Biological systems interactions protein residues. Medical search. Frequent questions

Linear and cyclic π systems bond to metals allowing organic complexes to bond to metals. (wikipedia.org)
Due to their mobility broadening their probability distributions, the vast majority of counterions around proteins, nucleic acids, and their complexes are unresolved even in high-resolution crystal structures. (utmb.edu)
The techniques developed in my laboratory have been applied to understand molecular flexibility, interactions between proteins and other molecules, and self-assembly behavior in complexes made from multiple proteins. (haverford.edu)
Biological systems of interest for us include regulatory proteins, membrane-associated proteins, bacteriosynthetic proteins, viral protein complexes, and aggregating peptides and proteins. (haverford.edu)
Computational analyses show that Zn(2+) and Cu(2+) form pentacoordinate complexes involving both the His4 and His8 residues of the N-terminal domain of one monomeric unit and the His84 and Asp105 residues of the other monomeric unit of the NGF active dimer. (cnr.it)
We started hypothesizing that the most obvious interpretation of interference was from subunit poisoning by wild type proteins with mutant proteins into complexes, where maximum signal output would require both the proteins to be in the active state persistently, and that having a wild type protein would be like a sort of flat tire and would be a much less efficient complex than a sort of double barreled mutant RAS. (cancer.gov)
However, less is understood about how RT crystallography may impact the conformational landscapes of protein-ligand complexes. (rcsb.org)
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)
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)

The in silico data provided insights into the molecular mechanism of the interaction between acetone molecules and the lysozyme protofibril, once acetone presented the best experimental results. (bvsalud.org)
In life, complex networks of molecular interactions involve electrostatic forces that influence structure and function of biological macromolecules. (utmb.edu)
We also use molecular dynamics simulations and frequency calculations to provide a computational picture of what our experimental data shows about protein structures. (haverford.edu)
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)
Im describes it as a "computational microscope" that enables scientists to understand molecular-level interactions that cannot be observed any other way. (medicalxpress.com)
They also built a viral membrane system of an S protein for molecular dynamics simulation. (medicalxpress.com)
The present study demonstrated the one example of biologically important and molecular self-assembly system is a collagen-DNA ordered aggregates which spontaneously forms in aqueous solution. (scialert.net)
In this paper is demonstrated that one example of the biologically important and molecular self-assembling complex system is a collagen-DNA ordered aggregates spontaneously formed in aqueous solutions. (scialert.net)
Mrevlishvili and Svintradze (2005a, b) is demonstrated that one example of biological important and molecular self-assembly complex system is the collagen-DNA ordered aggregate which is spontaneously formed in aqueous solution. (scialert.net)
The research activity focussed on experimental study of the structural and dynamic properties of short-lived intermediates of biologically important molecular systems and photoprocesses using novel techniques of magnetic resonance spectroscopy. (europa.eu)
Many molecular pathways in eukaryotic cells are modulated by specific signaling proteins that are controlled, by phosphorylation and dephosphorylation, through the activity of kinase and phosphatase enzymes. (biomedcentral.com)
Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. (elifesciences.org)
Here we explore the translation of biological composites to engineering applications, using a variety of tools including molecular modeling, AI and machine learning, and experimental synthesis and characterization. (mrs.org)
We also present case studies of protein material optimization using genetic algorithms, applied to 3D printed composites, molecular design, and a translation of protein folding to music and back. (mrs.org)
Here, we analysed two deep mutational scanning experiments to investigate the role of protein aggregation in molecular evolution. (frontiersin.org)
Here, we set to clarify this complex matter and question of whether aggregation is an important constraint in protein evolution that can be the discriminant between beneficial and detrimental situations by considering two cases: we studied molecular evolution of proteins in an endogenous vs. exogenous host. (frontiersin.org)
Molecular dynamics (MD) is a computer simulation of physical movements of atoms and molecules, widely used to study biological systems. (uiuc.edu)
Recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. (uiuc.edu)
Using molecular modeling, the impact of BQ and NAC-BQ adduction on cytochrome c was visualized, revealing the spatial rearrangement of critical residues necessary for protein-protein interactions. (elsevierpure.com)
In summary, a combination of mass spectroscopic, molecular modeling, and biochemical approaches confirms that electrophile - protein adducts produce structural alterations that influence biological function. (elsevierpure.com)
The 2003-2004 influenza season was severe in terms of ducted a molecular analysis of the HA1 region of the HA its impact on illness because of widespread circulation protein. (cdc.gov)
Protein structures are invaluable for biochemical studies and for mechanical or molecular mechanics calculations have become the understanding of how proteins work. (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)

