Proteins protein interaction domains and motifs. Medical search. Frequent questions

The nucleation-enhancing activity of Bud6 requires both a "core" domain that binds to the formin and a "flank" domain that binds monomeric actin. (nih.gov)
one binds in a groove at the barbed end of the actin monomer in a manner closely resembling the helix of WH2 domains, a motif found in many actin nucleation factors. (nih.gov)
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)
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)

Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. (embl.de)
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)

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)
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)

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)
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)
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)

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)
Members of this family also possess highly conserved ATPase and helicase domains, flanked by individually distinctive N and/or C-terminal motifs. (bellbrooklabs.com)

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)
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)
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)
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)

In budding yeast, the actin-binding protein Bud6 cooperates with formins Bni1 and Bnr1 to catalyze the assembly of actin filaments. (nih.gov)
Here, we describe the structure of the Bud6 flank domain in complex with actin. (nih.gov)
The Bud6 binding site on actin overlaps with that of the formin FH2 domain and is also incompatible with inter-subunit contacts in F-actin, suggesting that Bud6 interacts only transiently with actin monomers during filament nucleation. (nih.gov)
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)
For example, shank proteins are located further away from the membrane in the cytosolic faces of the PSDs, facing the actin cytoskeleton. (frontiersin.org)
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)

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)

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)
The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. (cipsm.de)
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)
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)
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)

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)

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)

As CXXC1 is orthologous to Saccharomyces cerevisiae Spp1 that links DSB sites to the DSB machinery on the chromosome axis, we propose that these molecular interactions involved in the regulation of meiotic DSB formation are conserved in mouse meiosis. (springer.com)
The substituted amino acid is located within the second C2HC motif in the conserved zinc finger domain of NANOS3 and in silico molecular modelling suggests destabilization of protein-RNA interaction. (hindawi.com)
This structure unveils the molecular basis for the interaction and cooperativity between the whole replicative polymerase and PCNA with an unprecedented level of detail. (pasteur.fr)
In addition, the crystal structure revealed the molecular composition of the surface of the head in the head-to-tail interaction, namely the discoidin domain. (uni-wuerzburg.de)

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)
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)
The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation. (embl.de)
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)
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)

A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta, KRAB-A interacting protein and tripartite motif protein 28). (embl.de)
The protein is a member of the tripartite motif (TRIM) family. (fishersci.com)

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)

Identification of two SH3-binding motifs in the regulatory subunit of phosphatidylinositol 3-kinase. (eu.org)
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)

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)
PDZ domains are protein-protein interaction modules that generally bind to the C termini of their target proteins. (rcsb.org)
The presence of a conserved acyl-CoA-binding domain in each ACBP enables it to bind acyl-CoA esters. (aocs.org)
Protein-protein interaction networks: how can a hub protein bind so many different partners? (tau.ac.il)
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)

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)

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

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)
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)
Like Rb protein, many of the proteins encoded by tumor suppressor genes act at specific points in the cell cycle. (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)
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)

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)
The C-terminal four amino acids of a prospective binding partner of a PDZ domain are typically the determinants of binding specificity. (rcsb.org)
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)
The NTD of the hGRα contains a major transactivation domain, termed activation function (AF)-1, which is located between amino acids 77 and 262 of the hGRα and is ligand-independent. (medscape.com)

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)
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)
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)
B) Functional domains of the hGR-alpha. (medscape.com)
The functional domains and subdomains are indicated beneath the linearized protein structures. (medscape.com)
[ 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)

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)

The identification of an inactivating missense mutation in NANOS3 suggests a mechanism for POI involving increased primordial germ cells (PGCs) apoptosis during embryonic cell migration and highlights the importance of NANOS proteins in human ovarian biology. (hindawi.com)
Mounting evidence suggests that the genetic disorders/mutation and diseases change not only the protein expression patterns but also membranes themselves. (lu.se)
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)

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)

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

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 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)
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)
The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II and III promoters, binding and splicing of RNA, and control of nucleolus function. (embl.de)
The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. (embl.de)
Repression of transcriptional activity by heterologous KRAB domains present in zinc finger proteins. (embl.de)

