Protein interaction domains and motifs. Medical search. Frequent questions

p53 bound to the SMRT deacetylase activation domain (DAD), which mediates HDAC3 binding and activation, and HDAC3 could attenuate p53 binding to the DAD region of SMRT. (nih.gov)
Although zinc fingers usually function by binding to DNA or RNA, the LIM motif probably mediates protein-protein interactions. (thermofisher.com)
Death-associated protein kinase (DAPK) is a stress-regulated protein kinase that mediates a range of processes, including signal-induced cell death and autophagy. (ed.ac.uk)
The protein encoded by this gene mediates transcriptional control by interaction with the activation function 2 (AF2) region of several nuclear receptors, including the estrogen, retinoic acid, and vitamin D3 receptors. (fishersci.com)
The platelet GP IIb/IIIa complex mediates platelet-to-platelet interactions (platelet aggregation). (medscape.com)

The PDZ domain of ZASP binds the C-terminus of alpha actinin-2 and ZMs bind the rod domain of alpha actinin-2. (wikipedia.org)
During its biogenesis KdpD binds to the signal recognition particle (SRP) of Escherichia coli that consists of a 48-kDa protein Ffh and a 4.5S RNA. (nature.com)
SRP is universally conserved in its core region that consists of a ribonucleoprotein particle, the SRP RNA (4.5S RNA in E. coli ) and the protein component SRP54 (Ffh in E. coli for "fifty-four-homolog") that binds to the conserved RNA domain IV 4 . (nature.com)
Identification of a protein that binds to the SH3 region of Abl and is similar to Bcr and GAP-rho. (eu.org)
Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. (embl.de)
Anteroposterior patterning in Drosophila melanogaster is dependent on the sequence-specific RNA-binding protein Smaug, which binds to and regulates the translation of nanos (nos) mRNA. (embl.de)
We show here that the SAM domain of Saccharomyces cerevisiae Vts1 binds RNA with the same specificity as Smaug and that Vts1 induces transcript degradation through a mechanism involving the cytoplasmic deadenylase CCR4. (embl.de)
The chromo-domain binds histone H3 tails methylated on lysine 9. (cipsm.de)
Crystal structures of the three molecular complexes revealed that IST1 binds to the MIT domains of VPS4, LIP5, and Spartin using two different mechanisms (MIM1 mode versus MIM3 mode). (rcsb.org)
These observations enabled us to deduce a preliminary binding code, which we applied to provide CHMP2A, a protein that normally only binds the MIT domain in the MIM1 mode, the additional ability to bind the MIT domain of Spartin in the MIM3 mode. (rcsb.org)
SELEX assays and footprinting data indicate that DEAF-1 binds to and activates Mtk and Drs regulatory DNAs via a TTCGGBT motif. (sdbonline.org)
DEAF-1 recognizes several TTCG motifs within the portion of the Dfd autoregulatory region termed 'module E.' In addition, DEAF-1 binds several similar motifs within a Dfd response element ( DRE ) from the 1.28 gene that enhances maxillary gene expression during embryogenesis (Pederson, 2000). (sdbonline.org)
FMRP is an RNA binding protein that binds to G quartet forming RNA using its RGG box motif. (auckland.ac.nz)
A loop from the N-terminal SH2 domain binds to the catalytic cleft of the phosphatase domain in the same SHP-2 molecule leading to an autoinhibited configuration (Hof et al. (lu.se)

PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. (wikipedia.org)
The information within the KdpD protein that confers SRP interaction was found in the amino-terminal cytoplasmic domain of KdpD, particularly at residues 22-48. (nature.com)
Within this sequence a Walker A motif is present at residues 30-38. (nature.com)
We found that the amino acid residues R22, K24 and K26 are important for SRP interaction, whereas the residues G30, G34 and G36, essential for a functional Walker A motif, can be replaced with alanines without affecting the affinity to SRP-FtsY and membrane targeting. (nature.com)
Furthermore, it is suggested that the binding of SRP to the signal sequence is promoted by the presence of basic amino acid residues through electrostatic interactions 18 . (nature.com)
SH3 (Src Homolgy 3) domains are small protein modules of about 50-60 residues. (eu.org)
The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. (embl.de)
Residues that compose the RNA-binding surface are conserved in a subgroup of SAM domain-containing proteins, suggesting that the function of the domain is conserved from yeast to humans. (embl.de)
repeat families are found in the conserved residues that form the hydrophobic domain core. (cellsignal.com)
The animal AE proteins consist of homodimeric complexes of integral membrane proteins that vary in size from about 900 amino acyl residues to about 1250 residues. (tcdb.org)
As part of the analyses, residues that are critical for LisH-dimerization and the head-to-tail binding, respectively, were identified, whose mutation specifically interfered with each of the interactions separately. (uni-wuerzburg.de)
For the binding site on the GABA(A) receptor, it was confirmed that the thirteen most C-terminal residues of the intracellular domain are critical for the binding of muskelin. (uni-wuerzburg.de)
In accordance with the strong conservation of these residues among the alpha subunits of the GABA(A) receptor, it could be shown that an interaction with muskelin in vitro is also possible for the alpha2 and alpha5 subunits. (uni-wuerzburg.de)
In addition, recent studies have revealed several GxxxG-containing TM domains that interact via alternative interfaces involving hydrophobic, polar, aromatic, or even ionizable residues that do not form recognizable motifs. (cipsm.de)
The selectivity of an individual SH2 domain is not sharply defined, and a range of residues is typically tolerated at each site following the phosphotyrosine. (lu.se)