Aromatic-aromatic interactions (π stacking): involves interactions of aromatic molecules with each other. (wikipedia.org)
The specifics for binding of π cyclic systems are much more complex and depend on the electrons, the HOMO, and the LUMO in each individual case of molecules. (wikipedia.org)
Applications to intrinsically disordered proteins and conformationally flexible nucleic acids are particularly useful because structure-based analysis of electrostatics is not straightforward for such molecules. (utmb.edu)
1. study of photochemical reactions involving proteins and protein related molecules. (europa.eu)
A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. (uni-luebeck.de)
This is particularly true of studies that have examined the arrangement of atoms in large molecules with elaborate structures like proteins or DNA. (elifesciences.org)
However, cells are densely packed with many different molecules and there is little proof that proteins keep the same structures inside cells that they have when they are studied alone. (elifesciences.org)
This model suggested new possible interactions between molecules inside cells that cannot currently be studied in real cells. (elifesciences.org)
There are conflicting data on whether KRAS protein molecules form dimers. (cancer.gov)
The atoms and molecules are allowed to interact, giving a view of the motion of the atoms and consequently of protein domains in the case of protein simulations. (uiuc.edu)
Next it is important to remove cofactors, ions, and water molecules not involved in the binding interactions. (stonybrook.edu)
It is suggested that the hemopexin domain facilitates binding to a variety of molecules and proteins, for example the HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs). (embl.de)
At neutral pH, where these residues are uncharged, we find no evidence of buried water molecules near the mutation site. (lu.se)

Crystal structures of protein kinases with bound substrate peptides show that substrate residues at positions -3 to +3 relative to the phosphorylated serine, threonine or tyrosine residue adopt an extended conformation and bind to a pocket in the catalytic domain of the protein kinase [ 8 ]. (biomedcentral.com)
Enzymatic digestion of protein into shorter peptides by sequence-specific proteases is a key step in mass spectrometry-based shotgun proteomics experiments. (asbmb.org)
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)
The use of synthetic peptides approved by the health authorities for vaccine, for cancer, and in drug delivery systems is increasing with these developments. (intechopen.com)
The aim of this book chapter is to review the recent developments in the use of peptides in the diagnosis of drug and vaccine systems and to present them to the reader with commercially available illustrations. (intechopen.com)

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)
Modification of a substrate protein via the covalent attachment of the C-terminal glycine of Ub to the ε-amino group of lysine residues in a substrate is termed ubiquitination. (ndltd.org)
Unlike, other PTM proteins, Ub can form polyUb chains at one or more of its seven lysine residues. (ndltd.org)
Unfortunately, the study of these chains have been limited by the inability to generate homogeneous polyUbs chains linked at known lysine residues. (ndltd.org)
Finally, mutagenesis of N1 showed that ubiquitylation occurs in a conventional lysine-dependent manner at multiple acceptor sites because only an N1 allele devoid of lysine residues remained unmodified. (ox.ac.uk)
To examine the role of water penetration, we have measured the 17O and 2H magnetic relaxation dis- persions (MRD) for the V66E and V66K mutants of staphylococcal nuclease, where glutamic acid and lysine residues are buried in predominantly apolar environments. (lu.se)

My main research interest is the development of new physical techniques for understanding conformational flexibility and structural switching in proteins. (haverford.edu)
We proposed to utilise CIDNP kinetics in proteins to determine the paramagnetic nuclear relaxation times and use them for site-specific determination of correlation times of intramolecular mobility of residues in different conformational states on the nanosecond time scale. (europa.eu)
The CusB protein is part of the CusCBA periplasmic Cu(I) efflux system in Gram-negative bacteria, and it was recently reported to play a key role in the functioning of the whole CusCBA system, in which conformational changes as well as the assembly/disassembly process control the opening of the transporter. (biorxiv.org)
Some residues were found to be in close proximity and displayed different interacting patterns due to conformational changes of the receptor upon ligand binding. (tennessee.edu)
We show that at RT, fewer ligands bind, and often more weakly - but with a variety of temperature-dependent differences, including unique binding poses, changes in solvation, new binding sites, and distinct protein allosteric conformational responses. (rcsb.org)
Overall, this work suggests that the vast body of existing cryo-temperature protein-ligand structures may provide an incomplete picture, and highlights the potential of RT crystallography to help complete this picture by revealing distinct conformational modes of protein-ligand systems. (rcsb.org)
Our results may inspire future use of RT crystallography to interrogate the roles of protein-ligand conformational ensembles in biological function. (rcsb.org)
Such buried ionizable groups destabilize the protein and may trigger conformational changes in response to pH variations. (lu.se)
On the other hand, the MRD data are consistent with a local conformational change in response to ionization of the internal residues. (lu.se)

π-metal interactions can also be involved directly with the function of ligands on the catalyst. (wikipedia.org)
By comparing the binding affinity of dansyl-proline with HSA and ovotransferrin, we demonstrated that FRET explains the quenching provoked by the interaction of ligands in albumin. (bvsalud.org)
To do so, I studied the interaction inside the protein among site-I ligands of HSA via fluorescence resonance energy transfer (FRET), synchronous fluorescence, red edge excitation shift (REES), and induced circular dichroism (ICD). (bvsalud.org)
Therefore, we attempt to check whether we'd elicit ligand-dependent behavioural reactions in em C. elegans /em by expressing mammalian GPCRs in the ASH and ADL gustatory neurons, because they are straight exposed to the surroundings allowing gain access to of proteins and peptide ligands towards the heterologous receptors. (exposed-skin-care.net)
This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. (uni-luebeck.de)
Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. (elifesciences.org)
DEC-205 (CD205), a member of the macrophage mannose receptor protein family, is the prototypic endocytic receptor of dendritic cells, whose ligands include phosphorothioated cytosine-guanosine (CpG) oligonucleotides, a motif often seen in bacterial or viral DNA. (uci.edu)
Much of our current understanding of how small-molecule ligands interact with proteins stems from X-ray crystal structures determined at cryogenic (cryo) temperature. (rcsb.org)
2018). Here, we have performed two RT crystallographic screens of PTP1B using many of the same fragments, representing the largest RT crystallographic screens of a diverse library of ligands to date, and enabling a direct interrogation of the effect of data collection temperature on protein-ligand interactions. (rcsb.org)
The binding cavities were predicted for both the proteins through blind and specific protein-ligand docking with their respective ligands and inhibitors and were found to be in accordance with the druggable sites predicted by DoGSiteScorer. (bvsalud.org)
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)

