Species hydrophobic residues in protein protein residues. Medical search. Frequent questions

One of the conserved hydrophobic interface residues, Tyr10 was mutated to Ala and the impact of this virtual mutation was estimated by additional MD simulations for the wild-type (WT) and mutant protein-peptide complexes. (ncbs.res.in)

These replacements also led to production of infective viruses that replaced the acidic residues introduced (E) by nonpolar amino acids, indicating that preservation of the hydrophobic interface is essential for virus replication. (asm.org)
1987). The deduced protein product is 113 amino acids in length and contains a sequential stretch of hydrophobic and hydrophilic residues at the carboxyl terminus. (marquette.edu)
The bZIP protein sequence contains 2 conserved bZIP domains with a total length of ~ 60-80 amino acids. (biomedcentral.com)
The second is a relatively poorly conserved leucine zipper region characterised by leucine in the last position of every seven amino acids, and hydrophobic residues at positions 3 and 4. (biomedcentral.com)
At the same time, majority of the amino acid residues that are non-essential have "mutated" (Figure 4, RBM residues not labeled with short red lines). (wearechange.org)
It is definitely known that principal amino-acid sequences dictate the tertiary buildings of proteins, but how foldable in to the indigenous condition occurs may be the subject matter of intense investigation still. (phytid.org)
Proteolytic cleavage by the ZMPSTE24 protease removes the last 15 amino acid residues and the hydrophobic farnesyl group to produce mature lamin A, which is found both at the NL and in the nuclear interior. (aad.org)
Here, we set out to identify amino acid residues responsible for glucosinolate transport activity of the main seed glucosinolate exporter UMAMIT29 in Arabidopsis thaliana . (frontiersin.org)
Transport activity assays of mutant variants with a single point amino acid substitution in each site UMAMIT29 suggest that five of these residues are critical for glucosinolate transport. (frontiersin.org)
The GRAVY value for a protein is calculated as the sum of hydropathy values of all the amino acids, divided by the number of residues in the sequence (Kyte and Doolittle, 1982). (surface-antigen.com)
Many bioactive peptides have in common structural properties that include a relatively short peptide residue length (e.g. 2-9 amino acids), possessing hydrophobic amino acid residues in addition to proline, lysine or arginine groups. (eurekaselect.com)
Exorphins, or opioid peptides derived from food proteins such as wheat and milk (e.g. exogenous sources) have similar structure to endogenous opioid peptides, with a tyrosine residue located at the amino terminal or bioactive site. (eurekaselect.com)
Proteins are composed of long chains of amino acids that fold on themselves to form three-dimensional structures. (elifesciences.org)
The 72-amino acid TEA DNA binding domains in mTEAD-2, 3, and 4 are approximately 99% homologous to the same domain in mTEAD-1, and all four proteins bind specifically to the same DNA sequences in vitro with a Kd value of 16-38 nM DNA. (embl-heidelberg.de)
The hOAT3 cDNA consisted of 2179 base pairs that encoded a 543-amino-acid residue protein with 12 putative transmembrane domains. (aspetjournals.org)

Replacements L38E and L41E, involving charge acquisition at residues predicted to contribute to the hydrophobic interface, reduced the dimerization signal in the protein ligation assay and prevented the detection of dimer/multimer species in both transiently expressed 3A proteins and in synthetic peptides reproducing the N terminus of 3A. (asm.org)
AD is traditionally characterised by the presence of two hallmark lesions of abnormal protein aggregates: (i) intracellular neurofibrillary tangles of tau protein, and (ii) extracellular amyloid plaques, primarily comprised of amyloid-β peptides, which are small hydrophobic protein fragments (39 to 42 residues) from the transmembrane protein APP. (diamond.ac.uk)
Bioactive Proteins and Peptides from Food Sources. (eurekaselect.com)
Antihypertensive peptides, known as Angiotensin I converting enzyme (ACE) inhibitors have been derived from milk, corn and fish protein sources. (eurekaselect.com)
Immunomodulatory peptides derived from tryptic hydrolysates of rice and soybean proteins act to stimulate superoxide anions (reactive oxygen species-ROS), which triggers non-specific immune defense systems. (eurekaselect.com)
Antioxidant properties that prevent peroxidation of essential fatty acids have also been shown for peptides derived from milk proteins. (eurekaselect.com)
Copper ions bind to biomolecules (e.g., peptides and proteins) playing an essential role in many biological and physiological pathways in the human body. (mdpi.com)
Most naturally occurring proteins and peptides from plants are considered safer than chemical drugs. (edu.in)
Similarly, bioactive peptides, which are specific protein fragments that are thought to have physiological health benefits, are good candidates for cosmeceutical components that provide enzyme-modulating activity. (dovepress.com)