LIM domains are highly conserved cysteine-rich structures containing 2 zinc fingers. (thermofisher.com)
Members of this family also possess highly conserved ATPase and helicase domains, flanked by individually distinctive N and/or C-terminal motifs. (bellbrooklabs.com)
Furthermore, two more highly conserved TWIST motifs NSEEE and WR were analyzed individually to find out their interacting proteins and their role in regulating the TWIST1 transcriptional activity. (uni-marburg.de)

LIM kinase-1 and LIM kinase-2 belong to a small subfamily with a unique combination of 2 N-terminal LIM motifs and a C-terminal protein kinase domain. (thermofisher.com)
Although the kinase domain of DAPK has a range of substrates that mediate its signalling, the additional protein interaction domains of DAPK are relatively ill defined. (ed.ac.uk)
1998). The Src SH2 domain has been shown to bind a phosphorylated tyrosine at the C-terminus of the same molecule resulting inactivation of enzyme activity by rearrangement of catalytic center in the kinase domain (reviewed in Hubbard et al. (lu.se)

PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. (wikipedia.org)
KdpD is a four-spanning membrane protein that has two large cytoplasmic domains at the amino- and at the carboxyterminus, respectively. (nature.com)
The protein is targeted to the inner membrane surface and is released after contacting the SRP receptor protein FtsY. (nature.com)
In contrast to the signal sequences of exported proteins, the bacterial SRP signal sequences are more hydrophobic and are mostly "uncleaved signal sequences" present in membrane proteins that remain in the final protein-chain as transmembrane anchor sequences. (nature.com)
In general, the signal for insertion into the inner bacterial membrane is located in the first hydrophobic transmembrane domain and insertion is catalysed by the Sec translocase and/or YidC insertase. (nature.com)
It is found in proteins involved in several biological processes as diverse as signal transduction pathways, cytoskeleton organization, membrane traffic or organelle assembly. (eu.org)
For example, shank proteins are located further away from the membrane in the cytosolic faces of the PSDs, facing the actin cytoskeleton. (frontiersin.org)
The rationale of this organization may be related to important roles of these proteins as "exchange hubs" for the signaling proteins for their migration from the subcortical cytosol to the membrane. (frontiersin.org)
In this review, the hypothesis is forwarded that nNOS delivered to subcortical cytoskeleton requires interactions with scaffolding proteins prior to docking at the membrane. (frontiersin.org)
A thesis is proposed here, based on rational argument that depletion of the cytoskeletal organizer protein shank3 may result in defective nNOS membrane localization, resulting in defective nitric oxide synthesis. (frontiersin.org)
The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. (cipsm.de)
AE1 is also activated by interaction with glycophorin which also functions to target it to the plasma membrane ( Young and Tanner, 2003 ). (tcdb.org)
The membrane-embedded C-terminal domains may each span the membrane 13-16 times. (tcdb.org)
All AE proteins are hypothesized to share a similar topology in the cell membrane. (tcdb.org)
The N -terminal transmembrane domain of ACBP1 and ACBP2 targets each protein to the endoplasmic reticulum (ER) and the plasma membrane while ACBP3 is targeted extracellularly. (aocs.org)
Using a GFP-tagged bri1-120 construct, we detected the bri1-120 protein in the plasma membrane, and showed that the phenotypic defects in the rosette leaves of bri1-301 , a kinase-inactive weak allele of BRI1 , can be restored by the overexpression of the bri1-120 proteins in bri1-301 . (biomedcentral.com)
Transmembrane (TM) helices of integral membrane proteins can facilitate strong and specific noncovalent protein-protein interactions. (cipsm.de)
Mutagenesis and structural analyses have revealed numerous examples in which the interaction between TM helices of single-pass membrane proteins is dependent on a GxxxG or (small)xxx(small) motif. (cipsm.de)
However, the actual interaction strength of motif-containing helices depends strongly on sequence context and membrane properties. (cipsm.de)
In multipass membrane proteins, GxxxG motifs can be important for protein folding, and not just oligomerization. (cipsm.de)
Our current knowledge thus suggests that the presence of a GxxxG motif alone is a weak predictor of protein dimerization in the membrane. (cipsm.de)
While many studies have been focused on the membrane structure, the dynamics of such systems are crucial for the function of the membrane including membrane bound proteins. (lu.se)
Native membrane derived polymer-supported lipid bilayers (nSLBs) are poised to bridge the gap between live cell experiments and traditional model membrane architectures that by offering a combination of accessibility by surface sensitive analytical instrumentation and a composition which more closely resembles cellular membranes by displaying a diversity of endogenous membrane proteins, lipids, and carbohydrates. (lu.se)
Due to the lack of detergent solubilization and reconstitution steps, the nSLBs created using this approach contain essentially all of the native lipids, as well as the membrane-associated proteins and carbohydrates from the donor membrane. (lu.se)