Furthermore, we have identified specific glutamic acid residues within cytochrome c as novel sites of NAC-BQ adduction. (elsevierpure.com)

We developed an innovative methodology to directly measure local electrostatic potentials for every residue of proteins and nucleic acids. (utmb.edu)
We use NMR spectroscopy for such characterizations of the positively or negatively charged groups of proteins and nucleic acids. (utmb.edu)
TDP-43 is a highly conserved, ubiquitously expressed, multifunctional nucleic acid-binding protein composed of two RNA recognition motifs (RRM), nuclear localization (NLS) and export signals (NES), and a carboxy-terminal glycine rich region. (nature.com)
The technique had high potential for determining the structural and magnetic resonance properties and the reactivity of the radicals of proteins, nucleic acids and their building blocks. (europa.eu)
However, chemical and enzymatic probing has lead to the idea that these tRNAs have retained the basic cloverleaf structure of canonical tRNAs but that they lack several conserved tertiary interactions leading to a weaker three-dimensional structure (4Watanabe Y.-I. Kawai G. Yokogawa T. Hayashi N. Kumazawa Y. Ueda T. Nishikawa K. Hirao I. Miura K.-I. Watanabe K. Nucleic Acids Res. (ncsu.edu)
However, small amounts of the aminoacylated 8U→C mutated hmtRNAMet could be isolated, permitting a limited investigation of additional steps in translation.In the mammalian mitochondrial system, the Met-tRNAMet must be formylated by the mitochondrial transformylase (MTFmt) to be used in initiation (19Spencer A.C. Spremulli L.L. Nucleic Acids Res. (ncsu.edu)
The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. (elifesciences.org)

Fragment of 6 × His-T1 lipase fusion was synthesized, cloned into the pGEX4T1 system, and expressed in Escherichia coli BL21 (DE3) pLysS, resulting in lipase-specific activity at 236 U/mg. (bvsalud.org)

The second factor, termed peptide specificity, describes the interaction between amino acid residues in the catalytic domain of the protein kinase and the substrate residues that surround the phosphorylated residue. (biomedcentral.com)
The relative contribution of substrate recruitment and peptide specificity to protein kinase substrate specificity varies between protein kinases. (biomedcentral.com)
However, it is recognised that for many protein kinase families, particularly those that phosphorylate Ser/Thr residues, peptide specificity is the major factor that determines substrate specificity. (biomedcentral.com)
The prediction of peptide specificity is therefore the basis for most of the available computational methods aimed at predicting substrates of protein kinases. (biomedcentral.com)
Progesterone receptor membrane component 1 (PGRMC1) is 195 residue membrane-bound protein which contains a short luminal peptide, a single N -terminal transmembrane domain, and a C -terminal cytochrome b 5 -related heme-binding domain ( Figure 1A ). (oncotarget.com)
Functional recognition of the modified human tRNA(UUU)(Lys3) anticodon domain by HIV's nucleocapsid protein and a peptide mimic. (ncsu.edu)
These opportunities are surveyed here against a background of the immunobiology of allergic sensitization and current state-of-the-art approaches to measurement of peptide/protein reactivity. (cdc.gov)
The information we gathered here allows us to understand more about the physical interactions of alpha-factor, Ste2p, and Gpa1p and provides us insights about the initiation and activation of the signal transduction pathway of a peptide ligand receptor. (tennessee.edu)

Despite the importance of ions as essential constituents of biological systems, how these ions interact with biological macromolecules and impact their functions is not well understood. (utmb.edu)
Biological macromolecules function in highly crowded cellular environments. (elifesciences.org)

2). Glycomics, the systematic study of all glycan structures in a biological system, relies on effective enzymatic and analytical techniques for correlation of glycan structure with function. (neb.com)
Other commonly used endoglycosidases such as Endoglycosidase H ( NEB #P0702 ) are not suitable for general deglycosylation of N -linked sugars, because it only deglycosylates glycoproteins containing primarily high mannose N -linked structures, as well as leaving one N -acetylglucosamine residue attached to the asparagine. (neb.com)
My group uses the vibrational bands of both natural and unnatural amino acids to determine the residue-level structural distribution of proteins with particularly dynamic structures. (haverford.edu)
For proteins that are building blocks in larger structures, the ability of the building blocks to adopt multiple shapes can allow the construction of complex biomolecular assemblies. (haverford.edu)
Vibrational spectroscopy is uniquely suited to observation of structural distributions, rather than just average protein structures. (haverford.edu)
The positions of highlighted regulatory phosphorylations observed in (B) below are indicated, as are the amino acids included in the NMR structure deposited as PDB 4X8Y, and the amino acid residues used to obtain crystal and NMR structures [ 4 ]. (oncotarget.com)
The predominant helical nature of the N and C-terminal extensions of FAM were predicted to form scaffolding structures, well suited to protein binding. (ndltd.org)
The association pathway from monomer to oligomer is critical in a range of biological processes and thus it is of a vital importance to elucidate both atomic-resolution structures of intermediates along the pathway as well as the structure of the final state. (lu.se)
The 3 D structures of these two target proteins were predicted via ab initio homology modeling followed by structures refinement and validation, as no structures were available till date. (bvsalud.org)
The most common strong alternative and complement to experimental methods to methods to obtain protein structures are X-ray crystallography obtain insight in biochemical processes. (lu.se)