Computer analysis of the DNA sequence of the 21C cDNA revealed a 76 percent 3$\sp\prime$ coding sequence similarity with the Drosophila acidic ribosomal protein gene, A1 (Qian et al. (marquette.edu)
Despite their different functions and only 23% sequence identity, the two proteins have very similar overall structures, displaying a previously unidentified fold comprised of a compact 12-stranded antiparallel β-sandwich wrapped in two short α helices. (uthscsa.edu)
Similar to what is observed for other viral proteins, S2 of SARS-CoV-2 shares a high sequence identity (95%) with S2 of ZC45/ZXC21. (wearechange.org)
Judging from this sequence analysis alone, we were convinced early on that not only would the SARS-CoV-2 Spike protein bind hACE2 but also the binding would resemble, precisely, that between the original SARS Spike protein and hACE223. (wearechange.org)
To test this, we aligned 97 protein sequences consisting of homologs of UMAMIT clade I from 27 plant species and created sequence logos containing the 51 residues identified in the structural analysis ( Supplementary Figure 1 ). (frontiersin.org)
In this study, a super-hydrophobic aluminum surface was prepared by nanosecond laser texturing and FAS modification in sequence. (flow3d.co.kr)
Recombinant protein encompassing a sequence within the center region of human RBPMS. (genetex.com)
The RNA recognition motif consists of two short stretches of conserved sequence, as well as a few highly conserved hydrophobic residues. (genetex.com)
5. Smith, M. J. and Koch, G. L. (1989) Multiple zones in the sequence of calreticulin (CRP55, calregulin, HACBP), a major calcium binding ER/SR protein. (bomiprot.org)
We prepared rabbit polyclonal antibodies against a peptide of proteins deduced from the available genome sequence and used them for immunoblotting and immuno-CLSM. (liveconscience.com)
The T-box is defined as the minimal region within the T-box protein that is both necessary and sufficient for sequence-specific DNA binding, all members of the family so far examined bind to the DNA consensus sequence TCACACCT. (embl-heidelberg.de)

Researchers wanted to examine Alzheimer's disease plaques to see if there was evidence of the protein-derived amyloid peptide converting non-reactive iron forms into reactive states. (diamond.ac.uk)
A cysteine peptidase is a proteolytic enzyme that hydrolyses a peptide bond using the thiol group of a cysteine residue as a nucleophile. (embl.de)
The addition of a Leu or Pro residue to the N-terminus of a His-His, dipeptide will enhance antioxidant activity and facilitate further synergy with non-peptide antioxidants (e.g. (eurekaselect.com)
hydrophobic stretch of an oleosin is sufficiently long (a transmembrane [PL bilayer] peptide has approximately 20-25 residues) to form a hairpin penetrating the surface PL monolayer of the LD in to the matrix. (liveconscience.com)
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)
1995), the molecular mechanism and the peptide group, suggesting that urea-peptide inter- whereby urea unfolds proteins has not been established. (lu.se)
Solvent denaturation is a result of altered protein-solvent vorably with water-peptide interactions. (lu.se)
Further, using a model peptide we demonstrate adduct formation with Cys as the preferred nucleophilic residue and PE(26:2) +2 oxygens, as one of the most reactive truncated PE-electrophiles produced. (cdc.gov)

I) A cofactor-A dimer (yellowish and gray) with conserved putative binding residues (crimson). (phytid.org)
Based on our model, we proposed a substrate-transporting cavity of UMAMIT29 defined by helix I to IV and VI-IX and selected 51 residues as putative substrate binding sites based on solvent accessibility ( Figure 1 ). (frontiersin.org)
The encoded protein has a single, putative RNA recognition motif in its N-terminus. (genetex.com)