In addition, ARVCF contains a predicted nuclear-targeting sequence suggesting that it may have a function as a nuclear protein. (nih.gov)
The core experimental aim of the project is to develop a new single-molecule spectroscopic method, dynamic single-molecule Metal Induced Energy Transfer (or dynamic smMIET), which will be suited to study the conformational dynamics of intrinsically disordered peptides (sequences of FG-repeat proteins from the nuclear pore), and of small folding protein motifs, in particular helix-turn-helix (HTH) and WW-domain motifs. (uni-goettingen.de)
Widespread domain in signalling and nuclear proteins. (embl.de)
The protease not only releases small peptides, such as the amyloid-β peptide, which drives Alzheimer's disease pathogenesis, but also intracellular domains, which can have critical functions in nuclear signaling. (cipsm.de)
Nuclear corepressor for KRAB domain-containing zinc finger proteins (KRAB-ZFPs). (abcam.com)
The bacterial sliding clamp is referred to as the b clamp, while the eukaryotic and archaeal sliding clamp protein is called the proliferative cell nuclear antigen (PCNA). (pasteur.fr)
These characteristics correlate with a distinct nuclear architecture, epigenetic signatures enriched for active chromatin marks and hyperdynamic binding of structural chromatin proteins. (biomedcentral.com)
While DDX5 is predominantly a nuclear protein, it can shuttle between the nucleus and the cytoplasm, depending upon cell cycle status, cell type, and given post-translational modification. (bellbrooklabs.com)
First, I focused on functional characterization of the NLS1 and NLS2 domains as potential nuclear localization signals in TWIST. (uni-marburg.de)
Additionally, to understand the role of the TWIST NLS2 in nuclear localization, amino acid at positions 73, 76 and 77 were substituted in this motif. (uni-marburg.de)
This synergistic effect is consistent with the observation that combined K38R (NLS1) and K76R (NLS2) mutants dramatically reduced nuclear localization, further suggesting that both NLS1 and NLS2 work together in regulating nuclear localization of TWIST protein. (uni-marburg.de)
The protein localizes to nuclear bodies and is thought to associate with chromatin and heterochromatin-associated factors. (fishersci.com)
At the cellular level, the actions of glucocorticoids are mediated by a 94-kd protein, the glucocorticoid receptor (GR). The human (h) GR belongs to the steroid/thyroid/retinoic acid superfamily of nuclear receptors and functions as a ligand-dependent transcription factor that regulates the expression of glucocorticoid-responsive genes positively or negatively. (medscape.com)
For example, the TP53 gene, located on chromosome 17, encodes a 53-kd nuclear protein that functions as a cell cycle checkpoint. (medscape.com)

ZASP functions to maintain structural integrity of sarcomeres during contraction, and has been shown to be involved in protein kinase A signaling. (wikipedia.org)
SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
Here, we studied the molecular interactions between IST1 and the three MIT domain-containing proteins to understand the structural basis that governs pairwise MIT-MIM interaction. (rcsb.org)
Cell wall proteomics, as well as numerous genetic or biochemical studies, have revealed the high diversity of CWPs, among which proteins acting on polysaccharides, proteases, oxido-reductases, lipid-related proteins and structural proteins. (mdpi.com)
Their N-terminal hydrophilic domains may interact with cytoskeletal proteins and therefore play a cell structural role. (tcdb.org)
In their work, the Unit of Structural Dynamics of Macromolecules presented the structure of the DNA-bound PolD-PCNA complex from P. abyssi at 3.77 Å using an integrative structural biology approach, combining cryo-EM, X-ray crystallography, protein-protein interaction measurements and activity assays. (pasteur.fr)
To establish a basis for understanding the mode of operation of muskelin, the aim of this thesis was an in-depth biochemical and structural characterization of muskelin and its interaction with the GABA(A) receptor. (uni-wuerzburg.de)
1993). Based on these results, together with structural analyses of different ligand-binding models, it is apparent that SH2 domains bind distinct but overlapping sequence motifs. (lu.se)
Mauno Vihinen is well-known for his experience and interest in investigating variations and their effects whether they emerge at molecular levels (DNA, RNA protein), in structural context or in the cellular networks and pathways. (lu.se)

Thus, inhibiting HOX-PBX interaction represents a potential strategy to prevent these malignancies, as demonstrated by the patented peptide HTL001 that is being studied in clinical trials. (mdpi.com)
We present the structures of eight unique PDZ domains crystallized using this approach and focus on four which provide information on selectivity (PICK1 and the third PDZ domain of DLG2), binding site flexibility (the third PDZ domain of MPDZ), and peptide-domain interactions (MPDZ 12th PDZ domain). (rcsb.org)
SmMIET is based on the distance-dependent quenching of the fluorescence emission of fluorescent molecules by metallic or semi-metallic thin films, and it requires labeling of the peptide/protein of interest by only one dye, in contrast to single-molecule Förster Resonance Energy Transfer, which requires labeling with a donor and an acceptor dye label. (uni-goettingen.de)
Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent chain and the ribosomal exit tunnel are critical. (cipsm.de)
Interestingly, we found that the G quartet recognition is necessary but not sufficient for the FMRP RGG box binding to this RNA target, indicating that additional interactions of the peptide, possibly with the stem and/or stem-G quartet junction region, are required. (auckland.ac.nz)
This review will summarize our current knowledge of the DAPK interactome, the use of peptide aptamers to define novel protein-protein interaction motifs, and how these new protein-protein interactions give insight into DAPK functions in diverse cellular processes, including growth factor signalling, the regulation of autophagy, and its emerging role in the regulation of immune responses. (ed.ac.uk)

ZASP belongs to the Enigma subfamily of proteins and stabilizes the sarcomere (the basic units of muscles) during contraction, through interactions with actin in cardiac and skeletal muscles. (wikipedia.org)
A role for myosin-I in actin assembly through interactions with Vrp1p, Bee1p, and the Arp2/3 complex. (eu.org)
Scar/WAVE-1, a Wiskott-Aldrich syndrome protein, assembles an actin-associated multi-kinase scaffold. (eu.org)
Formins are multidomain proteins defined by a conserved FH2 (formin homology 2) domain with actin nucleation activity preceded by a proline-rich FH1 (formin homology 1) domain. (biomedcentral.com)
In vitro, the FH2 domain competes with barbed-end capping proteins and is necessary and sufficient to nucleate actin polymerization, but the FH1 domain, which interacts with profilin-actin, funnels actin to the nucleation vicinity and confers full activity to the molecule [ 1 ]. (biomedcentral.com)
Actin-related protein 2/3 (Arp2/3) complex activation by nucleation promoting factors (NPFs) such as WASP, plays an important role in many actin-mediated cellular processes. (elifesciences.org)
These studies provide evidence that WASP and WIP play central roles in establishment of a robust multivalent SH3 domain-PRM network in vivo, giving actin assembly onset at endocytic sites a switch-like behavior. (elifesciences.org)
Actin is one of the most abundant proteins in yeast, mammalian and other eukaryotic cells. (elifesciences.org)
In yeast, a member of the WASP family of proteins promotes the assembly of actin filaments around the site where endocytosis will occur. (elifesciences.org)
To achieve this, WASP interacts with several other proteins including WIP and myosin, a motor protein that moves along actin filaments to generate mechanical forces. (elifesciences.org)
However, it was not clear how these proteins work together to trigger actin filaments to assemble at the right place and time. (elifesciences.org)
suggest that WASP and WIP play key roles in establishing the network of proteins needed for actin filaments to assemble during endocytosis. (elifesciences.org)

