Residues protein binding. Medical search. Frequent questions

Here we describe the first comprehensive fragment-based inhibitor exploration of an HSP70 enzyme, which yielded an amino-quinazoline fragment that was elaborated to a novel ATP binding site ligand with different physicochemical properties to known adenosine-based HSP70 inhibitors. (rcsb.org)
Crystal structures of amino-quinazoline ligands bound to the different conformational states of the HSP70 nucleotide binding domain highlighted the challenges of a fragment-based approach when applied to this particular flexible enzyme class with an ATP-binding site that changes shape and size during its catalytic cycle. (rcsb.org)
Cattle rhodopsin contains 348 amino acid residues. (wikipedia.org)
Based on the crystallographic structure an in vitro mutagenesis approach was conducted to identify amino acid residues which are relevant for FHL-1 and factor H binding by exchanging single or multiple residues in region 1 and the C-terminally located region 3. (ox.ac.uk)
and even the role of particular amino acid residues in the mechanism. (wikipedia.org)
In recent work we developed the first bioinformatic representation of protein dynamics, and are currently using this tool, in combination with earlier studies of the static physical properties of amino acid sequences, to elucidate basic mechanisms of protein folding. (rochester.edu)
Nrf2 consists of six functional Neh domains (Neh1-Neh6), from which, the amino-terminal Neh2 domain controls binding Keap1-the inhibitor protein Kelch-like ECH-associated protein 1, that is responsible for the cytosolic sequestration of Nrf2 under physiological conditions (Fig. 2 a). (springer.com)
The Nir/rdgB proteins contain a 180 amino-acids-long conserved region in the central part of the protein. (embl.de)
The three Nir proteins (Nir1, Nir2, and Nir3) bindto the amino-terminal domain of PYK2 via a conserved sequence motif located inthe carboxy terminus. (embl.de)
Now the BA.2.12.1 is a sublineage of BA.2, and it has two amino acid changes in the spike protein as compared to BA.2. (cdc.gov)
1992), A cluster of hydrophobic amino acid residues re. (xenbase.org)
A cluster of hydrophobic amino acid residues required for fast Na(+)-channel inactivation. (xenbase.org)
Amino acid residues required for fast Na(+)-channel inactivation: charge neutralizations and deletions in the III-IV linker. (xenbase.org)
Assays were performed for the quantity of isocyanate bound to protein, protein content, amino acid residues, and free amino groups. (cdc.gov)
The only significant change in amino acid residues recovered from HSA before and after reaction with HDI occurred in the lysyl residues. (cdc.gov)
Amino acid residue N100 in the fusion loop of E1 protein was identified as critical for binding. (cdc.gov)

To the best of our knowledge, there is no method that can predict the binding site of SAM in a given protein sequence. (edu.in)
Result: This manuscript describes a method SAMbinder, developed for predicting SAM interacting residue in a protein from its primary sequence. (edu.in)
All models were trained, tested, and evaluated on 145 SAM binding protein chains where no two chains have more than 40\% sequence similarity. (edu.in)
The full-length sequence of DAPK1 has 1,430 residues ( Farag and Roh, 2019 ), which consists of the catalytic domain (CD), the autoregulatory domain (ARD), eight ankyrin repeats, two P-loop motifs, the cytoskeletal binding domain, the death domain, and the serine-rich C-terminal tail. (frontiersin.org)
When enzymes bind multiple substrates, such as dihydrofolate reductase (shown right), enzyme kinetics can also show the sequence in which these substrates bind and the sequence in which products are released. (wikipedia.org)
The GYF sequence is part of a structurally unique bulge-helix-bulge motif that constitutes the major binding site for the CD2 tail. (embl-heidelberg.de)
Sequence-specific dynamic information in proteins. (rochester.edu)
Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins. (rochester.edu)
Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences. (rochester.edu)
Sequence determinants of protein architecture. (rochester.edu)
The discovery of the antioxidant response element (ARE) have led to the conclusion that the battery of genes, including glutamate-cysteine ligase (GCL), thioredoxin reductase 1 (Txnrd1), NAD(P)H-quinone oxidoreductase 1 (NQO1) and heme oxygenase-1 (HMOX1) is regulated through Nrf2 binding to this consensus binding sequence [ 3 ]. (springer.com)
Folding a protein sequence into its minimum-energy structure represents such a problem. (lu.se)
Protein folding, going from sequence to structure by mini- a quadratic Hamiltonian requires additional spin variables and mizing an energy function, represents a difficult optimization implementing interactions such as self-avoidance becomes problem. (lu.se)
SH2 domains mediate intramolecular recognition and intermolecular protein-protein association almost invariably by binding to phosphorylated tyrosine (pY) residues in specific sequence contexts. (lu.se)