Deciphering protein–protein interactions. (crossref.org)
Hence, a proline-binding module distinct from SH3 and WW domains regulates protein-protein interactions. (embl-heidelberg.de)
Replacements that favored (Q44R) or impaired (Q44D) the polar interactions predicted between residues Q44 and D32 did not abolish dimer formation of transiently expressed 3A, indicating that these interactions are not critical for 3A dimerization. (asm.org)
We demonstrate that cyclotides bind effectively and stably to different forms of Aβ structures hydrogen bonding and hydrophobic interactions. (ncbs.res.in)
Most of these essential residues are precisely preserved, including those involved in disulfide bond formation (C467, C474) and electrostatic interactions (R444, E452, R453, D454), which are pivotal for the structural integrity of the RBM (Figure 3C and 4). (wearechange.org)
Computational modelling of the interactions between these ligands and both wild type and mutant S1P 4 receptors showed excellent agreement with experimental data, therefore confirming the fundamental role of this residue in ligand recognition by S1P receptors. (biomedcentral.com)
Moreover, iron interactions with N-terminally acetylated α S, the physiologically relevant form of the human protein, will be addressed to shed light on the current understanding of protein dynamics and the physiological environment in the disease state. (hindawi.com)
MRD is among the few methods that can provide molecular-level informa- tion about protein solvation in native as well as denatured states, and it is used here to simultaneously monitor the interactions of urea and water with the unfolding protein. (lu.se)
1 nsec) interactions of urea and water with the native and denatured protein. (lu.se)
If this is the case, interactions, but it is not clear whether denaturants like urea then solvent denaturation can be driven simply by the ex- act directly by binding to the protein surface or indirectly by posure of more binding sites in the denatured protein perturbing solvent-mediated hydrophobic interactions or by (Schellman 1987). (lu.se)
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)

This may be the water molecule buried near the small hydrophobic folding core at the D-E turn in the native protein. (lu.se)

Based on a predicted model of UMAMIT29, we propose that the substrate transporting cavity consists of 51 residues, of which four are highly conserved residues across all the analyzed homologs of UMAMIT29. (frontiersin.org)
Based on distance-based protein folding tools, we predict the substrate-transporting cavity of UMAMIT29. (frontiersin.org)
We hypothesised that the transport cavity contains highly conserved residues that are key for the transport activity. (frontiersin.org)
The SMP domain is able to homo- or heterodimerize, harbors lipids in a hydrophobic cavity and mediates lipid transfer between the two adjacent bilayers independently of membrane fusion and fission reactions. (expasy.org)
The resulting elongated barrel-shaped cylindrical structure harbors a lateral opening and a central hydrophobic cavity where phospholipids can bind. (expasy.org)
An x-ray structure shows that the C-terminal domain of mitoguardin-2 has a hydrophobic cavity that binds lipids. (rupress.org)
10 nsec) to the protein even in 7.5 M urea, where the large internal binding cavity is disrupted and CD indicates a fully denatured protein. (lu.se)

When expressed as a recombinant protein in transfected cells, PV 3A cofractionates with endoplasmic reticulum markers ( 66 ), and its single transient expression can disrupt the secretory apparatus ( 23 ) and decrease major histocompatibility complex (MHC) class I expression ( 22 ). (asm.org)
Synaptotagmin-like Mitochondrial lipid-binding Proteins (SMP) domains are exclusively found at MCSs between different organelles such as endoplasmic reticulum (ER)-Mitochondrion, ER-Plasma membrane (PM) and Nucleus-Vacuole junctions. (expasy.org)
Metazoan PDZD8, a critical endoplasmic reticulum (ER)-mitochondria tethering protein. (expasy.org)
Lipid transport proteins at membrane contacts, where organelles are closely apposed, are critical in redistributing lipids from the endoplasmic reticulum (ER), where they are made, to other cellular membranes. (rupress.org)
The synthesis of three major endoplasmic reticulum proteins during lipopolysaccharide-induced differentiation of murine lymphocytes. (bomiprot.org)
Many proteins are made in a compartment within the cell called the endoplasmic reticulum and 'chaperone' proteins help them fold correctly. (elifesciences.org)
This leads to an increase in the number of unfolded proteins in the endoplasmic reticulum and so the cell increases the levels of chaperone proteins to cope with this. (elifesciences.org)
used biochemical techniques to study how an Hsp70 protein in the endoplasmic reticulum called BiP forms oligomers. (elifesciences.org)

