Identification interactions protein residues. Medical search. Frequent questions

Mutation of these residues lead to an ablation of Claudin1 association and a reduction in on HCV entry, further indicating the requirement of the Claudin1-CD81 complex in the entry process. (bham.ac.uk)
Although mutation of six conserved residues activated phenol hydroxylase in steady-state assays, the double mutant M37T/V77A, resulting from random mutagenesis, did not activate phenol hydroxylase. (concordia.ca)
Mutation on these residues can lead to new strains of coronavirus with different degrees of infectivity and virulence. (biorxiv.org)
Structurally, this mutation most likely impairs PROM1 protein stability, flexibility, and amino acid interaction network after changing the amino acid residue Leucine into Proline in the basic helix-loop-helix leucine zipper domain. (oncotarget.com)
Mutation of C273 or C288 in linker region resulted in higher level expression of Nrf2 protein in the absence of inducers. (cdc.gov)
At neutral pH, where these residues are uncharged, we find no evidence of buried water molecules near the mutation site. (lu.se)

Ectopic up-regulation of PTPRD in neuroblastoma dephosphorylates tyrosine residues in AURKA resulting in a destabilization of this protein culminating in interfering with one of AURKA's primary functions in neuroblastoma, the stabilization of MYCN protein, the gene of which is amplified in approximately 25 to 30% of high risk neuroblastoma. (biomedcentral.com)
Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180° rotations, or flips, which are mediated by transient and large-scale "breathing" motions that generate sufficient void volume around the aromatic ring. (lu.se)

We have also made available our software through different web servers, such as pyDockWeb for protein-protein docking, pyDockSAXS for the structural prediction of protein complexes using Small-Angle X-ray Scattering (SAXS) data in collaboration with Pau Bernadó (CBS, Montpellier), or OPRA for the identification of RNA-binding residues in proteins. (bsc.es)
More efficient identification of correct docking poses, especially in difficult cases such as weak interactions, multi-protein complexes or membrane proteins. (bsc.es)
The results indicate that the selected complexes remain highly stable throughout the 100-ns molecular dynamics simulation runs, displaying strong correlations with the binding of targeted ligands within the active site of the selected protein. (bvsalud.org)
Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. (leibniz-fli.de)
They either apply docking to estimate the structural and chemical fitness of the query compound to the target or extract a set of pharmacophores from protein-ligand complexes and check whether the query compound matches well with the pharmacophores. (biomedcentral.com)

Our method considers a variety of features including protein sequences, gene co-expression, functional association, and phylogenetic profiles. (nature.com)
To further aid covalent drug design, we extended a functional group mapping approach based on explicit solvent all-atom molecular simulations (SILCS: site identification by ligand competitive saturation) that intrinsically considers protein flexibility, functional group, and protein desolvation along with functional group-protein interactions. (nih.gov)
The phenotype of Bard1 null mice was found to be remarkably similar to that of Brca1 nulls, further emphasising the functional relationship between these two proteins. (bmj.com)
The research concentrates on understanding the structural and functional features of biologically relevant molecules and their interactions employing the tools of Structural Bioinformatics and Molecular Modeling. (biocev.eu)
The structure of an SfbI-5 peptide in complex with the second and third F1 modules from Fn confirms that the conserved FnBR residues play equivalent functional roles across bacterial species. (hud.ac.uk)
Scholars@Duke publication: Functional analysis of the simian immunodeficiency virus Vpx protein: identification of packaging determinants and a novel nuclear targeting domain. (duke.edu)
These approaches promise to enable researchers to assess, on a large scale, both expression level and functional state of the proteins that carry out most functions in a cell. (lu.se)
In our present view, these areas are found for systems where several types of macromolecules (proteins, polysaccharides or polyelectrolytes) and/or amphiphiles interact to form a functional or destructive unit. (lu.se)

To facilitate the design of this class of ligands, computational methods can be used to help identify reactive nucleophilic residues, frequently cysteines, on a target protein for covalent binding, to test various warhead groups for their potential reactivities, and to predict noncovalent contributions to binding that can facilitate drug-target interactions that are important for binding specificity. (nih.gov)
We closely collaborate with researchers within BIOCEV as well as with external groups on analysis of structural data, rational design of protein mutations, and design of ligands and inhibitors of studied proteins. (biocev.eu)
Development of novel computational methods and parameter optimization for description of designed ligands and inhibitors and their interactions. (biocev.eu)
The screens were conducted to discover new ligands of the proteins. (dundee.ac.uk)
Investigation of these ligands could further understanding of protein-ligand interactions with GBP and AcAChBP, as well as the physiological receptors GlyR and nAChR. (dundee.ac.uk)