In Jurkat T cells, over-expression of the isolated CD2BP2 domain binding to CD2 enhances the production of interleukin 2 on crosslinking of CD2 but not the T cell receptor. (embl-heidelberg.de)
Cellular receptor ACE2, serine protease TMPRSS2 and exopeptidase CD26 (also known as DPP4) are the three membrane bound proteins potentially implicated in SARS-CoV-2 infection. (ias.ac.in)
ESR11 studied the complex between the human adenovirus type 5 penton base capsid protein and its integrin receptor by cryo-electron microscopy, leading to a preliminary structure of the interaction of the complex, as well as a 4 Å structure of the penton base. (europa.eu)
Exocytosis of secretory or synaptic vesicles is executed by a mechanism including the SNARE (soluble N -ethylmaleimide-sensitive factor attachment protein receptor) proteins. (jneurosci.org)
The Nir/rdgB (N-terminal domain-interacting receptor/Drosophila retinal degeneration B proteins) family has been identified in a variety of eukaryotic organisms, ranging from worms to mammals. (embl.de)
Parafollicular (PF) cells secrete 5-HT in response to stimulation of a G-protein-coupled Ca 2+ receptor (CaR) by increased extracellular Ca 2+ (↑[Ca 2+ ] e ). (jneurosci.org)
The signaling complex which is composed of a transmembrane receptor, histidine protein kinase CheA and adaptor protein CheW plays an important role in chemotaxis signaling pathway. (ucsb.edu)
Chemoattractants or chemorepellents bind to the transmembrane receptor transmitted a signal to CheW and CheA. (ucsb.edu)
Here we want to investigate the interaction between the CheA and receptor protein by using mutagenesis and phosphorylation assay. (ucsb.edu)
Our results indicated that Tsr receptor mutant, I384A, interfered with the binding sites of the ternary complex. (ucsb.edu)
Residue I384 of Tsr receptor is important for binding to the proteins. (ucsb.edu)
There's a change at residue of 704, which is not within the receptor binding domain and therefore should not affect neutralization of the virus. (cdc.gov)
These toxins inhibit the release of neurotransmitters at the neuromuscular junction by cleaving soluble NSF attachment protein receptor (SNARE) complex proteins in nerve cells, which prevents the fusion of neurotransmitter containing vesicles to cell membranes 2 . (cdc.gov)

However, the trade-off with currently available matrices (GE Healthcare's excel and Roche's cOmplete) is a reduced binding capacity compared to NTA or IDA ligands. (genengnews.com)
Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. (lu.se)
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)

As both enzymes bind biphosphate substrates, each half barrel has a phosphate-binding motif, and HisF even exhibits limited HisA catalytic activity. (the-scientist.com)
One of the methods that have been proposed is a multiobjective optimization, in which protein stability and catalytic activity are simultaneously optimized [ 4 , 5 ]. (hindawi.com)
Several methods have been proposed to design novel stable proteins, such as multi-objective optimization, in which protein stability and catalytic activity are simultaneously optimized. (hindawi.com)
They usually appear in multidomain proteins, together with catalytic domains, or other protein binding modules, such as Src homology 3 (SH3), phosphotyrosine binding (PTB) or pleckstrin homology (PH) domains. (lu.se)

The heat shock protein 70s (HSP70s) are molecular chaperones implicated in many cancers and of significant interest as targets for novel cancer therapies. (rcsb.org)
Here, we performed large-scale molecular dynamics (MD) simulations of the DAPK1−CaM complex in the Ca 2+ -bound and-unbound states to reveal the importance of Ca 2+ . (frontiersin.org)
However, molecular weight is also important due to potential steric incompatibilities within protein cores. (hindawi.com)
Modelled protein-protein interaction (PPI) predicted strong molecular interaction between these two receptors and SARS-CoV-2 spike protein (S1 domain). (ias.ac.in)
Molecular interactions between ACE2-S and TMPRSS2-Sare crucial and preciously mediated by specific residues. (ias.ac.in)
The proteostasis network (PN) is an assembly of distinct dynamic molecular pathways that control the functionality of the proteome (proteome homeodynamics) during protein synthesis, folding, trafficking, and degradation. (hindawi.com)
Identification and characterization of new molecular partners for the protein arginine methyltransferase 6 (PRMT6). (embl.de)
The assembly of PRMT6 protein network allowed us to formulate functional hypotheses which led to the discovery of new molecular partners for the architectural transcription factor HMGA1a, a known substrate for PRMT6, and to provide evidences for a modulatory role of HMGA1a on the methyltransferase activity of PRMT6. (embl.de)
Here we describe the molecular cloning and characterization of a novelfamily of PYK2-binding proteins designated Nirs (PYK2 N-terminaldomain-interacting receptors). (embl.de)
We adopted a distinct approach aimed initially at interfering with protein-protein interactions of RAS, and other so-called undruggable targets like transcription factors, using molecular biology tools called intracellular antibodies that bind to target proteins inside cells. (cancer.gov)
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)
Antibody binding sites provide an adaptable surface capable of interacting with essentially any molecular target. (lu.se)
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)