The viral particle is composed of a protein capsid that contains a positive-sense RNA molecule of about 8,500 nucleotides that is infectious and encodes a single polyprotein, which is processed in infected cells by cis - and trans -acting viral proteases ( 55 ) to yield different polypeptide precursors and the mature viral proteins ( 9 , 62 ). (asm.org)
2009 MLDP doesn't have an extended hydrophobic polypeptide for steady association using the matrix of LDs. (liveconscience.com)
The toxin is a single polypeptide with an active (A) domain, a binding (B) domain, and a hydrophobic segment known as the T domain, which helps release the active part of the polypeptide into the cytoplasm. (medscape.com)

Indeed, we found that all in the latter group of proteins bind SAMD9. (uthscsa.edu)
As a result, isomerization of proline residues (peptidyl-prolyl isomerases) and the correct development of disulphide bonds (proteins disulphide isomerases) frequently bind and stabilize nonnative protein (Leroux, 2001). (phytid.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)
The presence of the interdomain linker makes it more difficult for unfolded proteins to bind. (elifesciences.org)

and 4) Reduction of progerin downstream toxic effects, an example being N-acetyl cysteine acting as a reactive oxygen species scavenger. (aad.org)
One of the most significant current discussions in Cu biochemistry relates to the mechanisms of the positive and negative actions of Cu ions based on the generation of reactive oxygen species, including radicals that can interact with DNA molecules. (mdpi.com)
Examples of these specific detoxification systems are the glyoxalase system, which removes the reactive aldehyde methylglyoxal, [3] and the various antioxidant systems that eliminate reactive oxygen species. (bionity.com)
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)

1984). These results suggest that the 3$\sp\prime$ sequences common to the genomic clones define a subset of Drosophila ribosomal proteins that share similar functional residues. (marquette.edu)
The reports on base sequences of spider silk protein genes have gained importance as the mechanical properties of silk fibers have been revealed. (bioone.org)

Upon ATP binding, large structural changes within the nucleotide-binding and transmembrane regions push conserved hydrophobic residues at the substrate entry site towards the periplasm and provide a model for polysaccharide translocation. (tcdb.org)
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)

A hydrophobic surface patch is created by motif residues that are highly conserved among a variety of proteins from diverse eukaryotic species. (embl-heidelberg.de)
SMP proteins are widespread amongst eukaryotic species with a particular enrichment in plants and features suggestive of species-specific functional variations. (expasy.org)

Gravy index score of proteins below are more likely globular (hydrophilic protein), while scores above are more probable membranous (hydrophobic protein). (surface-antigen.com)

There are many examples of biologically active food proteins, with physiological significance beyond the pure nutritional requirements that concern available nitrogen for normal growth and maintenance. (eurekaselect.com)

This enzyme catalyses the following chemical reaction Hydrolysis of proteins with broad specificity. (wikipedia.org)
Hydrolysis involves usually a catalytic triad consisting of the thiol group of the cysteine, the imidazolium ring of a histidine, and a third residue, usually asparagine or aspartic acid, to orientate and activate the imidazolium ring. (embl.de)
Conserved residues in the motor domain have been positioned within the framework provided by the recent crystal structures, thus helping to define those residues involved in actin and ATP binding, in hydrolysis and in conformational change. (embl.de)

The loops are characterized with functionally important negatively charged, positively charged, and hydrophobic residues, respectively, together forming a unique "three-fingered molecular claw. (uthscsa.edu)
This has revealed remarkably poor overall conservation at the site thought to be involved in actin binding, but several highly conserved residues have been identified that may be functionally important. (embl.de)

Homer proteins are components of postsynaptic density (PSD) and play a crucial role in coupling diverse target molecules. (jneurosci.org)
In this study, we revealed that Homer3 was phosphorylated by calcium/calmodulin-dependent protein kinase II (CaMKII) in Purkinje cells, and the phosphorylation reduces the affinity for Homer target molecules, resulting in change of the solubility. (jneurosci.org)
These proteins can be present in a cell as single molecules (monomers) or as a group of several chaperone molecules (oligomers). (elifesciences.org)
Polar compounds cannot diffuse across these cell membranes and the uptake of useful molecules is mediated through transport proteins that specifically select substrates from the extracellular mixture. (bionity.com)

In only one family of cysteine peptidases, is the role of the general base assigned to a residue other than a histidine: in peptidases from family C89 (acid ceramidase) an arginine is the general base. (embl.de)