The major subunits of the TOC complex (Toc75, Toc90 and Toc34) and TIC complex (Tic214, Tic20, Tic100 and Tic56), three chloroplast translocon-associated proteins (Ctap3, Ctap4 and Ctap5) and three newly identified small inner-membrane proteins (Simp1-3) have been located in the supercomplex. (nature.com)
The study of MscL, a highly convenient model system, will give us basic understanding and the first example of what type of intramolecular interactions, sequence motifs, and conformations make membrane proteins sensitive to a physiologically relevant mechanical stimulation. (usda.gov)
Mechanosensitive membrane proteins: Usual and unusual suspects in mediating mechanotransduction. (stanford.edu)
This Viewpoint, which accompanies a Special Issue focusing on membrane mechanosensors, discusses unifying and unique features of both established and emerging mechanosensitive (MS) membrane proteins, their distribution across protein families and phyla, and current and future challenges in the study of these important proteins and their partners. (stanford.edu)
MS membrane proteins are essential for tissue development, cellular motion, osmotic homeostasis, and sensing external and self-generated mechanical cues like those responsible for touch and proprioception. (stanford.edu)
As the field continues to grow, so too will the list of proteins suspected to function as mechanosensors and the diversity of known MS membrane proteins. (stanford.edu)

Several FnBR residues are highly conserved across bacterial species, and here we investigate their contribution to the interaction. (hud.ac.uk)

Viruses 14: v14040792 (2022)), and mapped 59 host protein interactions to the viral surface. (europa.eu)
1 , 2 Largely expressed on the surface of SARS-CoV-2, the spike (S) protein plays a crucial role in binding to the host angiotensin-converting enzyme 2 (ACE2) through the receptor-binding domain (RBD) and facilitating viral entry, 3 , 4 which is therefore considered as one of the most preferred targets against SARS-CoV-2. (biorxiv.org)
The different interactions between viral proteins and cellular host proteins are required for efficient replication of HIV-1. (biomedcentral.com)
In an attempt to study the host interacting protein of IN, we have identified a new interacting host protein PSF which is a splicing factor and elucidated its role in integration and viral replication. (biomedcentral.com)
Experimental as well as in silico analysis inferred that the host protein causes not only change in the integration events but also targets the incoming viral DNA or the integrase-viral DNA complex. (biomedcentral.com)
MD trajectory analyses provided a strong clue of destabilization of Integrase-viral DNA complex occurred due to PSF interaction with the conserved bases of viral DNA ends that are extremely crucial contact points with integrase and indispensable for integration. (biomedcentral.com)
The integration process is catalyzed by viral protein integrase which utilizes different host proteins for integration of viral DNA [ 1 ]. (biomedcentral.com)
Identification of these interacting host cellular protein provide better understanding of mechanism of viral replication and subsequently development of new therapeutic approaches. (biomedcentral.com)
The viral particle is composed of a protein capsid that contains a positive-sense RNA molecule of about 8,500 nucleotides that is infectious and encodes a single polyprotein, which is processed in infected cells by cis - and trans -acting viral proteases ( 55 ) to yield different polypeptide precursors and the mature viral proteins ( 9 , 62 ). (asm.org)
The viral genome encodes four structural capsid proteins (VP1 to VP4) and seven nonstructural (NS) proteins, the leader Lb/ab protease, and proteins encoded in the P2 (2B and 2C) and P3 (3A, 3B, 3C, and 3D) regions ( 9 ). (asm.org)
NS proteins are involved in crucial aspects of the viral cycle and pathogenesis, such as rearrangements of intracellular membranes required for endomembrane recruitment and the lysis of host cells ( 1 , 12 , 14 , 18 , 73 ). (asm.org)

Polypyrimidine tract binding protein and associated splicing factor (PSF) has diverse functions inside the cell such as transcriptional regulation, DNA repair, acts as nucleic acids binding protein and regulate replication and infectivity of different viruses. (biomedcentral.com)

