Protein protein interactions hydrophobic residues in protein protein residues. Medical search. Frequent questions

Triflin weighs 25 kDa and consists of 221 amino-acid residues. (wikipedia.org)
This domain is responsible for the selectivity of the protein and consists of two subdomains: N-terminal subdomain (Cys 167 to Cys 179) and C-terminal subdomain (42 amino-acids residues). (wikipedia.org)
Overexpression of SPC98 suppresses the temperature sensitivity conferred by mutations in region I but not the phenotypes conferred by mutations in the other two regions, suggesting that the amino terminus of Spc110p is involved in an interaction with the gamma-tubulin complex composed of Spc97p, Spc98p, and Tub4p. (sdbonline.org)
The glycine-rich region in UBQLN1 is rich in polar amino acids, whereas the same region in UBQLN2 is rich in hydrophobic residues. (syr.edu)
In addition, researchers have long shown that the element that gives rise to a protein's function is its three-dimensional structure - commonly referred to as the structure-function relationship - and that all the information needed to adopt this function/structure is stored and encoded in the amino acid sequence of the protein. (tugraz.at)
It was proposed as early as 1963 by Christian Anfinsen that the structure a protein adopts is always the lowest energy state accessible to its amino acid sequence. (tugraz.at)
This is essentially the protein structure prediction problem turned upside down, where a minimum energy structure for a given amino acid sequence is computed. (tugraz.at)
Computationally, protein design represents two interconnected problems: a) How do we score conformations of an amino acid chain and b) How can we sample all its degrees of freedom efficiently? (tugraz.at)
These problems are difficult to solve because sequence space for a typically sized protein (~200 amino acids) is vast (20200) and comprehensive sampling of it remains a challenge even with current computational power. (tugraz.at)
Protein design on the contrary allows for the exploration of this "dark matter" of amino acid sequence space (Figure 1). (tugraz.at)
It consists of 3 to 16 tandem repeats of 34 amino acids, mostly of small and large hydrophobic residues, that form ALPHA-HELIX pairs. (bvsalud.org)
Basic (primary) protein structure consists of long sequences of amino-acid molecules linked in a chain. (lbl.gov)
A protein motif 22 to 26 amino acids in length that binds POLY(ADP RIBOSE ) polymers through non-covalent interactions. (nih.gov)
For the human, immunodeficiency virus type 1 Gag protein, we recently reported that the membrane-binding domain resides within the N-terminal 31 amino acids and consists of two components: myristate and a cluster of basic residues, which together promote membrane binding in vitro and budding in vivo (W. Zhou, L. J. Parent, J. W. Wills, and M. D. Resh, J. Virol. (nih.gov)
Contrary to this opinion, it was alleged that protein folds are very common among random amino acid chains. (creation.com)
In Part 1 we address protein-folding experiments that are based on proteins constructed of very few but specified types of amino acids. (creation.com)
Three regularly spaced tryptophan or other hydrophobic amino acid residues form the core of this structure [ 8 ]. (biorxiv.org)
Three peptides, D1 (amino acid residues 175-201), D2 (a.a. 434-467), and TM (a.a. 1128-1159), corresponding to the spike protein (S) of severe acute respiratory syndrome corona virus (SARS CoV) were synthesized and their immunological functions were investigated in three different animals models (mice, guinea pigs, and rabbits). (scienceopen.com)
The major neutralizing epitope was located on the D2 peptide, and the amino acid residue was fine mapped to 434-453. (scienceopen.com)
In BALB/c mice T-cell proliferation assay revealed that only D2 peptide contained T-cell epitope, the sequence of which corresponded to amino acid residue 434-448. (scienceopen.com)
SARS-CoV E protein is an integral membrane protein with 76 amino acids (GenBank® accession no. (pdfroom.com)
The N-terminal amino group of Pro2 H-bonds with the carbonyl of Ala539 and its side chain makes hydrophobic interactions in the pocket. (eu.org)
All ferrocene‐steroid conjugates get engaged in hydrophobic interactions with LEU387, TYR411, LEU430, and ARG485 amino acid residues. (nsf.gov)
To enhance the activity on synthetic polyesters, the canonical amino acid methionine in Thermoanaerobacter thermohydrosulfuricus lipase (TTL) was exchanged by the residue-specific incorporation method for the more hydrophobic non-canonical norleucine (Nle). (frontiersin.org)
14 B23.1, the prevalent isoform in all tissues, 15 contains 294 amino acids, 16 whereas B23.2, a truncated protein, lacks the last 35 C-terminal amino acids of B23.1 and is expressed at very low levels. (haematologica.org)
USA Vol. 90, pp. 7686-7690, August 1993 Pharmacology Amino acid residues essential for biological activity of a peptide derived from a major histocompatibility complex class I antigen (glucose transport /ordered structure) JAN STAGSTED*, CLAUDIO MAPELLIt, CHESTER MEYERS', BRIAN W. MATTHEWS? (nih.gov)

An analysis of the affinities of structural analogues of HupA, correlated with their interactions with the protein, shows the importance of individual hydrophobic interactions between HupA and aromatic residues in the active-site gorge of AChE. (proteopedia.org)
Of special interest is the preferential enrichment of aromatic residues (for example, tryptophan [Trp]) in the interface between the hydrophilic aqueous phases and the hydrophobic bilayer core. (spectroscopyonline.com)
This has led to the notion of anchoring residues, in which the anchoring effect is thought to arise from the amphiphatic nature of interfacial aromatic residues (7,8). (spectroscopyonline.com)
In particular, we present markers relevant for lipid molecular conformations and markers for the conformation of anchoring aromatic residues. (spectroscopyonline.com)
Hydrophobic interactions via aliphatic and aromatic residues were formed during isoelectric precipitation. (oregonstate.edu)