Non-covalent interactions involving π systems are pivotal to biological events such as protein-ligand recognition. (wikipedia.org)
The interactions involved usually are non-covalent (such as metal-ligand bonds, hydrogen bonds, or van der Waals forces-hydrophobic interactions) (Whitesides and Boncheva, 2002). (scialert.net)
Current strategies utilised to review mammalian GPCR-ligand connections are mainly em in vitro /em systems, that are not often an accurate representation of em in vivo /em connections. (exposed-skin-care.net)
These moieties are critical in terms of their role in in-vivo safety and efficacy (pharmacodynamics and pharmacokinetics), protein folding, protein targeting and trafficking, ligand binding, stability, protein halfâ life regulation, and immunogenicity (8). (chromatographyonline.com)
We have used the pheromone alpha-factor receptor (Ste2p) of the yeast Saccharomyces cerevisiae as a model system to understand ligand binding, receptor activation, and G protein interaction. (tennessee.edu)
Another method to study ligand binding that we have adapted for use in our system is to incorporate a chemical crosslinker [3,4-dihydroxylphenylacetyl (DHPA)] into alpha-factor for periodate-mediated crosslinking to Ste2p. (tennessee.edu)
After ligand binding, signal transduction is mediated by the interaction of activated Ste2p with its G protein (Gpa1p). (tennessee.edu)
1 monomer of 1X70 with all waters and non standard residues deleted except for the ligand 715, which is colored light blue for clarity. (stonybrook.edu)
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)

Taxonomic distribution of proteins containing HX domain. (embl.de)

N -linked glycosylation occurs when glycans are attached to asparagine residues on the protein. (neb.com)
O -linked glycans are most commonly attached to serine or threonine residues through the N -Acetylgalactosamine residue. (neb.com)
In addition, they modeled all potential glycans (or carbohydrates) attached to the S protein. (medicalxpress.com)
Glycosylation refers to a sequence of events that take place in the Golgi body and the endoplasmic reticulum of the cells of the expression system (predominantly mammalian) that lead to post-translational addition and processing of carbohydrate or glycan moieties to the protein backbone (usually serine- or threonineâ linked glycosylation for O-linked glycans and asparagineâ linked glycosylation for N-linked glycans) (6). (chromatographyonline.com)
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. (uni-luebeck.de)

The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so determine the sequence surrounding the phosphorylation site. (biomedcentral.com)
Predikin now consists of two components: (i) PredikinDB, a database of phosphorylation sites that links substrates to kinase sequences and (ii) a Perl module, which provides methods to classify protein kinases, reliably identify substrate-determining residues, generate scoring matrices and score putative phosphorylation sites in query sequences. (biomedcentral.com)
New features in Predikin include the use of SQL queries to PredikinDB to generate predictions, scoring of predictions, more reliable identification of substrate-determining residues and putative phosphorylation sites, extended options to handle protein kinase and substrate data and an improved web interface. (biomedcentral.com)
In general, a protein kinase acts on a discrete set of substrates to ensure that signalling fidelity is maintained. (biomedcentral.com)
How a particular protein kinase recognises its substrate protein(s) is therefore a key question. (biomedcentral.com)
Two major factors determine the formation of a protein kinase-substrate complex [ 4 ]. (biomedcentral.com)
The first, termed substrate recruitment, encompasses any process that increases the effective concentration of the protein kinase substrate. (biomedcentral.com)
Perilipin 5 (PLIN5) is a lipid-droplet-associated protein that coordinates intracellular lipolysis in highly oxidative tissues and is thought to regulate lipid metabolism in response to phosphorylation by protein kinase A (PKA). (uci.edu)

3. modelling of non-enzymatic Deoxyribonucleic acid (DNA) repair via electron transfer from amino acids to the oxidised purine nucleotides that we recently found as a prototype of fast chemical repair of radiation induced damages of DNA and extending the findings to systems with increased complexity within the frame of proteomic research on peculiarities of recognition and processing of DNA substrate. (europa.eu)
The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids. (uni-luebeck.de)
In QENS experiments of protein solutions hydrogens act as reporters for the motions of methyl groups or amino acids to which they are bound. (lu.se)
H3N2 viruses continue to ding to specific amino acids of the HA protein that are drift from the vaccine strain and may remain as the domi- directly involved in the divergence of antigenically distinct nant strains during the 2005-2006 influenza season. (cdc.gov)