The main focus of our research is the development and optimization for High-Performing-Computing (HPC) of computational methodology for the structural and energetic characterization of protein interactions at molecular level. (bsc.es)
MS-based experiments have often represented to be invaluable tools for the assessment of the cleavage sites, but the reported MS-spectra always show a partial coverage of all the peptide fragments generated by the enzyme interaction, lacking a complete characterization. (cnr.it)

The salient features of Hombres are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission. (wikipedia.org)
The matching is com- plicated by the fact that there are protein modifications and the sequence databases store the unmodified sequences. (lu.se)

The ability to rank covalent molecular binders with similar warheads using SILCS ligand grid free energy (LGFE) ranking was also tested for several proteins. (nih.gov)
Recombinant human Midkine is a 13.4 kDa protein containing 123 amino acid residues including five intra-molecular disulfide bonds. (reliatech.de)
It has been hypothesized that conserved histidines in the class II fusion protein E of these viruses function as molecular switches and, by their protonation, control the fusion process. (rupress.org)
This review emphasizes the molecular mechanism of phytochemicals on PCa cells, the synergistic effects of compound-drug interactions, and stem cell targeting for PCa treatment. (bvsalud.org)
The methodology will include site-directed mutagenesis, covalent protein modifications, patch- clamp measurements, thermodynamic and kinetic analysis of dose-response curves and rates of transitions, videomicroscopy, and molecular modeling. (usda.gov)
Here, using atomistic molecular dynamics simulation, we study the correlations between the RBD dynamics with physically distant residues in the spike protein, and provide a deeper understanding of their role in the infection, including the prediction of important mutations and of distant allosteric binding sites for therapeutics. (biorxiv.org)
We applied time-independent component analysis (tICA) and protein connectivity network model, on all-atom molecular dynamics trajectories, to identify key non-RBD residues, playing crucial role in the conformational transition facilitating spike-receptor binding and infection of human cell. (biorxiv.org)
As a molecular mechanism, we demonstrate that PTPRD interacts with aurora kinase A (AURKA), an oncogenic protein that is over-expressed in multiple forms of cancer, including neuroblastoma. (biomedcentral.com)
In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. (lu.se)
A molecular model of the FMDV 3A protein, derived from the nuclear magnetic resonance (NMR) structure of the poliovirus 3A protein, predicted a hydrophobic interface spanning residues 25 to 44 as the main determinant for 3A dimerization. (asm.org)

The X-ray structure was remarkable it showed that the core of the protein is extremely negatively-charged and hydrophilic, not hydrophobic. (europa.eu)
The surface of the GABP alpha OST domain contains two predominant clusters of negatively-charged residues suggestive of electrostatically driven interactions with positively-charged partner proteins. (ubc.ca)

Forty years after the seminal work by Wagner and Wüthrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. (lu.se)
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)

Using the mutational analysis of recombinant subviral particles of tick-borne encephalitis virus, we provide direct experimental evidence that the initiation of fusion is crucially dependent on the protonation of one of the conserved histidines (His323) at the interface between domains I and III of E, leading to the dissolution of domain interactions and to the exposure of the fusion peptide. (rupress.org)
In this scenario, although the cleavage sites involved in the interaction of insulin with IDE are known, a convenient experimental method that is able to identify in a complete and unambiguous way, all the peptide fragments generated by such interaction has yet to be found. (cnr.it)
In this work, we report a new experimental procedure by which an unambiguous as well as complete assignment of all the peptide fragments generated by the interaction of insulin with IDE is described. (cnr.it)
Constructing glucagon like peptide-1 receptor fused with derivatives of GFP for visualizing protein-protein interaction in living cells. (leibniz-fli.de)
We describe a statistical measure, Mass Distance Fingerprint, for automatic de novo detection of predominant peptide mass distances, i.e., putative protein mod- ifications. (lu.se)
The need to keep track of protein modifications is readily recognized by the proteomics community, and few repositories of known peptide modifications have been created. (lu.se)
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)

BARD1, unlike BRCA1, also contains a centrally located sequence of three ankyrin repeats 11 that are found in many proteins involved in transcriptional regulation. (bmj.com)