Several HSP70 inhibitors have been reported, but because the majority have poor physicochemical properties and for many the exact mode of action is poorly understood, more detailed mechanistic and structural insight into ligand-binding to HSP70s is urgently needed. (rcsb.org)
Additionally, the structural data revealed a potential functional role for the ATP ribose moiety in priming the protein for the formation of the ATP-bound pre-hydrolysis complex by influencing the conformation of one of the phosphate binding loops. (rcsb.org)
Structural analysis further revealed that Ca 2+ removal caused the significant conformational changes at the DAPK1−CaM interface, especially the helices α1, α2, α4, α6, and α7 from the CaM and the basic loop and the phosphate-binding loop from the DAPK1. (frontiersin.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, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)
Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail. (nature.com)
SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
However, based on protein modeling, the best structural orthologs of Am069 are iron transport proteins from Cyanobacteria and Campylobacter jejuni. (usda.gov)
Structural stability, binding affinity and level of expression of these threeinteracting proteins are key susceptibility factors for COVID-19. (ias.ac.in)
At present it offers more information about protein-protein interaction dynamics than can be obtained with conventional structural biology techniques such as nuclear magnetic resonance (NMR) and X-ray crystallography. (the-scientist.com)
These observations demonstrate that the water relaxation dispersion in protein solutions is essentially due to a few structural water molecules buried within the protein matrix, but exchanging rapidly with the external water. (lu.se)

Modeling suggests that access to these titratable residues is blocked by a ladder of hydrophobic residues, and ATP-driven conformational changes open and close this hydrophobic seal to permit metal binding and release. (nih.gov)
The conservation of this arrangement of titratable and hydrophobic residues among ABC transporters of transition metals suggests a common mechanism. (nih.gov)
The HP model has favorable interactions between adjacent, not directly bound hydrophobic residues. (lu.se)

The Src homology 2 (SH2) domains are about 100 residues in length with an average of 28% pairwise residue identity (Pfam code PF00017). (lu.se)
Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)

We find that despite its broad metal-recognition profile, MntBC-A imports only manganese, whereas zinc can function as a high-affinity inhibitor of MntBC-A. Computational analysis shows that the transmembrane metal permeation pathway is lined with six titratable residues that can coordinate the positively charged metal, and mutagenesis studies show that they are essential for manganese transport. (nih.gov)
Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila . (nature.com)
Mutagenesis and NMR analysis demonstrated that the CD2 binding region of CD2BP2 includes a 17-aa motif (GPY[orF]xxxxM[orV]xxWxxx GYF), also found in several yeast and Caenorhabditis elegans proteins of unknown function. (embl-heidelberg.de)
Site directed mutagenesis experiments showed that reducing the positive charge of this surface-exposed region of the E protein DII correlated with improved Ae. (cdc.gov)

Deciphering protein–protein interactions. (crossref.org)
The absorbance spectrum of the chromophore depends on its interactions with the opsin protein to which it is bound, so that different retinal-opsin complexes will absorb photons of different wavelengths (i.e., different colors of light). (wikipedia.org)
Binding free energy calculations validated the decreased DAPK1−CaM interactions in the Ca 2+ -unbound state. (frontiersin.org)
Hydrophobicity was one of the most important physicochemical properties, due to the fact that it is involved in protein interactions, for example, by forming hydrophobic cores. (hindawi.com)
The eponymous FinO protein was discovered as a regulator of F plasmid conjugation nearly 50 years ago, and acts to bind a single partner sRNA called FinP to stabilize FinP and facilitate its interactions with its antisense partner, the mRNA encoding the major F plasmid transcription factor, TraJ 5 . (nature.com)
Hence, a proline-binding module distinct from SH3 and WW domains regulates protein-protein interactions. (embl-heidelberg.de)
Specific protein-protein interactions (PPI) are being identified thatexplains uniqueness of SARS-CoV-2 infection. (ias.ac.in)
Scientists at the Pacific Northwest National Laboratory in Richland, Wash., have used an established technique to observe real-time interactions between single protein molecules for the first time. (the-scientist.com)
Proposed by Peter Wolynes at the University of California, San Diego, 2 this theory states that weak interactions between relatively unstructured proteins initiate protein-protein binding. (the-scientist.com)
ESR12 studied the interactions of M-protein, the main virulence factor and adhesin of Streptococcus pyogenes. (europa.eu)
Using cutting-edge techniques, he identified novel interactions, suggesting previously unknown immune evasion strategies and that the protein interaction networks that form depend on the local microenvironment (Chowdhury et al. (europa.eu)
Viruses 14: v14040792 (2022)), and mapped 59 host protein interactions to the viral surface. (europa.eu)
The controversy would be solved if binding to closed syntaxin1 were shown to be stimulatory for vesicle fusion and/or additional essential interactions were identified between Munc18-1 and the fusion machinery. (jneurosci.org)