Alkaline Phosphatase (AP) and other nonspecific phosphatases are some of Nature's most impressive catalysts, achieving preferential transition state over ground state stabilization of more than 10²²-fold while utilizing interactions with only the five atoms attached to the transferred phosphorus. (rcsb.org)
MD has emerged as an important research methodology covering systems to the level of millions of atoms. (uiuc.edu)
mechanics (QM), in particular the Schr ¨odinger equation, allow us different proteins, e.g. alcohol dehydrogenase, blue copper proteins, to calculate any measurable property of a defined set of atoms. (lu.se)
In general, the computational load rises rapidly with the number of atoms and electrons considered and therefore, only rather small systems can be studied accurately. (lu.se)

Just like in an electrostatic interaction where a region of negative charge interacts with a positive charge, the electron-rich π system can interact with a metal (cationic or neutral), an anion, another molecule and even another π system. (wikipedia.org)
Frank, would you like to summarize the data from your lab, and from the RAS Initiative here at the FNL, that have influenced your thinking about how RAS proteins might interact? (cancer.gov)
Studies with other VACV Bcl-2 proteins, such as C6 or B14, revealed that although these proteins also interact with ubiquitin, these interactions are non-covalent. (ox.ac.uk)

The ubiquitin pathway is a highly conserved post-translational modification system best characterised for its roles in protein degradation and intracellular trafficking and is involved in a diverse spectrum of cellular processes. (ndltd.org)
We studied this interaction by replacing natural residues in the intracellular loop 3 of Ste2p and C-terminal end of Gpa1p with cysteine and then determining disulfide crosslinking between Ste2p and Gpa1p. (tennessee.edu)

PNGase F cleaves between the innermost GlcNAc and asparagine residues of high mannose, hybrid and complex oligosaccharides from N -linked glycoproteins (5), as shown in Figure 2. (neb.com)
A cooperative and competitive interaction between multiple enzymes, cell lines, and cell culture conditions causes processing of the oligosaccharide structure during which some of the already attached moieties like mannose are trimmed to yield a fiveâ residue core (Man3GlcNAc2), to which N-acetylglucosamine (GlcNAc), fucose, galactose, and N-acetylneuraminic acid (sialic acid or Neu5Ac) residues get added in a probabilistic fashion. (chromatographyonline.com)
Here we describe the 3.2 Å cryo-EM structure of human DEC-205, thereby illuminating the structure of the mannose receptor protein family. (uci.edu)

PNGase F digestion deaminates the asparagine residue to aspartic acid, leaving the oligosaccharide intact for further analysis. (neb.com)
The addition of a precursor 13-residue oligosaccharide moiety GlcNAc2Man8Gluc3 to the nascent polypeptide chain occurs in the endoplasmic reticulum, following which the assembly folds and acquires its secondary, tertiary, and quaternary structure. (chromatographyonline.com)
Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. (uni-luebeck.de)

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)

Protein profiles offer new insights into Duchenne muscular dystrophy. (asbmb.org)
Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. (uni-luebeck.de)

N-linked glycosylation occurs through the asparagine residues of the protein, while O-linked glycosylation occurs through serine or threonine. (neb.com)
We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. (biomedcentral.com)
The post-translational modification of proteins by phosphorylation of serine, threonine or tyrosine residues is a ubiquitous process in cellular regulation. (biomedcentral.com)

The consequence of these different polymerization sites is altered biological response with different polyUb linkages conferring different fates to target proteins. (ndltd.org)

The regulation of complex and dynamic signal transduction proteins contributes to the destination of targeting proteins and the signal transduction of cell growth, and exposure to parasites can also influence signaling pathways. (biomedcentral.com)
The signal transduction pathway of the receptor starts from sensing outside signal and then activates G proteins. (tennessee.edu)

These SP constitute an important ingredient of cell walls and get harvested by suitable extraction or precipitation method, followed by purification, characterization and biological studies (Fig. 2 ). (springer.com)
Characterization and interactions of nanoparticles in biological systems. (cdc.gov)

For structural analysis of asparagine-linked carbohydrates, sugars are released from the protein backbone by enzymes such as PNGase F ( NEB #P0704 ). (neb.com)
Protein kinases, the enzymes responsible for protein phosphorylation, make up almost 2% of protein-encoding genes in the human genome [ 1 ] and an estimated 30-50% of human proteins are phosphorylated [ 2 ]. (biomedcentral.com)
Predicted regulatory interaction sites for SH2- and SH3-domain proteins are in non-structured regions that could be available to cytoplasmic enzymes. (oncotarget.com)
Ubiquitylation is opposed by deubiquitylating enzymes (Dubs), and the ubiquitin specific peptidase (USP) class of Dubs remove ubiquitin from specific substrates, thereby affecting protein fate. (ndltd.org)

In this work, we present a different paradigm for predicting miRNA-regulated genes based on the encoded proteins. (frontiersin.org)

As with mammalian systems, GPCRs play a significant part in the recognition of sensory 1062368-24-4 supplier indicators, and these indicators are relayed in the cell by heterotrimeric G protein. (exposed-skin-care.net)
As opposed to mammalian chemosensory systems, the em C. elegans /em sensory neurons exhibit multiple GPCRs in each sensory neuron using many G subunits per neuron for sensory transduction, hence enabling the nematode to react particularly to different environmental cues only using several sensory neurons [2-4]. (exposed-skin-care.net)
Considering that mammalian GPCRs are a significant group of medication targets, it might be an advantage with an available em in vivo /em program to research GPCR interactions using its particular agonists and antagonists. (exposed-skin-care.net)
In particular, a number of the long range interactions between the D- and T-arms of the tRNAs appear to be missing.All 22 tRNAs that function in mammalian mitochondria are encoded in the mitochondrial DNA. (ncsu.edu)
iv) After fulfilling these three criteria, the product must be biosafe: not produce mammalian toxins that affect users and consumers, and have a host range that does not include crops and beneficial organisms, and in most cases that it will not spread from application sites or have environmental residues beyond those needed to control the target pest. (weizmann.ac.il)