Novatein Thermoplastic Protein (NTP) is a patented blend of blood meal (a highly aggregated protein) and processing additives which: reduce hydrogen bonding, break cross links between cysteine residues, disrupt hydrophobic interactions, and facilitate protein unfolding. (waikato.ac.nz)
Detergents: associate with non-polar residues and disrupt hydrophobic interactions. (rahulgladwin.com)

[ 4 , 5 ] The precise function of this domain has not been fully resolved but evidence suggests that, once bound by Ca 2+ , the region takes on a β-roll structure and actuates a protein-wide conformational change that both stabilizes the toxin and exposes specific peptide surfaces that facilitate interaction with host cell membranes. (medscape.com)
In this work, we employed a combination of biophysical and biochemical methods to characterize PPIs, with a focus on interactions between structured domains and intrinsically disordered regions or peptide substrates.The subject of Chapter two is prolyl isomerase Ess1, which is an essential enzyme found in Saccharomyces cerevisiae. (syr.edu)
Phosphorylates serine in the peptide sequence, Hyd-X-R-X(2)-S, where Hyd is a large hydrophobic residue. (nih.gov)
protein peptide interactions. (upmc.fr)
Identification and characterization of the putative fusion peptide of the severe acute respiratory syndrome-associated coronavirus spike protein. (scienceopen.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)
Using multidimensional heteronuclear-edited and hetero-nuclear-filtered NMR spectroscopy, we have solved the solution structure of a complex of human thioredoxin and a 13-residue peptide extending from residues 56-68 of p50, representing a kinetically stable mixed disulfide intermediate along the reaction pathway. (nih.gov)
The peptide adopts a crescent-like conformation with a smooth 110 degrees bend centered around residue 60 which permits it to follow the path of the cleft. (nih.gov)
In addition to the intermolecular disulfide bridge between Cys32 of human thioredoxin and Cys62 of the peptide, the complex is stabilized by numerous hydrogen-bonding, electrostatic and hydrophobic interactions which involve residues 57-65 of the NF kappa B peptide and confer substrate specificity. (nih.gov)
The peptide self-interaction suggests that the biological effects in cells, which result from inhibition of receptor and transporter internalization, may be due to the binding (tantamount to self-interaction) of the peptide to the homologous sequences in the al domain of the MHC class I molecule. (nih.gov)

Globular proteins can be described from a physical point of view as micelles with a hydrophobic core surrounded by a hydrophilic shell. (upmc.fr)
Globular proteins have been the best studied, being easier to isolate in vitro , separated from other cellular bio-chemical interactions. (creation.com)
Thousands of globular proteins are critically important, and are used as enzymes and for other purposes 8 . (creation.com)
9 To function at all, and reliably, globular proteins must fold into precise three dimensional structures. (creation.com)
Schwieters, ``Using the experimentally determined components of the overall rotational diffusion tensor to restrain molecular shape and size in NMR structure determination of globular proteins and protein-protein complexes}{J. Am. Chem. (nih.gov)

By NMR structure determination and docking approaches, we built a 3D model of the Snup13p-Rsa1p interface, suggesting that residues R-249, R-246 and K-250 in Rsa1p and E-72 and D-73 in Snu13p form a network of electrostatic interactions shielded from the solvent by hydrophobic residues from both proteins and that residue W-253 of Rsa1p is inserted in a hydrophobic cavity of Snu13p. (hal.science)
The Arg8 and Lys9 residues make salt bridges and electrostatic interaction with LSD1 respectively ( Forneris,2007 ). (eu.org)

Observations suggest that hydrophilic residues in IDRs are abundant and hydrophobic residues are scarce [ 4 ]. (biomedcentral.com)

The phosphoryl group is transferred from the histidine kinase to a highly conserved aspartic acid residue in the N-terminal receiver domain of the cognate response regulator 3 (Fig. S1a ). (nature.com)
The proline residue at this location is highly conserved, suggesting it is crucial for keeping protein gels liquid, Fawzi added. (alzforum.org)
In addition, each helix contains a highly conserved inward-facing polar residue at its center (either glutamine or arginine) that contributes to an ionic layer in the middle of the four-helix bundle. (jneurosci.org)
Sequence comparisons across animal phyla demonstrate that AMPD has a highly conserved C-terminal catalytic domain, and a divergent N-terminal region with probable roles in isoform-specific catalytic properties, protein-protein interactions, and subunit associations [ 13 , 14 ]. (hindawi.com)

Using the OmpR protein, we identify residues in the flexible linker and the C-terminal β-hairpin that enable associations of this archetypical response regulator with thioredoxin, but are dispensable for interactions of this transcription factor to its cognate sensor kinase EnvZ, DNA or RNA polymerase. (nature.com)
By using biophysical, molecular and imaging approaches, here, we identify residues needed for Snu13p/15.5K-Rsa1p/NUFIP interaction. (hal.science)