Proline-binding domain in CD2-binding protein. (embl-heidelberg.de)
A membrane-proximal proline-rich tandem repeat, involved in cytokine production, is recognized by the intracellular CD2 binding protein CD2BP2. (embl-heidelberg.de)
The rod-like tail starts with an invariant proline residue, and contains many repeats of a 28 residue region, interrupted at 4 regularly-spaced points known as skip residues. (embl.de)

The few changes within the group of essential residues are almost exclusively hydrophobic "substitutions" (I428àL, L443àF, F460àY, L472àF, Y484àQ), which should not affect either protein folding or the hACE2-interaction. (wearechange.org)

This portion of the protein is rich in glutamic and lysine residues and is highly conserved among several species examined. (marquette.edu)
The S1P receptors contain a conserved glutamic acid residue present within the third TM that corresponds to glutamine in the LPA receptors. (biomedcentral.com)

One clone hybridized to the Minute locus 5E, a region containing the gene for acidic ribosomal protein 7/8 (Burns et al. (marquette.edu)

Mutagenesis and NMR analysis demonstrated that the CD2 binding region of CD2BP2 includes a 17-aa motif (GPY[orF]xxxxM[orV]xxWxxx GYF), also found in several yeast and Caenorhabditis elegans proteins of unknown function. (embl-heidelberg.de)
Human sterile alpha motif domain-containing 9 (SAMD9) protein is a host restriction factor for poxviruses, but it can be overcome by some poxvirus host-range proteins that share homology with vaccinia virus C7 protein. (uthscsa.edu)
This gene encodes a member of the RNA recognition motif family of RNA-binding proteins. (genetex.com)

in poliovirus (PV), the interaction between the RNA replication complex and intracellular membranes appears to be accomplished by proteins 3A and 2C, which have membrane-binding properties ( 11 , 60 ). (asm.org)
Progerin lacks this crucial cleavage site, resulting in a permanently farnesylated protein that accumulates in, and causing thickening of, the nuclear membrane. (aad.org)
According to Kyte and Doolittle (1982) integral membrane proteins typically have higher GRAVY scores than do globular proteins. (surface-antigen.com)
hydrophobic residues with an occasional polar residue of integral proteins that pass across membrane are recognized as transmembrane (TM) domains. (surface-antigen.com)
Moreover anchoring to the membrane they participate in the functions of these proteins in some unspecified way (Ramasarma et al. (surface-antigen.com)
Diverse membrane-associated proteins contain a novel SMP domain. (expasy.org)
SMP-domain proteins at membrane contact sites: Structure and function. (expasy.org)
The human cellular prion protein (PrP C ) is a glycosylphosphatidylinositol (GPI) anchored membrane glycoprotein with two N-glycosylation sites at residues 181 and 197. (mdpi.com)
Analysis of the transcriptome identified several orthologues required for intra-erythrocytic survival and erythrocyte invasion, including the rhoptry neck protein 2 (RON2) and the apical membrane antigen-1 (AMA-1). (biomedcentral.com)
[2] In contrast, the diffusion of hydrophobic compounds across these barriers cannot be controlled and organisms therefore cannot exclude lipid -soluble xenobiotics using membrane barriers. (bionity.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)

The secondary structure analysis revealed that in all representative protein samples alpha helices dominated among all other elements. (surface-antigen.com)

Proteins that undergo maturation in the ER are stabilized SOS2 by chaperones such as calnexin and calreticulin, which are structurally related and identify glycosylated, nonnative proteins through lectin-like domains. (phytid.org)
A tetrameric form of α S has also been identified in human tissues that has been postulated as the inactive storage form of this structurally dynamic protein due to its aggregation resistance [ 6 , 7 ]. (hindawi.com)
AMA-1 and RON2 of P. gallinaceum are evolutionarily and structurally conserved, suggesting that these proteins may play essential roles for avian malaria parasites to invade host erythrocytes. (biomedcentral.com)

Generally favours hydrophobic residues in P1 and P1', but also accepts Lys in P1, which leads to activation of trypsinogen. (wikipedia.org)
Folding intermediates, and nonnative protein species generally, are aggregation-prone usually, both and in the congested cellular environment. (phytid.org)
Following strict statistics of structures in the PDB, scores below 0.17 corresponds to randomly chosen unrelated proteins whereas with a score higher than 0.5 assume generally the same fold. (surface-antigen.com)