As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. (ucsc.edu)
Antioxidant genes such as ferritin are transcriptionally activated in oxidative stress via the antioxidant responsive element (ARE), to which nuclear factor-E2-related factor 2 (Nrf2) binds and activates transcription. (embl.de)
The multifunctional regulator nuclear factor erythroid 2-related factor (Nrf2) is considered not only as a cytoprotective factor regulating the expression of genes coding for anti-oxidant, anti-inflammatory and detoxifying proteins, but it is also a powerful modulator of species longevity. (springer.com)
The major characteristics of Nrf2 are to some extent mimicked by Nrf2-dependent genes and their proteins including heme oxygenase-1 (HO-1), which besides removing toxic heme, produces biliverdin, iron ions and carbon monoxide. (springer.com)
The genome-wide search for disease-causing variations in the SH2 domains revealed eight genes: Bruton tyrosine kinase (BTK), SH2 domain-containing protein 1A (SH2D1A), Ras GTPase activating protein (RasGAP), tyrosine protein kinase Zap-70, SHP-2, the p85α subunit of the PIP3 kinase (PI3-K), signal transducer and activator of transcription 1α/β (STAT1) and STAT5B. (lu.se)

CaM binding to the ARD triggers large conformational arrangements of DAPK1 through the disruption of the CD−ARD association, generating a constitutively active kinase. (frontiersin.org)
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)
Dynamic and conformational switching in proteins. (rochester.edu)

Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (hindawi.com)
Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (hindawi.com)
We have extended our studies to encompass intrinsically disordered proteins, and are using the sequences of those proteins as an added resource in the study of folding and stability in proteins. (rochester.edu)
In earlier work, we have applied novel bioinformatic methods to the comparison of protein sequences and protein structures, and used the resulting data to address problems at the foundations of bioinformatics. (rochester.edu)
Global informatics and physical property selection in protein sequences. (rochester.edu)
Beyond supersecondary structure: the global properties of protein sequences. (rochester.edu)
NTA and IDA fix transition metal ions to the matrix, where they complex polyhistidine sequences on proteins of interest. (genengnews.com)

Ca 2+ /CaM binds to the death-associated protein kinase 1 (DAPK1) to regulate intracellular signaling pathways. (frontiersin.org)
It has been shown that this domain is found in a longer C terminal region that binds to PYK2 tyrosine kinase. (embl.de)
The protein tyrosine kinase PYK2 has been implicated in signaling pathwaysactivated by G-protein-coupled receptors, intracellular calcium, and stresssignals. (embl.de)
We tested the hypothesis that protein kinase C (PKC) participates in stimulus-secretion coupling. (jneurosci.org)
The ↑[Ca 2+ ] i activates a signaling cascade that involves, sequentially, calcium-calmodulin, nitric oxide synthase, guanylyl cyclase, and protein kinase G. This signal transduction pathway enables Cl − to pass through vesicular channels and act as a counterion for the transport of H + , so that the vesicles of secretogogue-stimulated cells become acidic. (jneurosci.org)
Functional modulation of brain sodium channels by protein kinase C phosphorylation. (xenbase.org)
We also ran QM/MM simulations on casein-kinase 2 (CK2), where the ligand and a few surrounding residues were treated at the QM level, and the rest of the system at the MM level. (lu.se)

Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. (ucsc.edu)
We believe that the present results resolve the long-standing controversy regarding the mechanism behind the spin relaxation dispersion of water nuclei in protein solutions, thus establishing oxygen-17 relaxation as a powerful tool for studies of structurally and functionally important water molecules in proteins and other biomolecules. (lu.se)

eLife, 2016) implied that the N-terminus of the magnesium transporter A (MgtA) protein (from hereon called Keif) is intrinsically disordered, but the advantage of this disordered feature to the function of the protein is still unknown. (lu.se)

Retinal is bound to opsins, which are G protein-coupled receptors (GPCRs). (wikipedia.org)
Opsins are prototypical G protein-coupled receptors (GPCRs). (wikipedia.org)
Most toxins bind to specific target cell receptors. (msdmanuals.com)