Identification of two SH3-binding motifs in the regulatory subunit of phosphatidylinositol 3-kinase. (eu.org)
This region of Fip1 is needed for the interaction with the Th1 subunit of the complex and for specific polyadenylation of the cleaved mRNA precursor. (nih.gov)
motifs of Protein Phosphatase 2A PR65/A subunit. (cellsignal.com)
The biochemical studies of the interaction of muskelin and the alpha1 subunit of the GABA(A) receptor demonstrated a direct binding with an affinity in the low micromolar range, which is mediated primarily by the kelch repeat domain in muskelin. (uni-wuerzburg.de)
In this study, we validated the interaction between the C4 protein encoded by tobacco leaf curl Yunnan virus (TbLCYnV) and the regulatory subunit ß of Nicotiana benthamiana SnRK1, i.e. (bvsalud.org)

18. Sanowar S, Singh P, Pfuetzner RA, Andre I, Zheng H, Spreter T, Strynadka NC, Baker D, Goodlett DR and Miller S. Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System. (lu.se)
This new approach has been shown to preserve mobility and enzymatic activity of transmembrane proteins in the resulting nSLB. (lu.se)

SH3 domains bind to proline-rich peptides that form a left-handed polyproline type II helix (PPII) in one of two opposite orientations. (eu.org)
The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains. (eu.org)
Our results demonstrate that SH3 (Src homology 3) domain-PRM (proline-rich motif) interactions involving multivalent linker proteins play central roles in concentrating NPFs at endocytic sites. (elifesciences.org)
For example, a region of WASP known as the proline-rich domain can bind to proteins that contain an "SH3" domain. (elifesciences.org)

Recently, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, yet the role of the major heterochromatin proteins in pluripotency is unknown. (biomedcentral.com)
I wanted to determine if the TWIST protein or its conserved motifs interact with other regulatory proteins to help to regulate the TWIST transcriptional activity. (uni-marburg.de)
In addition to their role in assembling activated complexes, particular SH2 domains also form intramolecular interactions that regulate enzyme activity. (lu.se)

The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. (wikipedia.org)

Here we demonstrate that PSRP1 is not a bona fide ribosomal protein, but rather a functional homologue of the Escherichia coli cold-shock protein pY. (cipsm.de)
The function of the acyl-CoA-binding domain in recombinant Arabidopsis ACBPs expressed in the bacterium Escherichia coli was established using site-directed mutagenesis followed by in vitro binding assays. (aocs.org)
The crystal structure of a C-terminal domain of enterohemorrhagic Escherichia coli type III effector NleH2 has been determined to 2.6 Å resolution. (northwestern.edu)

The amino-terminal NG domain of SRP is bound to the ribosomal proteins uL23 and uL29, next to the tunnel exit and the carboxy-terminal M domain to the ribosomal 23S RNA 6 . (nature.com)
Plastid-specific ribosomal proteins (PSRPs) have been proposed to play roles in the light-dependent regulation of chloroplast translation. (cipsm.de)

H untington, E longation Factor 3, PR65/ A , T OR) is found in the four diverse eukaryotic proteins for which the domain is named. (cellsignal.com)
Organisms within the archaeal domain of life possess a simplified version of the eukaryotic DNA replication machinery. (pasteur.fr)

repeats are found in proteins involved in translation including eIF4Gs, p97/DAP5, Paip-1, GCN1 and FRAP/mTOR. (cellsignal.com)

The ARVCF gene encodes a protein containing two motifs, a coiled coil domain in the N-terminus and a 10 armadillo repeat sequence in the midregion. (nih.gov)
This locus, however, also encodes a protein from an alternative reading frame, designated p19ARF. (medscape.com)

Collectively, these data highlight a biological role for SMRT in mediating DNA damage responses and suggest a model where p53 binding to the DAD limits HDAC3 interaction with this coregulator, thereby facilitating SMRT coactivation of p53-dependent gene expression. (nih.gov)
LIM domain binding 3 (LDB3), also known as Z-band alternatively spliced PDZ-motif (ZASP), is a protein which in humans is encoded by the LDB3 gene. (wikipedia.org)
Enhances transcriptional repression by coordinating the increase in H3K9me, the decrease in histone H3 'Lys-9 and 'Lys-14' acetylation (H3K9ac and H3K14ac, respectively) and the disposition of HP1 proteins to silence gene expression. (abcam.com)
When a cell needs to make a particular protein, it first copies the instructions from the matching gene into a molecule known as a messenger RNA (or an mRNA for short). (elifesciences.org)
The present study was thus undertaken to determine how TWIST1 gene mutations affect protein function. (uni-marburg.de)
TWIST belongs to class B bHLH proteins which are known to form stable heterodimers with members of class A bHLH transcription factors including gene products of E12 and E47, respectively. (uni-marburg.de)
The abnormal hypermethylation of the expanded CGG repeats causes the transcriptional silencing of the FMR1 gene and, consequently, the loss of the fragile X mental retardation protein (FMRP). (auckland.ac.nz)
The protein encoded by this gene belongs to the pyridine nucleotide-disulfide oxidoreductase family, and is a member of the thioredoxin (Trx) system. (cancerindex.org)
What does this gene/protein do? (cancerindex.org)
What pathways are this gene/protein implicaed in? (cancerindex.org)
[ 1 ] His prediction was subsequently supported by the cloning of the retinoblastoma tumor suppressor gene ( RB1 ) and by functional studies of the retinoblastoma protein, Rb. (medscape.com)
Genetic association studies, such as recent genome-wide association studies (GWAS), have provided a springboard for exploring the contribution of inherited genetic variation and gene/environment interactions in relation to disease. (cdc.gov)
Although many data sources for genes and diseases are in the public domain, finding published results with potential implications for understanding gene-disease relationships and gene-environment interactions is not a trivial task. (cdc.gov)
Gene Prospector is a Web-based application designed to help researchers prioritize and evaluate evidence for genes related to human disease or interactions with non-genetic risk factors. (cdc.gov)