Furthermore, a machine learning model was trained to quantify the effectiveness of various warhead groups for proteins using metrics from SILCS-MC as well as experimental model compound warhead reactivity data. (nih.gov)

The immune response relies on the interaction between the Fc (fragment crystallisable) region of the antibody and receptors on the immune cell surface. (genengnews.com)
Though researchers' attention and this Viewpoint focus on a few famous ion channels that are considered the usual suspects as MS mechanosensors, we also discuss some of the more unusual suspects, such as G-protein coupled receptors. (stanford.edu)
Infection of human cells by the novel coronavirus (SARS-Cov-2) involves the attachment of the receptor binding domain (RBD) of the spike protein to the peripheral membrane ACE2 receptors. (biorxiv.org)

Acetylases are now known to modify a variety of proteins, including transcription factors, nuclear import factors and alpha-tubulin. (embl-heidelberg.de)
6, 7 BRCA1 interacts with a variety of proteins and is involved in multiple cellular processes including DNA repair, transcription, and checkpoint control. (bmj.com)

A mutant form of the ribosomal protein L1 reveals conformational flexibility. (expasy.org)

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. (embl.de)
We propose that this might be a common feature of the interactions of IDRs, and is likely to pose a challenge for the development of small molecule inhibitors of FnBP-mediated adhesion to and invasion of host cells. (hud.ac.uk)
Data showed good corroboration between the techniques and highlighted some limitations when considering small molecule interactions. (dundee.ac.uk)
Exploiting published structures, the possibility to extend the small molecule scaffolds into empty pockets of the two proteins was examined. (dundee.ac.uk)
Protein tyrosine phosphatase receptor delta ( PTPRD ) is an important regulator of axon growth and guidance and is highly expressed in the central nervous system where it functions as a transmembrane homophilic neuronal cell adhesion molecule [ 1 ]. (biomedcentral.com)
Small molecule protein-protein interaction inhibitors as CNS therapeutic agents: current progress and future hurdles. (leibniz-fli.de)
Gamma-glutamyl carboxylase catalyzes carboxylation of glutamine to Gla residues in the amino-terminal portion of the molecule. (medscape.com)
Gamma-glutamyl carboxylase catalyzes carboxylation of Gla residues in the amino-terminal portion of the molecule. (medscape.com)
Because a uniform dielectric ionizable group in a protein relative to the pKa value of the continuum model is a very crude description of the highly same group in a small reference molecule in dilute aqueous heterogeneous protein interior, the dielectric coefficient, eP, solution. (lu.se)

Replacements L38E and L41E, involving charge acquisition at residues predicted to contribute to the hydrophobic interface, reduced the dimerization signal in the protein ligation assay and prevented the detection of dimer/multimer species in both transiently expressed 3A proteins and in synthetic peptides reproducing the N terminus of 3A. (asm.org)
These replacements also led to production of infective viruses that replaced the acidic residues introduced (E) by nonpolar amino acids, indicating that preservation of the hydrophobic interface is essential for virus replication. (asm.org)

11- 13 The finding of breast cancer associated mutations within the RING finger domain of BRCA1 , disrupting BRCA1/BARD1 interaction, 11, 14 and the occurrence of BARD1 missense mutations in breast cancer patients, 15- 17 implies participation of BARD1 in BRCA1 mediated tumour suppression. (bmj.com)
The analysis of mutations now allows us to narrow the search for functionally important regions to the short N-terminal helix, two transmembrane domains of the protein, and the loop between them. (usda.gov)
Significant research effort for drug design against COVID-19 is focused on the receptor binding domain of the spike protein, although this region is prone to mutations causing resistance against therapeutics. (biorxiv.org)
These residues can not only be targeted by broad spectrum antibodies and drugs, mutations in them can generate new strains of coronavirus resulting in future epidemic. (biorxiv.org)
6 Significantly, the sites in S protein have been demonstrated to be vulnerable to acquire mutations. (biorxiv.org)

Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. (embl.de)
The subsequent identification of activating amino acids in the generated "stand-alone" TrpA contributes to an understanding of allostery in TS. (uni-regensburg.de)