We present a crystal structure of SALL4 C-terminal zinc fingers with an AT-rich DNA sequence, which shows that SALL4 uses small hydrophobic and polar side chains to provide flexible recognition in the major groove. (nih.gov)
[ 2 ] The C-terminus contains an uncleaved secretion signal and the hallmark RTX domain, which is made up of several glycine- and aspartate-rich nonapeptide units with the consensus sequence GGXGXDXψX (ψ represents a bulky hydrophobic residue). (medscape.com)
We compared the sequences of UBQLN1 and UBQLN2 and identified a small glycine-rich region with significant sequence disparity between the two proteins. (syr.edu)
Right:) Illustrative representation of protein sequence space (grey). (tugraz.at)
Sequence analysis of native proteins shows that tight clusters of protein families can be identified (beige). (tugraz.at)
With the advent of protein sequence databases and their ever-increasing growth, it has become evident that nature only sampled an infinitesimal small subset of all possible sequences available. (tugraz.at)
Although considerable sequence diversity is observed among the different binding regions, these three classes of recognition motifs exist for many of the known CaM binding proteins. (embl-heidelberg.de)
were the first to apply bioinformatics techniques to the study of IDPs [ 4 ] by developing a program to predict regions with no defined 3D structure in a protein sequence, called PONDR [ 5 ]. (biomedcentral.com)
Investigating the biological and functional roles of effectors during plant-microbe interactions are accessible through bioinformatics and experimental approaches which can broaden our knowledge about structural biology, sequence motif and domain knowledge of effector proteins from filamentous microbes. (encyclopedia.pub)
De novo protein design (that is, design a sequence from scratch which will create a given fold) is probably one of the more complicated protocols in Rosetta. (rosettacommons.org)
20. Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis. (nih.gov)
We discuss the significance of the observations in light of the fact that the peptides have sequence similarity only to MHC class I molecules (4, 5) among known protein se- quences. (nih.gov)

Sarcoplasmic proteins were unfolded after extremely acidic and alkaline extraction, exposing tryptophan and aliphatic residues. (oregonstate.edu)

The prooncoprotein EWS binds calmodulin and is phosphorylated by protein kinase C through an IQ domain. (embl-heidelberg.de)
Apoplastic secreted effectors, such as secreted proteins (SP's), β-glucan, [ 7 ] or RiSLM that binds to chitin [ 8 ] , are known to play a role in early establishment of mycorrhiza-plant interaction. (encyclopedia.pub)
Human serum albumin (HSA) is a multi-domain protein that binds various ligands and aids in their transport, distribution, and metabolism in the circulatory system. (nsf.gov)

and the need for many protein sequences which fold into a single stable conformation. (creation.com)
We concluded that PA affects protein conformation more significantly compared to EGCg. (nsf.gov)
Dk-(61-85) is active only if it has assumed an ordered conformation prior to its interaction with cells (2). (nih.gov)

These hydrophobic residues might mediate the interaction with the target proteins and therefore receptor recognition. (wikipedia.org)
Three recognition motifs for CaM interaction are discussed in the context of experimental investigations of a variety of CaM target proteins. (embl-heidelberg.de)
We further identified top 5 compounds including cynarine, stigmasterin, kushenol, β -sitosterol, and (24S)-24-propylcholesta-5-ene-3 β -ol as putative key active compounds on the basis of their molecular docking scores with identified hub target proteins. (hindawi.com)

Apo-CaM favors the IQ3 and IQ4 motifs but not the IQ1 and IQ2 motifs that lack two hydrophobic residues for interactions with apo-CaM's hydrophobic pocket. (nih.gov)
Because CaM can bind with high affinity to a relatively small alpha-helical region of many proteins, success in clearly defining the essential elements of CaM binding motifs seems feasible and should provide a means of identifying CaM binding proteins. (embl-heidelberg.de)
A modified version of the IQ motif as a consensus for Ca2+-independent binding and two related motifs for Ca2+-dependent binding, termed 18-14 and 1-5-10 based on the position of conserved hydrophobic residues, are proposed. (embl-heidelberg.de)
Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. (scienceopen.com)
This includes translocated effector proteins containing RxLR motifs and crinklers (CRN's), which will be reviewed in more detail in the next chapter. (encyclopedia.pub)
Fawzi believes these regulatory principles may apply to numerous neurodegenerative disease proteins, as they contain motifs and mutations similar to those found in hnRNPA2 and FUS. (alzforum.org)
The nht, mia, sa and rye proteins contain histone fold domain dimerization motifs. (sdbonline.org)

IQ domain GTPase-activating scaffolding protein 1 (IQGAP1) mediates cytoskeleton, cell migration, proliferation, and apoptosis events. (nih.gov)
A structural motif present in a variety of proteins that mediates protein-protein interactions and assembly of multiprotein complexes. (bvsalud.org)
Finally, we identified a novel BH3-like region located in the C-terminal cytosolic domain of SARS-CoV E protein, which mediates its binding to Bcl-xL. (pdfroom.com)

[ 33-35 ] Bisecting the toxin are two internal lysine residues (K564 and K690) that become post-translationally lipidated (acylated) in the bacterial cytosol prior to secretion. (medscape.com)

The C-terminal subdomain consists of particles, including some hydrophobic residues that are exposed to the solvent. (wikipedia.org)

Cow's milk-based infant formulas are the most common substitute to mother's milk in infancy when breastfeeding is impossible or insufficient, as cow's milk is a globally available source of mammalian proteins with high nutritional value. (mdpi.com)
The large subunit of mammalian microsomal triglyceride transfer protein (MTP), which catalyzes the transport of triglyceride, cholesteryl ester, and phospholipid between phospholipid surfaces. (expasy.org)
Our study reveals the structural conservation and diversity necessary for the binding of IAPs by the Drosophila Hid/Grim/Reaper and the mammalian Smac proteins. (rcsb.org)

