. (asbmb.org)
This study investigated the multiproduct (fucoidans, ß-glucans, proteins, carotenoids, fatty acids, amino acids and polyphenols) valorization of the invasive macroalgae Ascophyllum nodosum within a green biorefinery concept using ultrasound (US), microwave (MW) treatment followed by supercritical CO2 (SC-CO2) with co-solvent and enzymatic extraction. (bvsalud.org)
In this study, the reactions of 4-methylbenzoquinone (4MBQ) with ß-lactoglobulin (ß-LG) and amino acids at neutral pH were investigated. (bvsalud.org)
In this study, the role of the His residue at position 39 in the M protein (M39) of dengue virus type 2 (DENV-2) in the virus life cycle was investigated. (microbiologyresearch.org)
The results of this study pinpoint a critical residue in the M protein that potentially plays a role in viral morphogenesis, secretion and entry. (microbiologyresearch.org)
Protein is an important part of everyone's lifehuman, but despite the fact that we live in the 21st century, when neural networks paint pictures, and 3D printers are full-fledged organs, scientists have not yet had the opportunity to fully study the protein. (vpchothuegoldenking.com)
Quasielastic incoherent neutron scattering (QENS) is a well-suited experimental method to study protein dynamics from the picosecond to several nanoseconds and in the Ångström length-scale. (lu.se)
This study investigated how these missed detections occurred to determine their effect on the surveillance of influenza. (who.int)

I will start by outlining the most common problems encountered during the expression of recombinant proteins in E. coli and specific solutions will be given for each problem. (neb.com)
The PEP synthetase regulatory protein (PSRP) from E. coli has been cloned and expressed [11]. (scirp.org)
We are studying the architectural proteins, HU and IHF from E.coli, which bind to the minor groove of DNA through two flexible β-strand regions. (wesleyan.edu)
The estimated half-life of proteins have been investigated in mammals, yeast and E. coli (see the table below). (qiagenbioinformatics.com)
The gene encoding ArsR/methyltransferase fusion protein, arsR M , was amplified and expressed in Escherichia coli BL21 (DE3), and this strain showed resistance to arsenic in the present of 0.25-6 mM As(III), aresenate, or pentavalent roxarsone. (biomedcentral.com)

We invoke various groups as potential proton acceptors-namely, the phosphate and leucyl amino groups of leucyl-adenylate, the A76 base of tRNA, and the Asp80 and Glu532 residues of the protein-and consider both metal-assisted and metal-free reactions. (nih.gov)
By combining the results from two-stage quantification, 4 or 5 orders of magnitude in dynamic range were achieved for the detection of the serotypes of BoNT/A, /B, /E, or /F. The effect of multiplexing the assay by mixing substrates for different BoNT serotypes into a single reaction was also investigated in order to reduce the numbers of the cleavage reactions and to save valuable clinical samples. (cdc.gov)

We then discuss how obesity leads to insulin resistance via a complex interplay among systemic fatty acid excess, microhypoxia in adipose tissue, ER stress, and inflammation. (jci.org)

Enzymatic digestion of protein into shorter peptides by sequence-specific proteases is a key step in mass spectrometry-based shotgun proteomics experiments. (asbmb.org)
However, US/MW pretreatment and enzymatic extraction did not improve the yields of proteins and free amino acids. (bvsalud.org)

Leucyl-tRNA synthetase catalyzes attachment of leucine amino acid to its cognate tRNA. (nih.gov)

The characterization of SC-CO2 extracts revealed that pretreatment with US and MW improved the 2-fold yield of carotenoids, total phenolics and fatty acids. (bvsalud.org)

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)
A chicken gene that produces a protein important for viral disease resistance was obtained and its DNA sequence was determined. (usda.gov)

Thus, studies on MscS began to identify the specific amino acid residues that are responsible for giving the channel its voltage sensitivity. (caltech.edu)
SPRY2 is a member of the signaling pathway-specific inhibition protein sprouty (SPRY) family. (spandidos-publications.com)
Results were correlated with immunoreactivity for USP7 (herpes virus-associated ubiquitin-specific protease 7) and SUMO2/3 (small ubiquitin-related modifier protein 2/3) as well as PTEN and p53 FISH gene status. (biomedcentral.com)
Tail-specific protease (Tsp) is a periplasmic enzyme that selectively degrades proteins bearing a nonpolar C-terminus. (embl.de)
Every protein holds specific and individual features which are unique to that particular protein. (qiagenbioinformatics.com)
However, no single test for protein C is 100% sensitive or specific for detecting abnormalities. (medscape.com)

Alpha-synuclein (aSyn) is a protein that, in humans, is encoded by the SNCA gene. (wikipedia.org)
To investigate the possible existence of a metallothionein (MT) gene, the library was screened with degenerate probes designed using plant MT cysteine-rich motifs. (portlandpress.com)
Fatty acids and gene expression responses to bioactive compounds in Atlantic salmon (Salmo salar L.) hepatocytes. (nel.edu)
Schiller Vestergren A, Trattner S, Mráz J, Ruyter B, Pickova J. Fatty acids and gene expression responses to bioactive compounds in Atlantic salmon (Salmo salar L.) hepatocytes. (nel.edu)
To investigate to what extent ETHE1 is responsible for EE, we analysed this gene in 29 patients with typical EE and in 11 patients presenting with early onset progressive encephalopathy with ethylmalonic aciduria (non-EE EMA). (bmj.com)

Similarly, the chromogenic assay is not dependent on the presence of protein S. (medscape.com)

RPA, replication protein A. (rupress.org)
This is accompanied by DNA double-strand break (DSB) induction and recruitment of the DNA repair proteins replication protein A, Rad51, and 53BP1 to damaged regions. (rupress.org)
Mutational analysis of several of these amino acids both in pUL105 and pUL70, proved that they are crucial for viral replication. (frontiersin.org)

New drugs targeting essential viral proteins other than pUL54 are therefore urgently needed. (frontiersin.org)

Anatomy10

Organisms13

Chemicals and Drugs105

Analytical, Diagnostic and Therapeutic Techniques and Equipment44

Phenomena and Processes82

Disciplines and Occupations2

Technology, Industry, Agriculture1

Information Science8

Health Care4

Sequences20

Interactions19

Cysteine residues3

Mutations10

Peptide10

Alanine2

Specificity8

Putative4

Functional15

Substitutions1

Physicochemical properties1

Hydrophobic4

Interaction8

Structural7

Receptor7

Nucleic2

Stability6

Globular proteins1

Consist5

Human serum a1

Alignment3

Mechanism9

Isoforms1

Histidine4

Homologous2

Biochemical2

Lysine1

Molecules5

Identification3

Tryptophan2

Epitopes2

Membrane9

Methods4

Modification3

Molecular7

Substitution2

Monoclonal antibody5

Cleaves1

Prediction7

Bacterial Proteins3

Superfamily2

Evolutionary1

Extensively investigated1

Covalently2

Catalytic site1

Bovine1

Found10

Analyses4

Mutagenesis3

Spectroscopy3

Composition4

Oxidative4

Disulphide1

Extracellular2

Compartmentalization1

Binds2

Nucleotide1

Study14

Coli5

Reactions2

Fatty acid1

Enzymatic2

Leucine1

Characterization1

Important2

Specific6

Gene5

Dependent on the presence1

Replication3

Viral1