The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. (mdpi.com)
In the same experimental system, IL-10 and BDNF gene expressions increased, and in HypoE22 cells, the extract decreased the extracellular dopamine level and increased the DAT gene expression due to the direct interaction of parthenolide with the DAT. (researchgate.net)
Despite technological advances, experimental methods to target identification remain laborious, expensive, and sometimes unsuccessful. (biomedcentral.com)

Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. (lu.se)
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)

The recent identification of enzymes that regulate histone acetylation has revealed a broader use of this modification than was suspected previously. (embl-heidelberg.de)
Protein tyrosine phosphatase receptor delta (PTPRD) is a member of a large family of protein tyrosine phosphatases which negatively regulate tyrosine phosphorylation. (biomedcentral.com)
Our findings support the notion that arsenic binds to different sets of Keap1 cysteine residues to regulate divergent functions in Nrf2 signaling. (cdc.gov)

Previous X-ray structural studies at ambient temperature described several different protein domains including a large cavity in each subunit of the dimeric protein. (rcsb.org)
We aim to develop and optimize computational algorithms for characterizing and understanding protein-protein interactions, which remains one of the most important challenges in Structural Biology. (bsc.es)
The workshop aimed at representing a virtual bridge between these two events, showing how to manage and elaborate structural and high-throughput proteomics data so that it may be integrated with information from other life sciences disciplines with the aim of reaching a richer description and a deeper understanding of mechanisms and interactions in the involved system: the human being and its physiological and pathological states. (biomedcentral.com)
In addition, we show by a combination of structural and site-directed mutagenesis studies that bromodomains can interact specifically with acetylated lysine, making them the first known protein modules to do so. (embl-heidelberg.de)

Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. (embl.de)
Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. (embl.de)
Identification of critical cysteine residues of Keap1 in arsenic-sensing and suppression of Nrf2. (cdc.gov)
Here we analyzed arsenic-Keap1 cysteine thiol interactions for Nrf2 activation. (cdc.gov)

Vertebrate insulin gene enhancer binding protein isl-1. (embl.de)
Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. (embl.de)
The vpx gene products of human immunodeficiency virus type 2 (HIV-2) and of the closely related simian immunodeficiency viruses from sooty mangabeys (SIVsm) and macaques (SIVmac) comprise a 112-amino-acid virion-associated protein that is critical for efficient virus replication in nondividing cells such as macrophages. (duke.edu)

Bacterial fibronectin-binding proteins (FnBPs) contain a large intrinsically-disordered region (IDR) that mediates adhesion of bacteria to host tissues, and invasion of host cells, through binding to fibronectin (Fn). (hud.ac.uk)

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)

They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. (embl.de)
Design and identification of stable protein folds suitable for mutagenesis. (biocev.eu)
Chen, L. J. & Li, H. M. Stable megadalton TOC-TIC supercomplexes as major mediators of protein import into chloroplasts. (nature.com)
Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways. (leibniz-fli.de)

8- 10 In attempts to identify new breast and ovarian cancer susceptibility genes, much research has focused on BRCA1 associated proteins. (bmj.com)

Protein-protein interactions (PPIs) play essential roles in many biological processes. (nature.com)
Foot-and-mouth disease virus (FMDV) nonstructural protein 3A plays important roles in virus replication, virulence, and host range. (asm.org)

5 , 7 - 9 More specifically, a study analyzing 10,022 SARS-CoV-2 genomes from 68 countries revealed 2969 different missense variants, with 427 variants in the S protein. (biorxiv.org)

Identification of protein-protein interactions (PPIs) is important for understanding how proteins work together in a coordinated fashion in a cell to perform cellular functions. (nature.com)
PPIs are essential for individual protein functions, forming various cellular pathways, and are also involved in the development of diseases. (nature.com)
Interactions may also occur with other molecules involved in antibody-dependent cellular cytotoxicity (ADCC) or complement-dependent cytotoxicity (CDC). (genengnews.com)
Various reports implicated host cellular proteins as a key factor that either interact directly with HIV-1 integrase (IN) or get involved in the integration process of virus resulting in the modulation of integration step. (biomedcentral.com)
The investigations in which I am currently involved range from understanding the dynamics of fundamental protein-protein interactions, cellular processes, the. (edu.au)
The investigations in which I am currently involved range from understanding the dynamics of fundamental protein-protein interactions, cellular processes, the geometrical morphological features of microfossils, to the interactions in systems at larger scales involving human subjects. (edu.au)