The p16INK4A protein is a cell-cycle inhibitor that acts by inhibiting activated cyclin D:CDK4/6 complexes, which play a crucial role in the control of the cell cycle by phosphorylating Rb protein. (medscape.com)

In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. (springer.com)
SRP is bound to the ribosome and is ready to interact with a nascent protein chain. (nature.com)
We find that the fission yeast homologues of Tristetraprolin/TTP and Pumilio/Puf (Zfs1 and Puf3) interact with Ccr4-Not via multiple regions within low-complexity sequences, suggestive of a multipartite interface that extends beyond previously defined interactions. (elifesciences.org)
This initial interaction (platelet adhesion) sets the stage for other adhesive reactions that allow the platelets to interact with other agonists in the vicinity of vessel injury, such as adenosine 5'-diphosphate (ADP), subendothelial collagen, and thrombin. (medscape.com)

A Cypher/ZASP mutation associated with dilated cardiomyopathy alters the binding affinity to protein kinase C". The Journal of Biological Chemistry. (wikipedia.org)
Using affinity chromatography coupled to multidimensional protein identification technology (MudPIT), DEAF-1 was identified as a candidate regulator. (sdbonline.org)
In this study we have performed a thermodynamic analysis of the interactions between the FMRP RGG box domain and Sc1, an RNA molecule which had been previously shown to be bound with high affinity by both the full-length FMRP and by its RGG box domain. (auckland.ac.nz)
1998). In both examples, the high affinity ligands can compete with the intramolecular interactions and release the catalytic domains for their in vivo targets. (lu.se)

2010 ). PRDM9 includes several functional domains, such as a DNA-binding zinc finger array, a histone lysine methyltransferase PR/SET (PRDI-BF1 and RIZ1 homology) domain, and a Krüppel-associated box (KRAB)-related domain. (springer.com)
2017) Characterization of the mammalian DEAD-box protein DDX5 reveals functional conservation with S. cerevisiae ortholog Dbp2 in transcriptional control and glucose metabolism. (bellbrooklabs.com)
The aim of my work is to characterize functional domains in TWIST protein, and to determine the interacting partner for TWIST and its motifs particularly NSEEE and WR. (uni-marburg.de)
B) Functional domains of the hGR-alpha. (medscape.com)
The functional domains and subdomains are indicated beneath the linearized protein structures. (medscape.com)

Here we report the production of full-length PfRH5 protein using a cGMP-compliant platform called ExpreS 2 , based on a Drosophila melanogaster Schneider 2 (S2) stable cell line system. (nature.com)
This work identifies Drosophila S2 cells as a clinically-relevant platform suited for the production of 'difficult-to-make' proteins from Plasmodium parasites, and identifies a PfRH5 sequence variant that can be used for clinical production of a non-glycosylated, soluble full-length protein vaccine immunogen. (nature.com)
The Nanos protein gradient in Drosophila, required for proper abdominal segmentation, is generated in part via translational repression of its mRNA by Smaug. (embl.de)

It has been recently reported that motor proteins like myosin Va play important role in transcytosis of nNOS. (frontiersin.org)
Evidence has suggested the role of motor proteins like myosin Va in transposition of nNOS within the nerve terminals to the membranes to facilitate nitrergic neurotransmission ( 11 , 12 ). (frontiersin.org)
The experiments show that WASP, myosin and WIP are recruited to sites where endocytosis is about to occur through specific interactions with other proteins. (elifesciences.org)

In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. (embl.de)
The 32-aa MYND domain (for myeloid, Nervy, and Deaf-1) contains non-DNA-binding zinc fingers that are thought to mediate protein-protein interactions (Gross, 1996). (sdbonline.org)

DDX5 is a 614 amino acid protein consisting of an N-terminal Q motif, an ATP binding Rec A-like domain, a hinge region, a Rec A-like helicase domain, and a C-terminal RGS-RGG motif. (bellbrooklabs.com)
Particularly, in the extracellular domain, regions near the 70-amino acid island are known to be critical to BR binding. (biomedcentral.com)
In comparison, the exact function of the leucine rich-repeats (LRR) region located before the 70-amino acid island domain in the extracellular cellular portion of BRI1 has not yet been described, due to a lack of specific mutant alleles. (biomedcentral.com)
Our results indicated that the extracellular LRR regions before the 70-amino acid island domain of BRI1 are important for the appropriate cellular functioning of BRI1. (biomedcentral.com)
In the presence of BR, BKI1 is released by the direct binding of BR to the 70-amino acid island region in the extracellular domain of BRI1 [ 7 ]. (biomedcentral.com)