Despite considerable experimental progress using nuclear magnetic resonance (NMR), electron spin resonance (ESR), and molecular modeling (9-12) in the investigation of the effect of anchoring aromatic (and polar) residues, many issues remain unresolved. (spectroscopyonline.com)
Acts as a 'third messenger' substrate of protein kinase C-mediated molecular cascades during synaptic development and remodeling. (embl-heidelberg.de)
The molecular basis of this protein-lipid interaction is poorly understood. (nih.gov)
A search for ligand binding sites with the docking program Molecular Operating Environment identified the ordered water network binding site, lined mainly with hydrophobic residues, suggesting an extended ligand binding surface for nonsubstrate ligands, the so-called ligandin site. (nih.gov)
However, many questions remain unresolved about the molecular mechanisms governing mycorrhiza-plant interaction-with one being how they can establish interaction with such a broad host spectrum. (encyclopedia.pub)
Protein kinases represent therefore a sound target for the molecular therapy of people affected by melanomas and their inhibition is now pursued as an effective and viable therapeutic strategy 14 . (nature.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)
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)
In the January 17 Molecular Cell, they reported that pathogenic mutations in the RNA-binding protein hnRNPA2 enhanced its propensity to form β-sheets, spurring fibrillization of droplets. (alzforum.org)
In these studies, the investigation of molecular interactions was restricted to the cleavage products produced by these proteases. (jneurosci.org)
However, it has been difficult to extend the study of precise molecular interactions among SNAREs to CNS synapses, where neurotransmitter is packaged in small, clear vesicles and transmitter release occurs on a faster time scale. (jneurosci.org)

Glycolipid transfer protein knockout disrupts vesicle trafficking to the plasma membrane. (nih.gov)
The hlyB and hlyD genes, along with the genetically unlinked tolC , encode an ABC transporter, membrane fusion/channel protein and outer membrane protein, respectively, which together form the type I secretion system through which HlyA is translocated. (medscape.com)
Although the importance of hydrophobicity for general anesthetic drug potency has long been established, it remains uncertain whether these "nonspecific" drugs act on membrane proteins directly or by modification of the physical properties of the lipid membrane or the lipid-protein interface. (aspetjournals.org)
Thus, it is important to understand the mechanics of RAS-membrane interaction not only to clarify RAS signal transduction, but also to facilitate future drug discovery efforts directed against RAS itself. (nih.gov)
It is becoming increasingly clear that lipids can modulate membrane-embedded protein function and vice versa. (spectroscopyonline.com)
Specifically, we will briefly review relevant Raman spectroscopic markers for lipids and proteins and how both kinds of markers can be used in the investigation of membrane-embedded proteins in fully hydrated liposomes. (spectroscopyonline.com)
The amphiphatic character of membrane-spanning proteins and lipid molecules implies that lipids and proteins self-assemble to avoid the high energetic cost of exposing hydrophobic moieties to water (1,2). (spectroscopyonline.com)
The interaction - hydrophobic coupling - between lipids and membrane proteins is generally only slightly stronger than the interactions between lipids (3,4), suggesting an important role for unspecific lipid-protein hydrophobic interactions (3). (spectroscopyonline.com)
The number of available high-resolution structures of integral membrane spanning proteins is increasing, and there is mounting evidence for regulation of membrane proteins by the host bilayer membrane through the hydrophobic coupling between membrane and proteins (4,5). (spectroscopyonline.com)
This not only raises specific questions as to how membrane-spanning proteins interact with the lipid bilayer, but also opens the possibility to design biomimetic membranes based upon integral membrane proteins incorporated into encapsulated-supported systems for sensor and separation purposes (6). (spectroscopyonline.com)
One of the specific questions relates to a peculiar feature of integral membrane proteins: namely, a preference for aromatic (for example, Trp) residues located in the interfacial region between the hydrophobic core and the hydrophilic surface of the membrane. (spectroscopyonline.com)
Liposomes present a versatile tool for investigating lipid-protein interactions where one can fully control the lipid composition, protein content, and aqueous phases on both sides of the liposomal membrane. (spectroscopyonline.com)
During retrovirus assembly, Gag proteins bind to the inner leaflet of the plasma membrane to initiate the budding process. (nih.gov)
The positively charged residues associate electrostatically with acidic phospholipids to stabilize membrane binding, while myristate provides membrane-binding energy via hydrophobic interactions. (nih.gov)
Here we demonstrate that the human immunodeficiency virus type 1 Gag membrane-binding domain can fully replace the membrane-targeting function of the N-terminal 100 residues of the non-myristylated Rous sarcoma virus (RSV) Gag protein. (nih.gov)
To further explore the importance of myristate and basic residues in membrane binding, we developed a gain-of-function assay whereby budding was restored to defective mutants of RSV Gag. (nih.gov)
Myristate provides additional membrane-binding energy, which is critical when a Gag protein is near the threshold of stable membrane association. (nih.gov)
Biological proteins are usually classified as fibrous, membrane and globular. (creation.com)
Membrane proteins probably make up the majority of all proteins found in the cell. (creation.com)
The structure of membrane proteins, however, is completely different when embedded in a membrane as to when in aqueous solution. (creation.com)
This makes it very difficult to study and characterize membrane proteins in their relevant state. (creation.com)

Here we report that EWS, a nuclear RNA-binding prooncoprotein, contains an IQ domain, is phosphorylated by protein kinase C, and interacts with calmodulin. (embl-heidelberg.de)
Stress-activated serine/threonine-protein kinase involved in cytokine production, endocytosis, reorganization of the cytoskeleton, cell migration, cell cycle control, chromatin remodeling, DNA damage response and transcriptional regulation. (nih.gov)
The exquisite specificity between a sensor kinase and its cognate response regulator ensures faithful partner selectivity within two-component pairs concurrently firing in a single bacterium, minimizing crosstalk with other members of this conserved family of paralogous proteins. (nature.com)

Chapter three studied the interdomain interactions that mediate the liquid-liquid phase separation (LLPS) of ubiquilin-2 (UBQLN2). (syr.edu)

SALL4 protein has a distinct preference for AT-rich sequences, recognised by a pair of zinc fingers at the C-terminus. (nih.gov)
However, unlike many characterised zinc finger proteins, SALL4 shows flexible recognition with many different combinations of AT-rich sequences being targeted. (nih.gov)
Given the sheer number of available and yet unexplored sequences, it is reasonable to argue that there are thousands of possibilities for designing novel proteins of high stability and arbitrary shape. (tugraz.at)
Creationist scientists and Intelligent Design proponents have drawn attention to the sparseness of native-like folded proteins among random polypeptide sequences. (creation.com)