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)

Traditional drugs interact with their target in a reversible equilibrium, while irreversible covalent drugs increase the drug-target interaction duration by forming a covalent bond with targeted residues and thus may offer a more effective therapeutic approach. (nih.gov)
For bioengineered therapeutic mAbs, the glycans are primarily attached to the asparagine Asn297 residue in the conserved Fc region of the antibody. (genengnews.com)
Large scale screening of therapeutic molecules and antibodies are underway aiming to target the spike protein and consequently prevent infection. (biorxiv.org)
Here, we introduce LigTMap, an online server with a fully automated workflow that can identify protein targets of chemical compounds among 17 classes of therapeutic proteins extracted from the PDBbind database. (biomedcentral.com)

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)

Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. (embl.de)

in poliovirus (PV), the interaction between the RNA replication complex and intracellular membranes appears to be accomplished by proteins 3A and 2C, which have membrane-binding properties ( 11 , 60 ). (asm.org)

By state-of-the-art sequencing ESR6&7 showed that Bartonella henselae adhesin A (BadA) is nearly 4000 residues long (not ≈3000), and with ESR12 determined which parts of this very long protein bound human fibronectin as a promising basis for novel antimicrobial therapies. (europa.eu)

Some LIM domains bind protein partners via tyrosine-containing motifs. (embl.de)
They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. (embl.de)
11 The functionally important BARD1/BRCA1 heterodimer formation is mediated by the RING finger motifs and has also been shown to markedly increase the stability of both proteins. (bmj.com)

a protein required for the differentiation of the set of six touch receptor neurons in this nematode. (embl.de)
Midkine (MK) and its functionally-related protein Pleiotrophin are heparin-binding neurotrophic factors that signal through the same receptor, known as anaplastic lymphoma kinase (ALK). (reliatech.de)
GBP is based on Aplysia californica acetylcholine binding protein (AcAChBP), a surrogate for the nicotinic acetylcholine receptor (nAChR). (dundee.ac.uk)
Ligand binding triggers receptor homo- and/or heterodimerization and autophosphorylation on key cytoplasmic residues. (joplink.net)
The phosphorylated receptor recruits adapter proteins like GRB2 which in turn activates complex downstream signaling cascades. (joplink.net)
Also directly phosphorylates other proteins like RGS16, activating its GTPase activity and probably coupling the EGF receptor signaling to the G protein-coupled receptor signaling. (joplink.net)

The cavity was free of any visible electron density for lipid molecules at room temperature, suggesting that only dynamic interactions exist with the protein. (rcsb.org)
The precise identification of the lipid type is difficult because of discontinuities in the electron density. (rcsb.org)
The conformations of the bound lipid and the interactions between protein and lipid provide insights into the factors governing lipoprotein formation. (rcsb.org)
Fig. 4: Arrangement of protein subunits and lipid molecules in the inner-membrane complex. (nature.com)

Conversely, broad spectrum therapeutics like drugs and monoclonal antibodies can be generated targeting these key distant regions of the spike protein. (biorxiv.org)
18 The human immune system started generating antibodies specific to residues outside RBD even at the earlier stage of the pandemic. (biorxiv.org)

It is thought to be related in amino acid sequence to segments of apolipoprotein B and the microsomal transfer protein responsible for the assembly of low-density lipoproteins. (rcsb.org)
They are prepared using mammalian cell culture, engineered to create a protein sequence comparable to the human variant. (genengnews.com)
The proposed method is novel because it works independently of protein sequence databases and without any prior knowledge about modifica- tions. (lu.se)
PTMs from this list in conjunction with a protein sequence and a few precursor masses. (lu.se)

S. cerevisiae hypothetical protein YKR090w. (embl.de)
In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX, Caenorhabditis elegans hypothetical protein ZK783.4, yeast protein YTA7). (embl-heidelberg.de)

Other representative plant species cover even less protein involved in known PPIs. (nature.com)

Impedance-based biosensors allowed ESR4 to show that only the glycosylated host protein vitronectin binds YadA (Meuskens et al. (europa.eu)