Protein conformation is critically linked to function and often controlled by interactions with regulatory factors. (cipsm.de)
Here we report the selection of camelid-derived single-domain antibodies (nanobodies) that modulate the conformation and spectral properties of the green fluorescent protein (GFP). (cipsm.de)
The position of helix αC and the lack of a conserved arginine within an equivalent HRD motif suggested that the NleH2 kinase domain's active conformation might not require phosphorylation. (northwestern.edu)

In the online version, these sections contain links to more information about proteins encoded by over 17,000 known or predicted human genes. (cshlpress.com)
Like Rb protein, many of the proteins encoded by tumor suppressor genes act at specific points in the cell cycle. (medscape.com)
The major part of his production relates to variations ranging from protein engineering to effects and mechanisms of variations in protein structures, genes and diseases. (lu.se)

In the last decades, HOX proteins have been extensively studied due to their pivotal role in transcriptional events. (mdpi.com)
The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. (embl.de)

The insertion of this motif into the Diptericin ( Dpt ) regulatory region confers DEAF-1 responsiveness to this normally DEAF-1-independent enhancer. (sdbonline.org)

This role involves its DNA-binding domain, which is composed of a tandem array of zinc fingers, and PRDM9-dependent trimethylation of histone H3 at lysine 4. (springer.com)
One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
In this "SRP pathway", an open question is how a signal sequence is recognized since no consensus motif exists and is relevant for SRP binding. (nature.com)
HOX proteins execute their activity by exploiting a cooperative binding to PBX proteins and DNA. (mdpi.com)
Association of p62, a multifunctional SH2- and SH3-domain-binding protein, with src family tyrosine kinases, Grb2, and phospholipase C gamma-1. (eu.org)
Evidence for SH3 domain directed binding and phosphorylation of Sam68 by Src. (eu.org)
Binding of Fyn to MAP-2c through an SH3 binding domain. (eu.org)
The C-terminal four amino acids of a prospective binding partner of a PDZ domain are typically the determinants of binding specificity. (rcsb.org)
In an effort to determine the structures of a number of PDZ domains we have included appropriate four residue extensions on the C termini of PDZ domain truncation mutants, designed for self-binding. (rcsb.org)
The binding of BDNF to the ectodomain of TrkB leads to phosphorylation of tyrosines 515 (Y515) and 816 (Y816) in the cytoplasmic domain of TrkB. (jneurosci.org)
The Plasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) has recently emerged as a leading candidate antigen against the blood-stage human malaria parasite. (nature.com)
These results suggest that the SAM domain might have a primary role in RNA binding. (embl.de)
Using homology modeling and site-directed mutagenesis, we have localized the RNA-binding surface of the Smaug SAM domain and have elaborated the RNA consensus sequence required for binding. (embl.de)
With the exception of ForI and ForC all other formins conform to the domain structure GBD/FH3-FH1-FH2-DAD, where DAD is the Diaphanous autoinhibition domain and GBD/FH3 is the Rho GTPase-binding domain/formin homology 3 domain that we propose to represent a single domain. (biomedcentral.com)
The FH1 domain is also a binding site for diverse SH3-domain containing proteins like Src-like non-receptor tyrosine kinases, WISH (WASP-interacting SH3 protein) and IRSp53 (insulin receptor substrate) in mammals, and Hof1p in yeast [ 6 ]. (biomedcentral.com)
containing proteins include the Ran-GTP binding importin and exportin cargo transport proteins. (cellsignal.com)
Polyglutamine-binding protein 1 ( PQBP1 ) is an RNA-splicing factor that, when mutated, in humans causes Renpenning syndrome, an X-linked intellectual disability disease characterized by severe cognitive impairment, but also by physical defects that suggest PQBP1 has broader functions in embryonic development. (xenbase.org)
RNA-binding proteins contribute to specificity by interacting with both Ccr4-Not and target mRNAs, but this is not fully understood. (elifesciences.org)
Although the C-terminal domain comprises a small percentage of the total protein, this domain in some cases (i) has PSD-95/Discs Large/ZO-1-binding motifs that may be important for protein-protein interactions (e.g. (tcdb.org)
KIN17, which is known as a DNA and RNA binding protein, is highly expressed in numerous types of human cancers and was discovered to participate in several vital cell behaviors, including DNA replication, damage repair, regulation of cell cycle and RNA processing. (spandidos-publications.com)
In plants cells, lipid-transfer proteins (LTPs) and acyl-CoA-binding proteins (ACBPs) have been identified as candidates for lipid transfer within the cell [reviewed in 1,2]. (aocs.org)
Currently, information on these larger proteins with acyl-CoA-binding domains is available from data mining of sequenced genomes. (aocs.org)
The presence of a conserved acyl-CoA-binding domain in each ACBP enables it to bind acyl-CoA esters. (aocs.org)
These six ACBPs map to four distinct classes based on the presence of other protein domains besides the conserved acyl-CoA-binding domain. (aocs.org)
ACBP3 lacks both ankyrin repeats and kelch motifs but it is larger (39.3 kDa) than ACBP6 (10.4 kDa), which is the smallest member and consists of only the acyl-CoA-binding domain. (aocs.org)
PCNA binding partners carry short motifs known as the PCNA-interacting protein-box (PIP-box). (pasteur.fr)
The Q motif is necessary for single-stranded RNA binding and for proper conformational dynamics in response to ATP binding and hydrolysis. (bellbrooklabs.com)
While both the ATP binding domain and the helicase domain share and cooperate in conformationally dictated ATP binding and hydrolysis, RNA binding, and helicase functions, the N-terminal Rec A-like domain principally orchestrates ATP binding and hydrolysis, while the C-terminal Rec A-like domain mainly controls RNA binding and helicase activities. (bellbrooklabs.com)
For the detailed studies of both binding events, the solution of a crystal structure of a fragment of muskelin, comprising the Discoidin domain and the LisH motif, was an important basis. (uni-wuerzburg.de)
This information enabled to map the amino acids contributing to binding, which showed that the binding site of the head-to-tail interaction coincides with the generic ligand binding site of the discoidin domain. (uni-wuerzburg.de)
It could be shown that recombinant muskelin assembles into a tetramer to which both interactions, the LisH-dimerization and the head-to-tail binding, contribute independently. (uni-wuerzburg.de)
We have determined that the association between the FMRP RGG box and Sc1 RNA is dominated by hydrophobic and hydrogen bond interactions, with minor contributions from electrostatic interactions, and that the FMRP RGG box binding increases the stability of the G quartet RNA structure significantly. (auckland.ac.nz)
The structure resembles those of protein kinases featuring the catalytic, activation, and glycine-rich loop motifs and ATP-binding site. (northwestern.edu)
The C-terminal PDZ-binding motif of NleH2 provided bases for interaction with host proteins. (northwestern.edu)
The TRIM motif includes three zinc-binding domains - a RING, a B-box type 1 and a B-box type 2 - and a coiled-coil region. (fishersci.com)
The human GR is a modular protein composed of distinct regions illustrated in panel B in the image below, as follows: (1) The amino-terminal A/B region, also called immunogenic or N-terminal domain (NTD) and (2) the C, D, and E regions, which correspond to the DNA-binding domain, the hinge region, and the ligand-binding domain, respectively. (medscape.com)
The AF-1 plays an important role in the interaction of the receptor with molecules necessary for the initiation of transcription, such as coactivators, chromatin modulators, and basal transcription factors, including RNA polymerase II, TATA-binding protein (TBP), and a host of TBP-associated proteins (TAFIIs). (medscape.com)
Tyrosine phosphorylated regions in proteins function as specific binding sites for the SH2 domains containing cellular signalling proteins. (lu.se)
Binding of SH2 domains to their in vivo targets recruits the SH2 domain-containing protein to its proper signalling complex and thereby initiates or regulates downstream signalling cascades (reviewed in Schlessinger and Lemmon, 2003). (lu.se)
Supporting these findings, different SH2 domains have been shown to compete for same binding target in vivo (e.g. (lu.se)
Platelet activation allows binding of these proteins, which bridges adjacent platelets. (medscape.com)