This process occurs though hydrophobic interactions between the microtiter plate and non-polar protein residues. (amrita.edu)
These are likely to be surface-exposed locations, and forcing them polar (or rather, not large hydrophobics) means that there will be less issues with aggregation of the proteins. (rosettacommons.org)
The residue affinity potential encodes the arrangement of hydrophobic, polar and charged residues in a simple potential term. (nih.gov)

Disulfide formation, hydrogen bonding via tyrosine residues, and hydrophobic interactions occurred under extreme pH extraction. (oregonstate.edu)

Two recent papers offer some insight into how a cell might regulate condensation and aggregation of proteins that undergo liquid-liquid phase transitions. (alzforum.org)

In designing a new ligand-binding protein or enzyme acting on a particular molecule, researchers have traditionally tried to repurpose natural proteins. (lbl.gov)
We performed a protein-ligand analysis between nicotine analogs and α7 nAChRs receptor using geometrical conformers, physicochemical characterization of the analogs and developed a manually curated neuroprotective datasets to analyze their potential activity. (openbioinformaticsjournal.com)
Protein‐ligand docking studies were performed using AutoDock Vina Program. (nsf.gov)

Our results support a model in which binding partners could regulate UBQLN2 LLPS and its LLPS-associated functions in cells by interacting with either the UBL or UBA domains of the protein. (syr.edu)
These data suggest that PKC may regulate interactions of EWS and other RNA-binding proteins with their RNA targets and that IQ domains may provide a regulatory link between Ca2+ signal transduction pathways and RNA processing. (embl-heidelberg.de)
Many of the SNAG motif-containing proteins regulate EMT in developmental stages and also in cancerous cells. (eu.org)
It is proposed that the products of the five Drosophila genes encoding testis TAF homologs collaborate in an alternative TAF-containing protein complex to regulate a testis-specific gene expression program in primary spermatocytes required for terminal differentiation of male germ cells (Hiller, 2004). (sdbonline.org)
To identify proteins that might collaborate with the dTAF5 homolog can to regulate expression of specific target genes in Drosophila spermatocytes, the expression and function of other TAF II homologs in the Drosophila genome were investigated (Hiller, 2004). (sdbonline.org)

At this level of resolution, distinct conformations of the alkyl chain of S-hexyl glutathione are observed, reflecting the nonspecific nature of the hydrophobic substrate binding site (H-site). (nih.gov)
In histone H3, the residues at the positions Arg2, Thr6, Arg8, Lys9, and Thr11 are critical for binding as LSD1 substrate ( Lin,2010 ) and the SNAG domain of other transcription factors shares identical residues at positions Arg3, Arg8, and Lys9 and make similar contacts with LSD1. (eu.org)

The authors discuss the feasibility of using Raman spectroscopic markers for the study of lipid-protein complexes in model systems and review relevant Raman spectroscopic markers for lipids and proteins. (spectroscopyonline.com)
A particular area of biophysical research in which Raman spectroscopy has great potential is the study of lipid-protein interactions. (spectroscopyonline.com)
In this article, we will discuss the feasibility of using Raman spectroscopic markers for the study of lipid-protein complexes in model systems. (spectroscopyonline.com)
Raman spectroscopy has immediate appeal in the study of lipid-protein interactions because it is a noninvasive and nondestructive technique, and the excitation wavelength can be chosen to be below the absorption frequency of water (13). (spectroscopyonline.com)
But with increased sensitivity and recent developments in instrumentation, Raman spectroscopy is experiencing a revival in many research areas, including the study of lipids and lipid-protein complexes (14-19). (spectroscopyonline.com)
Here, we first discuss the technical challenges and relevant Raman spectroscopic markers for investigating the role of lipid-protein interactions in fully hydrated protein-vesicle samples. (spectroscopyonline.com)
Lipovitellin is the major lipid-protein complex found in the yolk of egg-laying animals, and is involved in lipid and metal storage. (expasy.org)
Lipid-protein interactions in lipovitellin. (expasy.org)

It reads different epigenetic marks on the histone proteins and suppresses gene expression by converting di-methylated H3K4 to mono- and un-methylated H3K4 through amine oxidation ( Shi,2004 ). (eu.org)
20 Through its N-terminal hydrophobic domain, NPM also exerts a chaperone activity, preventing protein aggregation in the nucleolus, favoring histone and nucleosome assembly, 21 - 23 and increasing acetylation-dependent transcriptional activity. (haematologica.org)

Thermodynamic parameters demonstrated that the protein‐ferrocene interactions are spontaneous, highly entropic, and hydrophobic. (nsf.gov)

We find that specific mutations in the acetylcholine receptor pore-forming M2 domains enhance the sensitivity of the receptor to the general anesthetics isoflurane, hexanol, and octanol, suggesting that these agents act by binding directly to a discrete protein site at or near these residues. (aspetjournals.org)
The sensitivity of the receptor to block by general anesthetics increases with increased hydrophobicity of these residues, demonstrating that hydrophobic forces dominate the interaction of drugs with their protein site. (aspetjournals.org)
In addition to SIGLEC receptors, the lab recently began to investigate the potential interaction between C-type lectin receptor, CD62L, and HIV-1 envelope protein, gp120. (nih.gov)

the protein condenses into liquid-like droplets at low temperature and returns to one soluble phase at high temperature. (syr.edu)
How Does a Neuron Avoid Aggregation of Liquid Protein Droplets? (alzforum.org)
Researchers believe that many proteins linked to neurodegenerative diseases function when condensed into liquid droplets. (alzforum.org)
Unfortunately, for reasons that elude scientists, those droplets can harden into toxic protein aggregates. (alzforum.org)
Meanwhile, researchers led by Jared Sterneckert at Technische Universität Dresden, Germany, found that revving up autophagy, a cellular disposal system, helped shrink RNA stress granules by degrading FUS, another protein that forms liquid droplets. (alzforum.org)
Salt forced hnRNPA2 LCDs to condense into droplets, likely held together by hydrophobic bonds. (alzforum.org)