The N-glycans must be cleaved from the protein using the enzyme PNGase-F. You achieve this cleavage by incubation for three hours at 37 °C. The cleaved N-glycans must then be purified from the cleavage solution by solid phase extraction (SPE). (genengnews.com)
Moreover, findings suggest an evolutionary trajectory that describes the transition from a primary metabolic enzyme regulated by an interaction partner to a self-reliant, stand-alone, secondary metabolic enzyme. (uni-regensburg.de)
This led to the purification and subsequent identification of each defective enzyme. (medscape.com)

Among others, we have developed software for prediction of protein-protein complex structure by docking simulations, identification of binding sites on protein surfaces, or prediction of hot-spot residues from energy calculations. (bsc.es)

ccPDB: The ccPDB database is designed to provide service to scientific community working in the field of function or structure annotation of proteins. (wikipedia.org)

In the present study, we have identified a new HIV-1 integrase interacting protein, polypyrimidine tract binding protein and associated splicing factor (PSF) through pull down assay and co immunoprecipitation of IN with mammalian cell protein. (biomedcentral.com)

Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. (embl.de)
MK plays an important regulatory role in epithelial-mesenchymal interactions during fetal development and in postnatal lung development. (reliatech.de)

The treatment of protein flexibility is currently a major bottleneck in protein docking. (bsc.es)
Data from the study of N-methylbicuculline suggest that it is promiscuous due to the flexibility of the orthosteric binding site of pLGIC members as well as the number of interactions the ligand can form, therefore a favourable orientation can always be adopted. (dundee.ac.uk)

Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. (embl.de)

Deciphering protein–protein interactions. (crossref.org)
Deciphering soluble and membrane protein function using yeast systems. (leibniz-fli.de)

Acetylation regulates many diverse functions, including DNA recognition, protein-protein interaction and protein stability. (embl-heidelberg.de)
Identification of key protein residues involved in recognition and strength of interaction. (biocev.eu)

ESR13 studied the three-dimensional structure of a protein subunit that polymerizes into filaments to drive secretion of 15 different toxins and enzymes in the bacterium Dickeya dadantii. (europa.eu)
Although globally resembling ubiquitin, the GABP(x fragment differs in its secondary structure topology and thus appears to represent a new protein fold that we term the OST (On-SighT) domain. (ubc.ca)
The glycan structure attached to the protein during glycosylation is particularly important because it affects biological activity. (genengnews.com)
The actual structure can affect the level of interaction.Efficiently generate glycosylation profiles with a single-vendor solution. (genengnews.com)
There is even a conserved structure, the bromodomain, that recognizes acetylated residues and may serve as a signalling domain. (embl-heidelberg.de)
BARD1 was originally identified through its interaction with BRCA1, with which it has a closely related domain structure. (bmj.com)
Protein farnesyltransferase: structure and implications for substrate binding. (expasy.org)
Similarities in chemical structure and binding poses of compounds that were shown to bind the target proteins were investigated. (dundee.ac.uk)
In order to give an insight into the manner of interaction of IDE with its substrates, several papers have focused on the structure of the IDE/insulin complex. (cnr.it)
Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. (lu.se)

Anatomy10

Organisms11

Chemicals and Drugs109

Analytical, Diagnostic and Therapeutic Techniques and Equipment46

Phenomena and Processes78

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science10

Health Care4

Mutation6

Tyrosine residues2

Complexes5

Functional8

Ligands5

Membrane proteins6

Highly conserved1

Viral11

Nucleic acids1

Characterization2

Sequences2

Molecular10

Negatively-charged2

Properties of proteins2

Peptide7

Involved in transcriptional1

Metrics1

Receptors3

Variety of proteins2

Conformational flexibility1

Molecule9

Hydrophobic2

Mutations5

Amino acids2

Experimental3

Chains3

Regulate3

Structural4

CYSTEINE4

Gene3

Intrinsically disordered1

Positively-charged1

Stable4

Genes1

Roles2

Variants1

Cellular6

Capsid1

Therapeutic4

Lysine1

Interact1

Intracellular1

Human fibronectin1

Motifs3

Receptor6

Lipid4

Antibodies2

Sequence4

Hypothetical protein2

Species1

Binds1

Enzyme3

Calculations1

Annotation1

Mammalian cell1

Regulatory2

Flexibility2

GTPase1

Deciphering2

Recognition2

Structure10