Analogous Pi binding measurements with a protein tyrosine phosphatase suggest the generality of this ground state destabilization mechanism. (rcsb.org)

whereas enzymatic methods are much gentler and can provide complete sugar removal with no protein degradation. (neb.com)

The accuracy and efficiency with which tRNA decodes genomic information into proteins require posttranscriptional modifications in or adjacent to the anticodon. (ncsu.edu)
We compare genomic models and observe that our protein model outperforms, whereas a unified model improves on both. (frontiersin.org)
In the genomic pool of the Leptospira interrogans many hypothetical proteins are still uncharacterized. (bvsalud.org)

Ubiquitin (Ub) is a small, 76 amino acid, and post-translational modification (PTM) protein in eukaryotes. (ndltd.org)
Ubiquitylation is a covalent post-translational modification that regulates protein stability and is involved in many biological functions. (ox.ac.uk)

Protein kinases and their substrates regulate essentially all cellular processes through complex regulatory networks, in which phosphorylated proteins act as switches that tune the response of the cell to environmental stimuli. (biomedcentral.com)
Figure 1: PGRMC1 is phosphorylated on key regulatory amino acid residues. (oncotarget.com)
This occurs through specific modulation of regulatory proteins during the host-pathogen interaction, especially proteins with roles in pathogenesis [ 27 ]. (biomedcentral.com)

To better understand electrostatic interactions of biomolecules, characterizations of their charged moieties are essential. (utmb.edu)
All or other nearby charged groups, the pKa shift of a buried pH-dependent properties of proteins are ultimately governed residue is dominated by the large electrostatic self-energy by the electrostatic interactions of ionizable side chains. (lu.se)
2004). The effect of electrostatic interactions is usually polarization effects in the protein are subsumed in an quantified in terms of the shift, DpKa, of the pKa value of an apparent dielectric constant, eP. (lu.se)

The heptapeptide sequence from -3 to +3 that best binds to the pocket is determined by the physicochemical nature of the residues in the catalytic domain that line the pocket and contact the substrate. (biomedcentral.com)

In chemistry, π-effects or π-interactions are a type of non-covalent interaction that involves π systems. (wikipedia.org)
Our research field is biophysical chemistry of proteins, DNA, and their interactions. (utmb.edu)
JOURNAL OF BIOLOGICAL CHEMISTRY, 283(49), 34445–34456. (ncsu.edu)
I am a member of the Biological Chemistry research group . (exeter.ac.uk)

PNGase F hydrolyzes nearly all types of N-glycan chains from glycopeptides/ proteins. (neb.com)
and 31 P nuclei of phosphate anions of DNA, RNA, and phosphorylated protein side chains. (utmb.edu)
In response, our laboratory has developed a system that creates polyUb chains through bacterial expression and 'synthetic' building blocks. (ndltd.org)
Proteins may be modified with mono-ubiquitin or ubiquitin chains. (ox.ac.uk)
Now that we the receptor by itself, we have to clean up the rest of the receptor by adding any missing side chains, dealing with multiple occupancies and mutated residues, and protonating and calculating partial charges. (stonybrook.edu)
The ionizable amino acid side chains of proteins are usually located at the surface. (lu.se)
Most ionizable side chains reside at the protein surface, parent physical significance. (lu.se)

Thus, this model system will be useful in identifying pathways downstream of TDP-43 that mediate dendritic arborization, which may provide potential new avenues for therapeutic intervention in ALS/FTD. (nature.com)
Copper is required for many biological pathways, but sometimes it can harm the cell. (biorxiv.org)

The "spike" or S protein facilitates viral entry into host cells. (medicalxpress.com)
The researchers say this is of particular importance because the S protein plays a central role in viral entry into cells, making it a main target for vaccine and antiviral drug development. (medicalxpress.com)
The team recommends reading the preprint paper, "Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane," before using any of the models. (medicalxpress.com)
Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane (2020). (medicalxpress.com)

Viruses have evolved multiple mechanisms to perturb the cell ubiquitin system and manipulate it to their own benefit. (ox.ac.uk)
The interaction between N1 and ubiquitin occurs at endogenous protein levels during VACV infection and following ectopic expression of N1. (ox.ac.uk)
Taken together, we described a previously uncharacterized modification of the VACV protein N1 that provided a new layer of complexity to the biology of this virulence factor, and provided another example of the intricate interplay between poxviruses and the host ubiquitin system. (ox.ac.uk)

However, in eukaryotic most proteins are post-translationally modified. (neb.com)

A. Schematic representation of the PGRMC1 protein showing the position of secondary structural elements common to PGRMC1 and related cytochrome b 5 fold proteins [ 1 ]. (oncotarget.com)
Consequently, BQ-adducted cytochrome c fails to initiate caspase-3 activation in native lysates and also inhibits Apaf-1 oligomerization into an apoptosome complex in a purely reconstituted system. (elsevierpure.com)