The BbCRASP-1 protein is the first bacterial factor H/FHL-1-binding protein for which the atomic structure has been solved. (ox.ac.uk)
This makes them suitable for the purification of proteins from eukaryotic samples, thereby extending the use of polyhistidine proteins from bacterial to more complex expression systems. (genengnews.com)
Botulinum neurotoxins (BoNTs) are bacterial proteins that cause the life-threatening disease botulism 1 . (cdc.gov)
However, capsule-specific opsonic antibodies can bind to the bacterial capsule and facilitate phagocytosis. (msdmanuals.com)

We targeted two methionine residues (M227 and M241) that are essential for the proper function of CusB. (biorxiv.org)
Its initiating methionine residue is post-translationally removed. (ucsc.edu)

In opsins, retinal binds covalently to a lysine in the seventh transmembrane helix through a Schiff base. (wikipedia.org)

Upon Ca 2+ binding, CaM is capable of interacting with hundreds of protein targets to regulate the wealth of intracellular signaling pathways. (frontiersin.org)
It was identified in the human intracellular protein termed CD2 binding protein 2 (CD2BP2), which binds to a site containing two tandem PPPGHR segments within the cytoplasmic region of CD2. (embl-heidelberg.de)
A membrane-proximal proline-rich tandem repeat, involved in cytokine production, is recognized by the intracellular CD2 binding protein CD2BP2. (embl-heidelberg.de)
Our work on intracellular antibody fragments as tools for analysis of protein complexes argued that these macromolecules could also be employed for target validation in diseases and then as guides for target-specific surrogate compounds as inhibitors. (cancer.gov)

This gene encodes a nuclear polyglutamine-binding protein that is involved with transcription activation. (nih.gov)
This gene encodes a cytoplasmic ribosomal protein that is a component of the 60S subunit. (ucsc.edu)
KJ892031 - Synthetic construct Homo sapiens clone ccsbBroadEn_01425 RPL22 gene, encodes complete protein. (ucsc.edu)
This phenotype co-segregates with either of two frameshift mutations, 1988delAGAG and 2469delGTCA, in ESPN , which encodes a calcium-insensitive actin-bundling protein called espin. (bmj.com)
The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)

The first EGF-like module of human coagulation factor IX contains a single functionally important calcium ion binding site. (lu.se)

Keap1 is a cysteine-rich protein, known to be anchored to actin cytoskeleton [ 5 ], serving as an adaptor protein for the Cul3-dependent E3 ubiquitin ligase complex. (springer.com)
They are classified based on the positions of key cysteine residues. (fishersci.com)
this response is mediated by oxidation of the cysteine residue on its DNA binding domain, which enhances DNA binding. (lu.se)

CX3CL1 is a CX3C chemokine known to induce adhesion and migration of leukocytes mediated by a membrane-bound and soluble form respectively. (fishersci.com)

We have now shown the dissociation constant for this site to be approximately 160 microM in a recombinant protein fragment consisting of residues 1-85 in human fIX. (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)

Dihydrofolate reductase from E. coli with its two substrates dihydrofolate (right) and NADPH (left), bound in the active site. (wikipedia.org)
Each serotype of BoNT hydrolyzes their protein substrates at different peptide bonds. (cdc.gov)

Whereas most fluorescent labels require genetic modification of target proteins, I-SO attaches covalently to the protein of interest and changes its fluorescence during a binding event. (the-scientist.com)

Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. (nih.gov)
The chemical compound series that was developed in this work is a pan-RAS series binding to all the RAS isoforms [12] because the binding pocket is found in KRAS, HRAS and NRAS. (cancer.gov)

Other choices include calmodulin-binding peptide, Strep-tag (oxtapeptide binding to streptavidini), chitin-binding domain, and FLAG-tag (another octapeptide that binds to anti-FLAG mAbs). (genengnews.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)

This type of information can be loosely divided into two families: (i) the available three-dimensional structures of macromolecules deposited within the Protein Data Bank and (ii) the relative invariance of elementary chemical properties such as bond lengths, bond angles, chiral volumes and planes. (iucr.org)

propose that an ancestral protein motif was duplicated and fused to produce the HisA isomerase enzyme, before a second duplication and further evolution yielded the more complex HisF synthase activity. (the-scientist.com)
A hydrophobic surface patch is created by motif residues that are highly conserved among a variety of proteins from diverse eukaryotic species. (embl-heidelberg.de)
Identification of a proline-binding motif regulating CD2-triggered T lymphocyte activation. (embl-heidelberg.de)