Ultimately, we are aiming to be able to routinely and robustly design catalytic or small molecule binding proteins of arbitrary shapes. (tugraz.at)
Strutural modelling of TTL revealed that residues Met-114 and Met-142 are in close vicinity of the active site and their replacement by the norleucine could modulate the catalytic activity of the enzyme. (frontiersin.org)

This modulation can take both specific and nonspecific forms, but the underlying framework is defined by the amphiphatic nature of lipids and proteins. (spectroscopyonline.com)
The ideal blocking buffer will bind to all potential sites of nonspecific interaction, eliminating background altogether, without altering or obscuring the epitope for antibody binding. (amrita.edu)

Project 1 aimed to determine which effectors are engaged by each of the mutant proteins, solve the structures of mutant RAS proteins complexed with relevant effectors, and identify new opportunities for small-molecule therapeutics. (nih.gov)
Computational design of novel protein structures is a promising tool to make superior biological materials with tailor-made properties, new pharmaceuticals or complex fine chemicals. (tugraz.at)
Over the last couple of years, tremendous progress has been made in this direction with many novel protein structures designed from scratch. (tugraz.at)
This causes a protein to fold into compact, characteristic shapes (secondary structures), such as alpha helices and beta (β) sheets. (lbl.gov)
In the latter, parallel protein strands line up so that bonds can form between the strand edges, creating relatively flat, sheet-like structures. (lbl.gov)
Previously, the computational design of proteins from scratch had been limited to structures that were too compact to accommodate cavities. (lbl.gov)
In this work, researchers deciphered the key rules that determine the shape of structures formed by β sheets in natural proteins. (lbl.gov)
The researchers then incorporated these rules into existing computational protein design methods and built new types of protein structures having the shapes they were targeting. (lbl.gov)
Interpretation and analysis of the crystallographic data showed that the experimental protein structures were very close to the computational models, validating the new design approach. (lbl.gov)
A globular protein is classically presented, from a structural point of view, as a succession of regular secondary structures (strands and helices) connected by loops. (upmc.fr)
However, subsequent research has shown that there are many proteins without specific 3D-structures under physiological conditions, so-called intrinsically disordered proteins (IDPs). (biomedcentral.com)
Furthermore, it can also predict a core region of IDPs forming definite 3D structures through interactions, such as dimerization. (biomedcentral.com)
Surprisingly, IDPs exhibit their functions through interactions with another protein despite their lack of well-defined structures. (biomedcentral.com)

Stability of a position by respect to mutation can be done by comparing the free energies of the native and mutated proteins, D D G. Several tools are available, either as included in a web server, or as an executable file. (upmc.fr)
SPROUTS: a database for evaluation of the protein stability upon point mutation. (upmc.fr)
Up to four main types of melanoma may be described, differentiated by anatomic sites and clinical features, as well as by distinctive genomic alterations including amplification, deletion and mutation of selected genes encoding for particular protein kinases. (nature.com)
By contrast, the P298L mutation associated with Paget's disease of bone replaces a hydrophobic proline with another hydrophobic residue. (alzforum.org)

PKC phosphorylation of these proteins also inhibits their binding to RNA in vitro. (embl-heidelberg.de)
Moreover, we found that SARS-CoV E protein interacted with Bcl-xL in vitro and endogenous Bcl-xL in vivo and that Bcl- xL interaction with SARS-CoV E protein was mediated by BH3 (Bcl-2 homology domain 3) of Bcl-xL. (pdfroom.com)
18. Binding of human nucleotide exchange factors to heat shock protein 70 (Hsp70) generates functionally distinct complexes in vitro. (nih.gov)
In collaboration with Jon Lorsch's group, we demonstrated that segments/residues in eIF1, eIF1A, tRNAi and 18S rRNA, which are implicated genetically in TC recruitment, also stimulate the rate of this reaction in a fully reconstituted yeast in vitro translation system. (nih.gov)

We hypothesized that SARS-CoV encodes a small envelope E protein that is homologous with MHV E protein, thus inducing T-cell apoptosis. (pdfroom.com)
The gene NPM1 that encodes for nucleophosmin (NPMI) is translocated or mutated in various lymphomas and leukemias, forming fusion proteins (NPM-ALK, NPM-RARa, NPM-MLF1) or NPM mutant products. (haematologica.org)