The 72 residues from the nonpolar stretch with regards to hydrophobicity are conserved among oleosins of varied species as well as the conservation can be highest in the Pro knot (PX5SPX3P with X being truly a highly non-polar residue). (liveconscience.com)
Oleosins can be found in higher and primitive vegetation including lycophytes (deduced through the genome series of genome includes a series that could encode an oleosin-like proteins (known as "oleolike" with this report) which includes the quality 12-residue Pro-knot series of the oleosin but just short nonpolar hands (eight and four residues). (liveconscience.com)

The viral genome encodes four structural capsid proteins (VP1 to VP4) and seven nonstructural (NS) proteins, the leader Lb/ab protease, and proteins encoded in the P2 (2B and 2C) and P3 (3A, 3B, 3C, and 3D) regions ( 9 ). (asm.org)

hydrophobic stabilization of the folded protein. (lu.se)

Based on the obtained result, high aliphatic index in P-ATPases indicated structural stability of this protein in both families. (surface-antigen.com)
TM-score is a metric for measuring the structural similarity of two protein models. (surface-antigen.com)

In current research, transmembrane domains of P-ATPase families were studied in topology prediction (Fig. 3) and the number of transmembrane domains was predicted in different insect species. (surface-antigen.com)
however three species of P-ATPase13A3 families had the most number of transmembrane domains with 11 of them which were including: Bt-13A3, Bm-13A3 and Tc-13A3. (surface-antigen.com)

It was identified in the human intracellular protein termed CD2 binding protein 2 (CD2BP2), which binds to a site containing two tandem PPPGHR segments within the cytoplasmic region of CD2. (embl-heidelberg.de)

1992. Deltamethrin residues in milk and tissues of lactating dairy cows. (cdc.gov)

The major constituent of LBs is aggregated α -synuclein ( α S), an intrinsically unfolded protein predominantly localized in the presynaptic regions of dopaminergic neurons. (hindawi.com)

The mutation activates an alternative splice site, resulting in accumulation of an abnormal lamin A-derived protein named progerin. (aad.org)
We tested whether mutation of this "ligand selectivity" residue to glutamine could confer LPA-responsiveness to the related S1P receptor, S1P 4 . (biomedcentral.com)
Mutation of this residue to glutamine confers LPA responsiveness with preference for short-chain species. (biomedcentral.com)

To be useful, these nascent proteins must shield their shown hydrophobic residues and MGCD0103 pontent inhibitor adopt an accurate tertiary framework. (phytid.org)

Adv. Protein Chem. (crossref.org)

In the present study, the role of this residue in determining ligand selectivity for the S1P 4 receptor was examined. (biomedcentral.com)
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)
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)

The key residues of the claw are not conserved in two C7 family members that do not antagonize SAMD9 but are conserved in distantly related C7 family members from four poxvirus genera that infect diverse mammalian species. (uthscsa.edu)
Taken together, our data indicate that diverse mammalian poxviruses use a conserved molecular claw in a C7-like protein to target SAMD9 and overcome host restriction. (uthscsa.edu)
Mammalian Extended-Synaptotagmins (E-SYTs), ER-resident proteins that act as tethers inking the ER and PM membranes into close apposition. (expasy.org)

We identify mitoguardin-2, a mitochondrial protein at contacts with the ER and/or lipid droplets (LDs), as a lipid transporter. (rupress.org)

We further studied the collinearity between these genes and related genes of six other species. (biomedcentral.com)
In general, most genes that encode antigens of Plasmodium parasites are highly polymorphic and encode proteins that are important targets for host protective antibody responses [ 5 ]. (biomedcentral.com)

Pretreatment of cells with the strong nucleophile, 2-mercaptoethanol, prevented the formation of PE-lipoxidated proteins and blocked ferroptotic death. (cdc.gov)

The simulation results and the images captured by high-speed camera were highly consistent, which indicated that the computational fluid dynamics (CFD) is an effective method to predict the droplet motion on super- hydrophobic surfaces. (flow3d.co.kr)

Silks are composed principally of proteins with a predominance of alanine, serine and glycine and silk proteins are able to undergo irreversible transformations from soluble protein to insoluble fibres. (bioone.org)
These readily undergo iron-catalyzed secondary free radical reactions leading to truncated products which retain the signature PE headgroup and which can readily react with nucleophilic moieties in proteins via their truncated electrophilic acyl chains. (cdc.gov)
In cells stimulated to undergo ferroptosis we identified PE-truncated species with sn-2 truncations ranging from 5 to 9 carbons. (cdc.gov)
Our results indicate that several dozens of proteins for each cell type, are PE-lipoxidated in HT-22, MLE, and H9c2 cells and M2 macrophages after they were induced to undergo ferroptosis. (cdc.gov)