Mapping the mutations onto the atomic structure of BbCRASP-1 reveals that, in contrast to earlier assumption, the C-terminal mutations act indirectly on FHL-1 and factor H binding, whilst the region 1 mutations map the site of direct complement regulator interaction. (ox.ac.uk)
Ponatinib binds the BRAF dimer and stabilizes a distinct αC-helix conformation through interaction with a previously unrevealed allosteric site. (nature.com)
Proteolytic cleavage of viral spike (S)-protein and ACE2 byTMPRSS2 began the entire host-pathogen interaction initiated with the physical binding of ACE2 to S-protein. (ias.ac.in)
The researchers found that the two proteins fluctuated between bound and loosely associated states, in support of the so-called fly-casting mechanism of protein-protein interaction. (the-scientist.com)
In conclusion, binding of Munc18-1 to closed syntaxin1 stimulates vesicle docking and a distinct interaction mode regulates the consecutive priming step. (jneurosci.org)
We wondered if these difficulties could be overcome by focussing on the antibody combining site (i.e. the part of antibody interacting with antigen) to guide the derivation of chemical compounds that would be surrogates of the antibody, because the combining site is the part relevant to the protein-protein interaction between antibody and antigen. (cancer.gov)
The corollary is that the specific interaction interface between the antibody fragment with target protein would be mimicked by the chemical compound surrogates. (cancer.gov)
In the first Abd technology application, we used a competitive surface plasmon resonance (cSPR) method [9] that depends on high affinity interaction of the antibody fragment with GTP-bound RAS. (cancer.gov)
protein interaction has still not emerged. (lu.se)

The encoded protein contains a WW domain. (nih.gov)
VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
Likewise, the ProQ/FinO domain-containing protein RocC of Legionella pneumophila interacts with only one trans -acting sRNA (RocR) to repress post-transcriptionally multiple mRNA targets 6 . (nature.com)
Similarly, a minimal ProQ/FinO domain protein, NMB1681, has been shown to bind a range of structured RNAs in Neisseria meningitidis 15 . (nature.com)
Proline-binding domain in CD2-binding protein. (embl-heidelberg.de)
Taxonomic distribution of proteins containing GYF domain. (embl-heidelberg.de)
The complete taxonomic breakdown of all proteins with GYF domain is also avaliable . (embl-heidelberg.de)
Click on the protein counts, or double click on taxonomic names to display all proteins containing GYF domain in the selected taxonomic class. (embl-heidelberg.de)
We solved the solution structure of the CD2 binding domain of CD2BP2, which we name the glycine-tyrosine-phenylalanine (GYF) domain. (embl-heidelberg.de)
Thus, the architecture of the GYF domain may be widely used in protein-protein associations. (embl-heidelberg.de)
Am069, the A. marginale ortholog of FbpA lacks predicted iron binding residues based on the NCBI conserved domain database. (usda.gov)
includes residues 201 to 321 of WASP, which contains the CRIB domain essential for Cdc42 binding. (the-scientist.com)
You put [a] domain with the dye hanging on it into a live cell, and it will respond to the endogenous protein, so you don't have to overexpress endogenous material, [or] modify the endogenous material to see what's going on," Hahn explains. (the-scientist.com)
The Tudor domain protein p100-TSN reads the symmetric methylation mark, and binding of p100-TSN downregulates E2F-1 apoptotic activity. (embl.de)
The DDHD domain is 180 residues long and contains four conserved residues that may form a metal binding site. (embl.de)
The domain is named after these four residues. (embl.de)
This domain is found in retinal degeneration B proteins, as well as a family of probable phospholipases. (embl.de)
This domain contains four conserved residues, DDHD, which may form a metal-binding site. (embl.de)
The DDHD domain is found in the central part of Nir/rdgB proteins, as well as the C-terminal part of the phosphatidic acid-preferring phospholipase A1. (embl.de)
The primary structures of Nirs reveal six putativetransmembrane domains, a region homologous to phosphatidylinositol (PI) transfer protein, and an acidic domain. (embl.de)
The E1 domain contains a growth factor-like or heparin-binding (residues 28-123) and Cu-binding (residues 124-189) subdomains. (proteopedia.org)
The Z-binding domain is involved in the oligomerizatin of APP. (proteopedia.org)
The domain organization of the analysed proteins. (lu.se)
Although SH2 domain containing proteins have been shown to have redundant functions in the cellular signaling networks, proteins with defective SH2 domains either have a crucial role during cell development process or they regulate multiple signaling cascades. (lu.se)

It is a critical component of eukaryotic and prokaryotic cellular functions and is indispensable for nucleic acid synthesis, protein production, and energy generation. (usda.gov)

A mutation that diminished Munc18 binding to syntaxin1 in vitro attenuated the vesicle-docking step but rescued vesicle priming in excess of docking. (jneurosci.org)
In conclusion, critical residues important for maintaining a human antigen-specific binding site during the process of in vitro antibody evolution were defined. (lu.se)