addressed this question by studying yeast cells with genetic mutations affecting one or more of these proteins. (elifesciences.org)
These mutations allowed to investigate the interplay of these interactions during oligomerization. (uni-wuerzburg.de)
Scope includes mutations and abnormal protein expression. (cancerindex.org)

Specificity of p47phox SH3 domain interactions in NADPH oxidase assembly and activation. (eu.org)
The four residue extensions, which represent known specificity sequences of the target PDZ domains and cover both class I and II motifs, form intermolecular contacts in the expected manner for the interactions of PDZ domains with protein C termini for both classes. (rcsb.org)
Our results also indicate that the G quartet RNA recognition is not a general feature of the RGG box motif but rather carries some sequence, protein and/or RNA, specificity. (auckland.ac.nz)

29. Rämisch S, Lizatović R, André I. Automated de novo phasing and model building of coiled-coil proteins. (lu.se)

Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs), generated by SPO11 and accessory proteins (de Massy 2013 ). (springer.com)
Across every domain of life, polymerase holoenzyme accessory proteins play an integral role in achieving the extraordinary efficacy and accuracy of the replicative polymerase complex. (pasteur.fr)

This may involve significant role of "shank," named for SRC-homology (SH3) and multiple ankyrin repeat domains, in nitric oxide synthesis. (frontiersin.org)
The FH2 (formin homology 2) domain is the defining feature of all formins. (biomedcentral.com)
In most fungal and metazoan formins the FH1-FH2 core is accompanied by a less well conserved N-terminal FH3 (formin homology 3) domain involved in targeting [ 14 ]. (biomedcentral.com)

ForC lacks a FH1 domain, ForI lacks recognizable GBD/FH3 and DAD domains and ForA, E and J have additional unique domains. (biomedcentral.com)

ZASP interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. (wikipedia.org)
This protein also interacts with all three members of the myozenin family. (wikipedia.org)
In S. cerevisiae , this interaction is at least in part provided by Spp1 that directly interacts with both methylated H3K4 near DSB sites and the axis-localized protein Mer2 (Acquaviva et al. (springer.com)
Meltrin alpha cytoplasmic domain interacts with SH3 domains of Src and Grb2 and is phosphorylated by v-Src. (eu.org)
In the Fip1 protein that is a component of a yeast pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase. (nih.gov)

The protein is a member of the tripartite motif (TRIM) family. (fishersci.com)
Tripartite Motif Containing 13 (TRIM13), a member of TRIM proteins, is deleted in multiple tumor types, especially in B-cell chronic lymphocytic leukemia and multiple myeloma. (cancerindex.org)

DSB sites are preferentially located within chromatin loops, while several proteins that are required for DSB formation (Rec114, Mei4, and Mer2) localize on the chromosome axis (Blat et al. (springer.com)

Processive phosphorylation of p130Cas by Src depends on SH3-polyproline interactions. (eu.org)
Phosphorylation of residue Y515 promotes association of TrkB with the adaptor protein Shc and activation of PI3-kinase (PI3K)/Akt, MAPK signaling pathways whereas phosphorylation of residue Y816 promotes association of phospholipase Cγ1 (PLCγ1) and signaling mediated by IP3 and DAG ( Reichardt, 2006 ). (jneurosci.org)
AE1 and NBCe1), and (iii) may provide sites for regulation of transporter function via protein kinase A phosphorylation (e.g. (tcdb.org)