NS proteins are involved in crucial aspects of the viral cycle and pathogenesis, such as rearrangements of intracellular membranes required for endomembrane recruitment and the lysis of host cells ( 1 , 12 , 14 , 18 , 73 ). (asm.org)

Some of these responses reflect activation of G protein-coupled receptors of the endothelial differentiation gene (Edg) family. (biomedcentral.com)

The eukaryotic proteins are more complicated than the bacterial enzyme complexes. (tcdb.org)

Besides, the motion process of droplet impacting super-hydrophobic surface was systematically analyzed via the optimization of simulation calculation grid and the simulation method of volume of fluid (VOF). (flow3d.co.kr)
And the motion mechanism of the droplet on super-hydrophobic surface was clearly revealed in this paper. (flow3d.co.kr)

Natural bioactive compounds derived from plant species show promising therapeutic properties to combat the emerging resistance in microbial pathogens, which can be exploited as next generation anti-infective drugs. (nature.com)

The aliphatic index of a protein is defined as the relative volume occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine). (surface-antigen.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)
M.Kaukonen, P. Söderhjelm, J. Heimdal & U. Ryde, "A QM/MM-PBSA method for estimates of free energies in proteins", J. Phys. (lu.se)

Does not clot milk This enzyme is found in a variety of Aspergillus species. (wikipedia.org)

2002). Cellular quality control chemical substance or Physical strains that are as a result of heat range adjustments, contact with proteotoxic realtors, or other circumstances that are conducive to proteins misfolding induce a ubiquitous, defensive, cellular tension response. (phytid.org)

SAdV-6, SAdV-18, and SAdV-20) were also completely Committee on Taxonomy of Viruses has 1 defi ned species, sequenced. (cdc.gov)

Vaccuum energies and QM ESP charges are calculated from a wavefunction polarised by the surrounding protein and solvent. (lu.se)

As an initial type of defence against harming cellular insults, many chaperones, including Hsp70s and sHsps, can stabilize protein undergoing denaturation and invite their refolding when the strain provides subsided. (phytid.org)
The etiology of Parkinson's disease (PD) is linked with cellular inclusions in the substantia nigra pars compacta region of the brain that are enriched in the misfolded presynaptic protein α -synuclein ( α S) and death of the dopaminergic neurons. (hindawi.com)
This is since these species are derived from normal cellular constituents and usually share their polar characteristics. (bionity.com)
[ 1 ] More recently, Van den Velde and colleagues have suggested that species of corynebacteria would be more correctly identified based on their cellular fatty acid profiles (ie, for the C14 to C20 fatty acids). (medscape.com)

A molecular model of the FMDV 3A protein, derived from the nuclear magnetic resonance (NMR) structure of the poliovirus 3A protein, predicted a hydrophobic interface spanning residues 25 to 44 as the main determinant for 3A dimerization. (asm.org)
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)
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)

Anatomy11

Organisms10

Chemicals and Drugs106

Analytical, Diagnostic and Therapeutic Techniques and Equipment44

Phenomena and Processes82

Disciplines and Occupations6

Technology, Industry, Agriculture3

Information Science11

Health Care4

Interface residues1

Amino15

Peptides9

Sequence11

Peptide8

Putative3

Interactions11

Small hydrophobic1

Cavity7

Endoplasmic reticulum8

Polypeptide3

Bind4

Reactive4

Sequences2

Substrate2

Eukaryotic species2

Hydrophilic1

Physiological1

Hydrolysis3

Functionally important2

Molecules4

Cysteine1

Proline3

Almost exclusively1

Glutamic2

Acidic1

Motif3

Membrane11

Helices1

Structurally3

Generally3

Nonpolar2

Protease1

Stabilization1

Structural2

Transmembrane domains2

Binds1

19921

Predominantly1

Mutation3

Inhibitor1

Chem1

Ligand5

Mammalian3

Mitochondrial protein1

Genes2

Nucleophile1

Highly1

Undergo4

Intracellular1

Gene1

Complexes1

Droplet2

Bioactive1

Chains1

Free energies2

Milk1

Induce1

Viruses1

Solvent1

Cellular4

Molecular3