The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
however, these fusions actually involve a ribosomal protein L22 pseudogene located at 3q26, and this gene actually maps to 1p36.3-p36.2. (ucsc.edu)
Transcriptional regulation of the human ferritin gene by coordinated regulation of Nrf2 and protein arginine methyltransferases PRMT1 and PRMT4. (embl.de)
Furthermore, an explanation for the observed restricted germline gene usage in certain antibody responses against protein epitopes is provided. (lu.se)

Several of these corresponding residues in the mouse monoclonal antibody are known to interact with the antigen. (lu.se)

Cells express a pool of thousands of different proteins that need to be tightly controlled for proper cellular structure, organization, and function. (hindawi.com)
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)

Additional domains are: Kunitz-type protease inhibitor (residues 287-344) and Zn-binding (residues 672-687). (proteopedia.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)

Protein phosphorylation is the most common post-translation modification of proteins and regulates many biological processes. (lu.se)

Copper shows low specificity and high yield, whereas cobalt is on the other end of the spectrum, generating extremely pure proteins but lower yield. (genengnews.com)
Six to eight histidines are typically used to increase specificity over intrinsic histidine in contaminating proteins. (genengnews.com)
NTA is a tetravalent ligand providing greater specificity but lower yield, while IDA is trivalent-less selective but generally providing more protein. (genengnews.com)
The importance of several of these conserved residues was supported by their presence in a mouse monoclonal antibody with a known structure and the same epitope specificity. (lu.se)
Protein drugs are increasingly important in drug development worldwide due their high specificity, potency, and low toxicity. (lu.se)

This represents a approximately 10-fold increase in affinity as compared with the isolated EGF module (residues 46-85). (lu.se)
The Gla module (here with Glu instead of Gla) thus increases the affinity of the EGF module calcium ion binding site. (lu.se)
Each of two mutations, V46E and Q50E, made to investigate whether the extra negative charge would increase the affinity of the calcium binding site manifested a negligible increase in affinity. (lu.se)
Affinity tagging, a popular method for capturing or immobilizing proteins, has several incarnations, none more popular than polyhistidine tagging. (genengnews.com)
After expression, the protein is captured by means of immobilized metal affinity chromatography (IMAC). (genengnews.com)

Oxidative stress generated during such stressful conditions may damage DNA and proteins, and as a consequence the cellular processes are disturbed. (springer.com)

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)

We are interested in computational studies of protein folding and dynamics, and particularly in the information about protein physics which is available through bioinformatic studies. (rochester.edu)
Protein conformation fluctuation dynamics is a stochastic process," says lead investigator H. Peter Lu, a staff scientist at PNNL. (the-scientist.com)
For both proteins, the oxygen-17 relaxation depended only very weakly on pD, showing that ionic residues do not perturb hydration water dynamics more than other surface residues. (lu.se)
For metal- powerful methods to obtain and compare reaction and activation loproteins, a third method to obtain local information about the energies for suggested enzyme mechanisms and they can also provide atomic details about the protein dynamics. (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)

Binding experiments and mutational analyses have demonstrated the critical importance of the GYF tripeptide in ligand binding. (embl-heidelberg.de)

In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
More recently, the application of RNA-seq technologies has enabled the elucidation of the biological partners and targets of several ProQ/FinO family proteins. (nature.com)
While these studies have built the case that certain ProQ/FinO family members bind to only a very limited number of partners in a highly specific manner, other family members appear to have multiple biological sRNA targets. (nature.com)
Lectins are unique proteins of varying biological importance. (nih.gov)

Calcium binding to the first EGF-like module of human factor IX in a recombinant fragment containing residues 1-85. (lu.se)
EGF-like module}}, language = {{eng}}, number = {{2}}, pages = {{100--104}}, publisher = {{Wiley-Blackwell}}, series = {{FEBS Letters}}, title = {{Calcium binding to the first EGF-like module of human factor IX in a recombinant fragment containing residues 1-85. (lu.se)
We exploited the specific binding of the antibody fragment and were able to identify RAS-binding compounds in antibody-competition assays (illustrated in Fig.1). (cancer.gov)
When the antibody fragment is bound to RAS, it serves as a competitor of compounds binding to the same region. (cancer.gov)
Using CDR shuffling, residues important for the assembly of mucin-1 specific paratopes were defined by random recombination of the complementarity determining regions derived from a set of mucin-1 specific clones, previously selected from an antibody fragment library. (lu.se)

Opsins without the retinal binding lysine are not light sensitive. (wikipedia.org)
The number of recovered lysine residues was the same in unconjugated HSA as in TDI HSA conjugates. (cdc.gov)