Genetic disruption of TrkB-Shc signaling had no effect on severity of SE yet partially inhibited activation of the prosurvival adaptor protein Akt. (jneurosci.org)
Mounting evidence suggests that the genetic disorders/mutation and diseases change not only the protein expression patterns but also membranes themselves. (lu.se)

PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain. (springer.com)
The heterochromatin-enriched HP1 proteins play a critical role in regulation of transcription. (cipsm.de)
Previous studies have indicated that KIN17 is involved in global genome repair, DNA replication, transcription and regulation of the cell cycle as part of a multi-protein complex. (spandidos-publications.com)
The CDK4-cyclinD complex normally phosphorylates the retinoblastoma protein (Rb protein), leading to release of the E2F transcription factor and cell cycle progression. (medscape.com)

They occur in a large number of functionally diverse proteins mainly from eukaryotes. (embl.de)
All the analysed SH2 domains have a typical SH2 domain fold consisting of a large anti-parallel β-sheet sandwiched between two α-helices The central β-sheet divides the domain into two functionally separate sides. (lu.se)

This Special Issue, "Plant Cell Wall Proteins and Development", will cover a selection of recent research topics in the field of cell wall biology focused on cell wall proteins and their roles during development. (mdpi.com)
2007). These proteins are important for the regulation of intracellular pH (pH i ) and play crucial roles in the epithelial absorption of HCO 3 - (e.g., in the renal proximal tubule) and secretion of HCO 3 - (e.g., in the pancreatic duct). (tcdb.org)

TcMYC2a was also found to bind with TcJAZ3 in yeast, which was a homolog of Arabidopsis JASMONATE ZIM-domain JAZ proteins, indicating that TcMYC2a had a similar function to AtMYC2 of JA signal transduction. (frontiersin.org)

We found that TRIM13 mRNA and protein expression was reduced in NSCLC tissues and cell lines in comparison to paired non-cancerous tissues and a human normal bronchial epithelial cell line, respectively. (cancerindex.org)
Alternative splicing of the primary transcript gives rise to the 2 mRNA and protein isoforms, hGR-alpha and hGR-beta. (medscape.com)

ACBP4 and ACBP5 show conservation in a domain of five kelch motifs, which also enable interaction with protein partners. (aocs.org)

and the four long isoforms have three C-terminal LIM domains. (wikipedia.org)

The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. (embl.de)

Two critical functions of IE1 are inhibition of SUMOylation of Promyelocytic leukemia protein (PML) and transactivation of viral promoters. (ncbs.res.in)
Here we demonstrate that the sterile-alpha motif (SAM) domain of Smaug functions as an RNA-recognition domain. (embl.de)
The C-terminal RGS-RGG (Arg-Gly-Ser-Arg-Gly-Gly) motif modulates DDX5-specific biological functions through its interaction with RNA and DDX3. (bellbrooklabs.com)
The functions of NSEEE, NLS1, NLS2, and conserved WR motifs are poorly understood at present. (uni-marburg.de)

Here, we show that truncation of the KRAB domain of mouse PRDM9 leads to loss of PRDM9 function and altered meiotic prophase and gametogenesis. (springer.com)

This is a PFAM domain. (embl.de)

These methods dramatically increase the likelihood of producing proteins that cannot fold or assemble appropriately. (cipsm.de)
The frameshift mutation results in the formation of a truncated protein which cannot fold properly, promoting aggregation, and subsequent deposition in tubular cells. (medscape.com)

This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologues. (embl.de)
Structures of a significant number of SH2 domains both in isolation and bound to various target molecules have been determined by X-ray crystallography and NMR spectroscopy. (lu.se)
20. Sgourakis NG, Lange OF, DiMaio F, André I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D. Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings. (lu.se)

Full length human recombinant protein of human LIMK1 produced in HEK293T cell. (thermofisher.com)

Here, TcMYC2a was identified to contain a basic helix-loop-helix (bHLH)-leucine zipper domain, a bHLH-MYC_N domain, and a BIF/ACT-like domain. (frontiersin.org)
Evolutionary alignment of Twist proteins from different species, indicate TWIST contain 4 additional conserved regions such as NSEEE, NLS1, NLS2, and WR-domain besides the bHLH motif. (uni-marburg.de)
The bHLH domain is thought to be responsible for heterodimerization with other bHLH proteins such as E12 protein or SEF2 protein. (uni-marburg.de)

Anatomy15

Organisms13

Chemicals and Drugs88

Analytical, Diagnostic and Therapeutic Techniques and Equipment42

Phenomena and Processes88

Disciplines and Occupations4

Information Science15

Health Care2

Mediates5

Binds14

Residues15

Highly conserved3

Kinase domain3

Membrane24

Nuclear14

Structural9

Peptide6

Actin12

Subunit5

Transmembrane2

Proline-rich4

Regulate3

Cysteine-rich1

Escherichia3

Ribosomal proteins2

Eukaryotic2

Found in proteins involved1

Encodes a protein2

Gene14

Complexes1

Interact4

Affinity4

Functional5

Drosophila3

Myosin3

Mediate2

Amino acid5

Conformation3

Genes3

Transcriptional2

Regulatory1

Binding41

Mutations3

Specificity3

Coiled coil1

Accessory proteins2

Homology3

Recognizable1

Interacts5

Tripartite2

Chromatin1

Phosphorylation3

Genetic2

Transcription4

Functionally2

Roles2

Signal transduction1

MRNA and protein2

Kelch1

Isoforms1

Ankyrin repeat1

Functions4

KRAB1

PFAM1

Fold2

Structures3

Recombinant1

BHLH3