Amyloid aggregates arise from either the partial or complete loss of the native protein structure or the inability of proteins to attain their native conformation. (bvsalud.org)

FLIM-FRET analysis of protein-protein interactions showed that PLIN5 S155 phosphorylation regulates PLIN5 interaction with adipose triglyceride lipase at the lipid droplet, but not with α-β hydrolase domain-containing 5. (uci.edu)

MARV assembles and buds from the host cell plasma where MARV matrix protein (mVP40) dimers associate with anionic lipids at the plasma membrane inner leaflet and undergo a dynamic and extensive self-oligomerization into the structural matrix layer. (uci.edu)

Finally, we found the residues K170, D236, R311, and R357 in GtrR that are crucial to its biological function, any single mutation leading to completely abolishing GtrR activity. (ntu.edu.sg)
More knowledge of the underlying mechanism is needed to attain a full understanding of CusB functioning, which is associated with targeting specific and crucial residues in CusB. (biorxiv.org)
The analysis also revealed that the functional domains, families and protein-protein interacting partners identified in both proteins are crucial for the survival of the bacteria. (bvsalud.org)

We are working on three areas of research: 1) Biomolecular Electrostatics , 2) Protein-DNA Dynamics , and 3) HMGB1 Biochemistry . (utmb.edu)
Developed by Wonpil Im, a professor in Lehigh's Department of Biological Sciences and Bioengineering Department, CHARMM-GUI ( graphical user interface ) is a program that simulates complex biomolecular systems simply, precisely and quickly. (medicalxpress.com)

Engineered resonance energy transfer (RET) between a mTurquoise2 fluorescent protein and FMN-bound As LOV2 increases switch sensitivity. (nature.com)
The HP model has favorable interactions between adjacent, not directly bound hydrophobic residues. (lu.se)

Despite the numerous, well-described functions and interactions of TDP-43, it is not well understood exactly which TDP-43-dependent cellular processes become defective in ALS/FTD and contribute to disease etiology. (nature.com)
Background G-protein-coupled receptors (GPCRs) play an essential role in lots of natural processes and represent a significant class of drug targets. (exposed-skin-care.net)
2. investigation of structure, i.e. surface accessibility and confinement, and dynamic processes, i.e. intermolecular electron and proton transfer, in native and ill defined partly folded and denatured states of proteins as promising new applications. (europa.eu)
The cyber twins can be used to simulate complex biological processes and deduce effects of medical treatments. (hep.com.cn)
The endocrine system-the other communication system in the body-is made up of endocrine glands that produce hormones, chemical substances released into the bloodstream to guide processes such as metabolism, growth, and sexual development. (medscape.com)

As a bacterial enhancer-binding protein (bEBP), GtrR is composed of an N-terminal receiver domain, a central ATPases associated with diverse cellular activities (AAA+) ATPase σ54 -interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. (ntu.edu.sg)
These proteins display interactions and are involved in the regulation of the cellular cytoskeleton. (biomedcentral.com)
The majority of proteins function as monodispersed ordered species dissolved in intra- or extra-cellular aqueous fluids. (frontiersin.org)
In the current research, we performed extensive in silico analysis to prioritize the potential hypothetical proteins of L. interrogans serovar Copenhageni via stepwise reducing the available hypothetical proteins (Total 3606) of the assembly to only 15, based on non-homologous to homosapien, essential, functional, virulent, cellular localization. (bvsalud.org)

Here, we combine in-vitro structural measurements, which used EPR spectroscopy and UV-Vis measurements, with cell experiments to explore the role of the various methionine residues in CusB. (biorxiv.org)
However, despite growing biological and clinical significance, little is known about the structural arrangement of this receptor or any of its family members. (uci.edu)
A general property of disordered proteins is their structural expansion that results in a high macromolecular flexibility. (lu.se)

The mitochondrial genome encodes 13 proteins necessary for energy production, two rRNAs and all of the 22 tRNAs required for the synthesis of these proteins (1Attardi G. Int. Rev. Cytol. (ncsu.edu)

A actividade realízase no marco do proxecto Iberphenol, proxecto que, explican desde a organización do congreso, naceu ao abeiro do Programa de Cooperación Transfronteiriza Interreg V-A España-Portugal (Poctep) 2014-2020 co obxectivo de pór en marcha unha rede ibérica de investigación en polifenois con aplicación na industria. (uvigo.es)

Given the strengths of the zebrafish system as a developmental tool, the zebrafish orthologue of Fam, usp9 was identified and found to be highly conserved. (ndltd.org)
Given the similarities between the mouse and zebrafish systems, a series of cross-species experiments were conducted to determine whether exogenous expression of highly conserved regions of FAM, could cause dominant-negative phenotypes in developing zebrafish embryos. (ndltd.org)

Anion-π interactions: interaction of anion with π system Cation-π interactions: interaction of a cation with a π system C-H-π interactions: interaction of C-H with π system: These interactions are well studied using experimental as well as computational techniques. (wikipedia.org)
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)

These findings suggest that parasite proteins are able to inhibit erythroid cell growth by down-regulation of ezrin phosphorylation, leading to ineffective erythropoiesis ultimately resulting in severe malarial anaemia. (biomedcentral.com)
One approach that has been recently suggested is to inhibit copper transporters in prokaryotic systems. (biorxiv.org)