Zinc-binding proteins such as zinc finger proteins can be captured by zinc-bound resins. (genengnews.com)
The light chain is a zinc-metalloprotease which is responsible for the cleavage of three SNARE complex proteins including SNAP-25 (Synaptosome-associated protein of 25 kDa), synaptobrevin-2 (also termed VAMP-2) and syntaxin. (cdc.gov)

Pathogens use adhesins to colonize tissues and cause infections, to bind host molecules for immune evasion and, for bacteria, to create antibiotic-resistant biofilms on implanted devices. (europa.eu)
This difference was ascribed to the abscence, in ubiquitin, of highly ordered internal water molecules, which are known to be present in BPTI and in most other globular proteins. (lu.se)
The relaxation data indicate that the internal water molecules of BPTI exchange with bulk water on the time-scale 10-8 to 10-6 second thus lowering the recently reported upper bound on the residence time of these internal water molecules by four orders of magnitude, and implying that local unfolding occurs on the submicrosecond time-scale. (lu.se)
The water molecules residing at the surface of the two proteins were found to be highly mobile, with an average rotational correlation time of approximately 20 picoseconds. (lu.se)

To test our hypothesis that histone H4R3 and H3R17 methylation regulates ferritin transcription, H4R3 and H3R17 protein arginine (R) methyltransferases 1 and 4 (PRMT1 and PRMT4) were investigated. (embl.de)

However, the use of mutant expression in the presence of endogenous protein left it unclear how the observed effects were related to the defect of vesicle docking in (M)unc18-1 knock-outs. (jneurosci.org)

Furthermore, it is important and challenging to accurately model the large entropic contribution to ligand-binding free energies. (lu.se)
This entropy largely stems from the fluctuation of the protein and ligand. (lu.se)

This inhibition reflects the binding of Munc18-1 to a closed conformation of the target-SNARE syntaxin1. (jneurosci.org)

Both of these tags improve fusion protein solubility and expression levels but exhibit immunogenicity for purposes of raising antiprotein antibodies. (genengnews.com)
First that RAS is indeed druggable (as many labs have now shown, in particular KRASG12C binding compounds [13-15]) and that antibodies could indeed be used to guide the isolation of chemical matter with our Abd technology. (cancer.gov)

AK097075 - Homo sapiens cDNA FLJ39756 fis, clone SMINT2018681, moderately similar to 60S RIBOSOMAL PROTEIN L22. (ucsc.edu)
BC058887 - Homo sapiens ribosomal protein L22, mRNA (cDNA clone MGC:64893 IMAGE:6141451), complete cds. (ucsc.edu)

Resonance Group, Chemical of the globular proteins bovine pancreatic trypsin inhibitor (BPTI) and Center, Lund University ubiquitin in aqueous solution. (lu.se)

Alternative approach to protein structure prediction based on sequential similarity of physical properties. (rochester.edu)

In polyhistidine tagging, 6 to 10 histidine residues are added recombinantly to either the protein's C- or N-terminus. (genengnews.com)

Vitamin K is an essential, lipid-soluble vitamin that plays a vital role in the production of coagulation proteins. (medscape.com)

Conversely, expressing the Munc18-2 isoform, which also displays binding to closed syntaxin1, rescued vesicle docking identical with Munc18-1 but impaired more downstream vesicle priming steps. (jneurosci.org)

Insight into how these proteins recognize their cognate RNAs initiated with FinO. (nature.com)

Anatomy12

Organisms11

Chemicals and Drugs92

Analytical, Diagnostic and Therapeutic Techniques and Equipment48

Phenomena and Processes90

Disciplines and Occupations2

Technology, Industry, Agriculture1

Information Science10

Health Care5

Amino16

Sequence14

Receptor13

Ligands3

Catalytic4

Molecular15

Structural12

Hydrophobic residues3

Homology2

Mutagenesis4

Interactions13

Genes5

Conformational3

Sequences7

Kinase7

Structurally2

Intrinsically disordered1

Receptors3

Bacterial4

Methionine2

Transmembrane1

Intracellular4

Encodes5

Functionally important1

Cysteine3

Membrane bound1

Recombinant protein1

Complexes1

Substrates2

Target proteins1

Isoforms2

Peptide2

Macromolecules1

Motif3

Interaction9

Domain24

Nucleic1

Vitro2

Gene4

Antigen1

Different proteins2

Protease1

Crystallography1

Phosphorylation1

Specificity5

Affinity5

Cellular1

Crucial1

Dynamics5

Experiments1

Biological4

Fragment5

Lysine2

Zinc2

Molecules4

Regulates1

Endogenous protein1

Ligand2

Conformation1

Antibodies2

Homo2

Lund University1

Prediction1

Histidine1

Soluble1

Conversely1

Cognate1