The first 163 residues of the N-terminal domain forms an α-β-α sandwich core. (wikipedia.org)
This domain is comparable with group 1 plant pathogenesis-related protein (PR-1). (wikipedia.org)
The structure of a mutant immunoglobulin-binding B1 domain of streptococcal protein G (GB1), which comprises five conservative changes in hydrophobic core residues, was determined by NMR spectroscopy and X-ray crystallography. (rcsb.org)
Taxonomic distribution of proteins containing IQ domain. (embl-heidelberg.de)
The complete taxonomic breakdown of all proteins with IQ domain is also avaliable . (embl-heidelberg.de)
Click on the protein counts, or double click on taxonomic names to display all proteins containing IQ domain in the selected taxonomic class. (embl-heidelberg.de)
In a protein containing partially disordered regions, a domain region is likely to be ordered, thus it is unlikely that a disordered region would be part of any domain. (biomedcentral.com)
In addition to its critical role in viral replication, PL pro removes post-translational modifications like ubiquitin and interferon-stimulated gene product 15 (ISG15) from host proteins through its deubiquitinase domain, leading to host immunosuppression and increased ability of the virus to evade the host antiviral immune response. (fortunejournals.com)
The split transcription factor is built from the plant-derived optical dimer PhyB and PIF3, which is fused to a DNA-binding domain based on the catalytically dead Cas9 protein (dCas9) and a transactivation domain. (optobase.org)
The inhibitor of apoptosis protein DIAP1 suppresses apoptosis in Drosophila, with the second BIR domain (BIR2) playing an important role. (rcsb.org)
The amine oxidase (AO) domain of LSD1 is responsible for its interaction with SNAG. (eu.org)
We have mapped a Jagged/Serrate-binding site to specific residues within the 12th EGF domain of human and Drosophila Notch. (plymouth.ac.uk)
Förster resonance energy transfer (FRET) was used to determine inter- and intra-domain distances in the protein with and without EGCg and palmitic acid (PA). (nsf.gov)
In solution, the enzyme protein arginine methyl transferase 1 modified four arginine residues in hnRNPA2's low-complexity domain. (alzforum.org)
1. Regulatory inter-domain interactions influence Hsp70 recruitment to the DnaJB8 chaperone. (nih.gov)
3. Class-specific interactions between Sis1 J-domain protein and Hsp70 chaperone potentiate disaggregation of misfolded proteins. (nih.gov)
6. The four hydrophobic residues on the Hsp70 inter-domain linker have two distinct roles. (nih.gov)
15. J-domain protein chaperone circuits in proteostasis and disease. (nih.gov)

Progress in the characterization of processed full length KRAS4B and its interaction with cellular membranes stands as a highlight of the RAS Initiative to date. (nih.gov)

For these experiments cross-connected The expressed proteins and immunoprecipitated complexes ended up analysed by immunoblotting. (adenosine-receptor.com)
TSC1delex proteins have been co-expressed with TSC2 and HATBC1D7 in transfected HEK 293T cells, and TSC1-TSC2-TBC1D7 complexes were immunoprecipitated with an anti-myc tag antibody. (adenosine-receptor.com)

The initial findings were with 25-residue peptides, but it was found subsequently that the eight N-terminal residues could be removed without loss of activity (1). (nih.gov)

Purified Tub4p complex contains one molecule of Spc98p and Spc97p, and two or more molecules of Tub4p, but no other protein. (sdbonline.org)
Curved β sheets are basic building blocks of many protein cavities that, by serving as binding sites for other molecules, are essential to protein function. (lbl.gov)

Alternation in the glycolipid transfer protein expression causes changes in the cellular lipidome. (nih.gov)
Calmodulin (CaM) is recognized as a major calcium sensor and orchestrator of regulatory events through its interaction with a diverse group of cellular proteins. (embl-heidelberg.de)
Many investigations have focused on defining the region of interaction between CaM and its cellular targets and the action of CaM on target protein function. (embl-heidelberg.de)
MYB transcription factors are named after an Avian myeloblastosis virus protein (v-Myb) which is a modified version of the cellular c-Myb and causes the activation of oncogenes [ 1 ]. (biorxiv.org)
Optogenetic systems use genetically encoded light-sensitive proteins to control cellular processes. (optobase.org)
Human thioredoxin is a 12 kDa cellular redox protein that plays a key role in maintaining the redox environment of the cell. (nih.gov)
Under native conditions, both in resting and proliferating cells, over 95% of cellular NPM protein exists as an oligomer. (haematologica.org)

One of the small serum proteins (SSP-2), a substance produced by Trimeresurus flavoviridis itself, has high affinity for Triflin, and may thus work as a defensive mechanism against accidental self-poisoning, suggesting a possible role for SSP-2 as an antidote to triflin. (wikipedia.org)
Docking simulations provided corroborating evidence for these binding interactions and indicated multiple high-affinity modes of binding. (nih.gov)
The crystal structure of the complex of AChE with optically pure HupA at 2.5 A resolution shows an unexpected orientation for the inhibitor with surprisingly few strong direct interactions with protein residues to explain its high affinity. (proteopedia.org)

14. A DNAJB chaperone subfamily with HDAC-dependent activities suppresses toxic protein aggregation. (nih.gov)

We now show that systematic alanine substitution in D'-(69-85) identifies residues that are essential for biological activity. (nih.gov)

The alpha-helical structure was converted to beta-sheet following acidic extraction, whereas alkaline treatment did not disturb the alpha-helical structure of sarcoplasmic proteins. (oregonstate.edu)

After analyzing classic protein formations and running folding simulations, researchers designed a series of novel proteins with curved β sheets, inspired by naturally occurring protein superfamilies. (lbl.gov)

Figure 1: (Left:) Differences in structure prediction and de novo protein design. (tugraz.at)
I am trying to learn how to preform De novo Protein Design. (rosettacommons.org)

Protein-protein interactions (PPIs) play central roles in most biological processes. (syr.edu)

The protein encoded by this gene is similar to bovine and porcine proteins which accelerate transfer of certain glycosphingolipids and glyceroglycolipids between membranes. (nih.gov)
Description of the protein which includes the UniProt Function and the NCBI Gene Summary. (nih.gov)
To test this hypothesis, a cDNA encoding SARS-CoV E protein was created using whole gene synthesis. (pdfroom.com)
4 Nucleophosmin is an essential protein, since inactivation of the gene encoding for nucleophosmin ( NPM1 ) in the mouse germ line leads to developmental defects that cause embryonic death in mid-gestation. (haematologica.org)