Proteomics, the systematic study of proteins in biological systems, has expanded the knowledge of protein expression, modification, interaction and function. (neb.com)

Duchenne muscular dystrophy, or DMD, is characterized by progressive muscle degeneration and weakness due to the alterations of the dystrophin protein that keeps muscles intact. (asbmb.org)

Thus, biomaterials have been harnessed to generate filtration systems and other water treatment options. (ncsu.edu)

Defects in these networks result in a variety of disease states making protein kinases important targets for drug design [ 3 ]. (biomedcentral.com)
The work predicted two unique hypothetical proteins of L. interrogans as a potential druggable targets for designing of inhibitors for them.Communicated by Ramaswamy H. Sarma. (bvsalud.org)

These ions electrostatically influence thermodynamics and kinetics of macromolecular interactions. (utmb.edu)

We conclude that protein function is informative across species in predicting post-transcriptional miRNA regulation in living cells. (frontiersin.org)

Arene-perfluoroarene interaction: electron-rich benzene ring interacts with electron-poor hexafluorobenzene. (wikipedia.org)

These included proteins associated with the extracellular matrix and muscle function, many of which had not been reported in previous studies. (asbmb.org)
In structure-function research using a -panel of somatostatin-14 analogues, we recognized key residues mixed up in conversation of somatostatin-14 with Sstr2. (exposed-skin-care.net)
How biomolecules efficiently function in real biological environments with crowding and significant chemical and physical heterogeneity remains a fundamental question in biology ( Minton, 2001 ). (elifesciences.org)
We targeted two methionine residues (M227 and M241) that are essential for the proper function of CusB. (biorxiv.org)
Loss of solubility and aggregation can lead to the partial or complete abrogation of protein function. (frontiersin.org)
By contrast, in the case of TEM-1 beta-lactamase mutations, aggregation is linked to a decreased cell fitness due to inactivation of protein function. (frontiersin.org)
Any situation, such as mutations or anomalous expression, could result in disruption of these beneficial interactions with consequent aggregation and depletion of normal function. (frontiersin.org)
Protein folding, going from sequence to structure by mini- a quadratic Hamiltonian requires additional spin variables and mizing an energy function, represents a difficult optimization implementing interactions such as self-avoidance becomes problem. (lu.se)
The concept of endocrine function thus was expanded to paracrine, autocrine, juxtacrine, and intracrine functions, whereas the classic endocrine system included the traditional endocrine axes. (medscape.com)

For anticoagulation potency, the formation of the SP/protease protein complex and the associated non-specific polar interaction between the negatively and positively charged groups in the polysaccharide and protein is responsible for anticoagulant activity. (springer.com)
Understanding the interaction between the T-cell receptor on CD4 + T cells and HLA-II cancer-specific epitopes on GBM cells is vital for the development of immunotherapies. (asbmb.org)
The level of protein phosphorylation at specific sites varies from less than 1% to greater than 90%, depending on conditions [ 26 ]. (biomedcentral.com)
Except in specific cases where protein translocation or other visualised downstream phenomena are targeted, it is hard to know whether an actuator has been switched. (nature.com)
aggregation can be required in specific cases to increase the functionality of a biological system. (frontiersin.org)
Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. (uci.edu)
We present evidence for the first time of a specific, high affinity interaction between TIMP-4 and the C domain of human gelatinase A and show that TIMP-4 binds both progelatinase A and the C domain in a similar manner to that of TIMP-2. (embl.de)
The docking interactions were found within the active functional domains for both the proteins while for Hypothetical Protein 2, the same residues were involved in interactions with Cytidine-5'-triphosphate in blind and specific docking. (bvsalud.org)
The endocrine system consists of endocrine glands that produce and secrete hormones into the blood stream to reach and act on target cells of specific organs. (medscape.com)

Anatomy8

Organisms8

Diseases1

Chemicals and Drugs60

Analytical, Diagnostic and Therapeutic Techniques and Equipment50

Phenomena and Processes86

Disciplines and Occupations24

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture13

Information Science21

Health Care11

Complexes9

Molecular23

Molecules13

Peptides5

Lysine6

Conformational9

Ligands11

Glutamic acid1

Nucleic7

Escherichia1

Peptide8

Macromolecules2

Structures10

Ligand11

Distribution of proteins1

Glycans5

Kinase8

Amino acids4

Atoms4

Interact3

Intracellular2

Mannose3

Oligosaccharide3

Intrinsically disordered1

Insights2

Serine3

Target proteins1

Signal transduction2

Characterization2

Enzymes4

Genes1

Mammalian5

Tyrosine1

Enzymatic1

Genomic3

Post-translationa2

Regulatory3

Electrostatic interactions3

Substrate1

Chemistry4

Chains7

Pathways2

Viral4

Ubiquitin3

Eukaryotic1

Cytochrome2

Conformation1

Regulates1

Dimers1

Crucial3

Biomolecular2

Bound2

Processes5

Cellular4

Structural3

Encodes1

20201

Highly conserved2

Experimental2

Inhibit2

Proteomics1

Dystrophin1

Generate1

Targets2

Kinetics1

Regulation1

Interacts1

Function9

Specific9