We show that conserved hydrophobic and charged residues on the surface of thioredoxin serve as a docking station for structurally diverse response regulators. (nature.com)
Here we show that the promiscuous interactions of response regulators with thioredoxin foster the flow of information through otherwise highly dedicated two-component signaling systems, thereby enabling both the transcription of Salmonella pathogenicity island-2 genes as well as growth of this intracellular bacterium in macrophages and mice. (nature.com)

Apolipophorin II/I, apolipoprotein B, vitellogenin, and microsomal triglyceride transfer protein genes are derived from a common ancestor. (expasy.org)
For example, an alternate form of TAF4 (TAF4b -- formerly hTAF II 105) highly expressed in granulosa cells was found to associate with TBP and TAF1 in a large, TFIID-like protein complex in ovarian extracts (Freiman, 2001) and to be required for normal follicular development and for expression of a number of genes in developing ovarian follicles in mice (Hiller, 2004 and references therein). (sdbonline.org)

For the first time, biophysical interaction studies were carried out using bovine serum albumin (BSA) and human serum albumin (HSA) for these polymers which are not yet reported in the literature. (nsf.gov)

Emerging roles for human glycolipid transfer protein superfamily members in the regulation of autophagy, inflammation, and cell death. (nih.gov)
9. Roles of intramolecular and intermolecular interactions in functional regulation of the Hsp70 J-protein co-chaperone Sis1. (nih.gov)
Many findings have revealed a complex scenario of NPM functions and interactions, pointing to proliferative and growth-suppressive roles of this molecule. (haematologica.org)

The present structure is an illustrative example of how proteins exploit the breadth of conformational space. (rcsb.org)

Docking studies corroborated the experimental data, and the binding interactions are hydrophobic. (nsf.gov)

We further discuss the case of p53, a tumor-suppressor protein, which is the most significant protein among cell cycle regulatory proteins. (biomedcentral.com)
Bcl-2 is a Bcl-xL homologue and the founding member of the Bcl-2/Bcl-xL apoptosis regulatory protein family [15]. (pdfroom.com)

Acidic extraction induced denaturation and aggregation of sarcoplasmic proteins to a greater extent than did alkaline treatment. (oregonstate.edu)

Additionally, bulges, bends, and other protrusions into the space (e.g. side chains that branch off of the main protein chain) can shape the cavity into a unique pocket into which only a complementary shape will fit, like a hand into a glove. (lbl.gov)
Side chains of Arg3 and Ser4 bind deeply into the LSD1 cleft and make several H-bonding interactions with the surrounding protein residues. (eu.org)

Four of the five secondary structure elements present in the monomeric wild type GB1 structure are retained in the tetrameric structure, although their intra- and intermolecular interactions are altered. (rcsb.org)

The oligomeric state and quaternary structure of the mutant protein are drastically changed from the wild type protein. (rcsb.org)
The narrow processing window is characteristic of the material's semi-crystalline nature which arises from residual protein secondary structure (α-helices and β-sheets). (waikato.ac.nz)
This work developed a suitable foaming method and an understanding of the role of protein secondary structure and rheology for Novatein, which can be foamed despite its high β-sheet content. (waikato.ac.nz)
To verify that the resulting proteins had the desired properties and adopted the modeled structure, the researchers experimentally characterized them with a variety of techniques. (lbl.gov)
It has been shown over the past years that these MIR are key residues, not for the function, but for the structure, and deeply buried in the core of the protein. (upmc.fr)
It had long been thought that a protein exhibits its specific function through its own specific 3D-structure under physiological conditions. (biomedcentral.com)
The technique in our study may also serve as a means of predicting a disordered region which would become an ordered structure when binding to another protein. (biomedcentral.com)
Anfinsen's discovery [ 1 ] that a protein exhibits its specific function through its own specific 3D-structure under physiological conditions dominated protein research for many years. (biomedcentral.com)
The structure of the Cyt c-554 is compared with those of other Cyts c, and possible interactions of this protein with its electron transport partners are discussed. (elsevierpure.com)
Circular dichroism (CD) established that EGCg affects protein secondary structure more significantly than PA. (nsf.gov)
We have brilliant colleagues who are in the forefront of their respective research and focused on an understanding of protein structure and dynamics, and how we might understand how life actually works by probing these things at an intimate level of detail. (nih.gov)

As a result, the bonds between proteins can be weakened to promote structural changes such as depolymerization. (go.jp)

Alternatively, protein A or protein G-enzyme conjugates may be preferable when screening monoclonal antibodies. (amrita.edu)

Anatomy10

Organisms11

Chemicals and Drugs99

Analytical, Diagnostic and Therapeutic Techniques and Equipment48

Phenomena and Processes83

Disciplines and Occupations7

Technology, Industry, Agriculture2

Information Science13

Health Care4

Amino26

Aromatic residues5

Disrupt hydrophobic interactions2

Peptide10

Globular proteins5

Electrostatic2

Hydrophilic residues1

Highly conserved4

Identify residues2

Sequence12

Tryptophan1

Binds3

Conformation3

Target proteins3

Motifs7

Mediates3

Lysine1

Solvent1

Mammalian3

Molecular11

Membrane21

Kinase3

Mediate1

Sequences4

Polar3

Tyrosine1

Aggregation of proteins1

Ligand3

Regulate5

Substrate2

Lipid-protein8

Histone2

Entropic1

Receptor3

Droplets6

Catalytic2

Nonspecific2

Structures13

Mutation4

Vitro4

Encodes2

Domain18

Characterization1

Complexes2

Peptides1

Molecules2

Cellular7

Affinity3

Suppresses1

ALANINE1

Alpha-helical1

Novel proteins1

Novo protein design2

Biological1

Gene4

Thioredoxin2

Genes2

Biophysical1

Roles3

Conformational1

Experimental1

Regulatory2

Acidic1

Chains2

Intermolecular interactions1

Structure11

Bonds1

Conjugates1