Our Bayesian framework may also result in more accurate statistical potentials for additional modeling applications, thus affording better leverage of the experimentally determined protein structures. (nih.gov)
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)
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)
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)

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)
Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. (embl.de)
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)
29. Rämisch S, Lizatović R, André I. Automated de novo phasing and model building of coiled-coil proteins. (lu.se)

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)
KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. (embl.de)
We report the characterization of three novel members of the KRAB-domain containing C2-H2 zinc finger family (ZNF133, 136 and 140). (embl.de)
KRAB (Kruppel-associated box) is an evolutionarily conserved protein domain found N-terminally with respect to the zinc finger repeats that encodes the DNA binding domain. (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)

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)
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)
the E-value for the KRAB domain shown below is 8.06e-19. (embl.de)
The KRAB domain is generally encoded by two exons. (embl.de)
A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. (embl.de)
The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. (embl.de)
There are 50777 KRAB domains in 49028 proteins in SMART's nrdb database. (embl.de)
Taxonomic distribution of proteins containing KRAB domain. (embl.de)
The complete taxonomic breakdown of all proteins with KRAB domain is also avaliable . (embl.de)
Click on the protein counts, or double click on taxonomic names to display all proteins containing KRAB domain in the selected taxonomic class. (embl.de)

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)
addressed this question by studying yeast cells with genetic mutations affecting one or more of these proteins. (elifesciences.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)

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)

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)

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)

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 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)
This may involve significant role of "shank," named for SRC-homology (SH3) and multiple ankyrin repeat domains, in nitric oxide synthesis. (frontiersin.org)

This locus, however, also encodes a protein from an alternative reading frame, designated p19ARF. (medscape.com)

Meltrin alpha cytoplasmic domain interacts with SH3 domains of Src and Grb2 and is phosphorylated by v-Src. (eu.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)

Evidence for SH3 domain directed binding and phosphorylation of Sam68 by Src. (eu.org)
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)

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)

Consequently, motif quality is a major determinant of mRNA stability for Puf3 targets in vivo and can be used for the prediction of mRNA targets. (elifesciences.org)
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 more mRNA copies it makes, the more protein it can produce. (elifesciences.org)
A simple way to control protein production is to raise or lower the number of these mRNA messages, and living cells have lots of ways to make this happen. (elifesciences.org)
The second screening of the yeast clones suggested some promising candidates protein as interacting partners with the NSEEE motif such as ETV5, SURF4, Spastin, Metalloproteinase 2, and ALR-like protein mRNA. (uni-marburg.de)
Alternative splicing of the primary transcript gives rise to the 2 mRNA and protein isoforms, hGR-alpha and hGR-beta. (medscape.com)

These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. (embl.de)
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)

The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [ ( PUBMED:9007998 ) ] involved in many biological processes. (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)

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)
RNA-binding proteins contribute to specificity by interacting with both Ccr4-Not and target mRNAs, but this is not fully understood. (elifesciences.org)

The present study was thus undertaken to determine how TWIST1 gene mutations affect protein function. (uni-marburg.de)
These mutations allowed to investigate the interplay of these interactions during oligomerization. (uni-wuerzburg.de)

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

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

Statistical potentials have been widely used for modeling whole proteins and their parts (e.g. sidechains and loops) as well as interactions between proteins, nucleic acids and small molecules. (nih.gov)

Association of p62, a multifunctional SH2- and SH3-domain-binding protein, with src family tyrosine kinases, Grb2, and phospholipase C gamma-1. (eu.org)
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)

Tyrosine phosphorylated regions in proteins function as specific binding sites for the SH2 domains containing cellular signalling proteins. (lu.se)

Anatomy15

Organisms13

Chemicals and Drugs88

Analytical, Diagnostic and Therapeutic Techniques and Equipment42

Phenomena and Processes88

Disciplines and Occupations4

Information Science15

Health Care2

Binds15

Mediates3

Residues14

Escherichia4

Highly conserved2

Nuclear14

Actin16

Conformation3

Membrane18

Structural9

Eukaryotic2

Molecular4

Chromatin5

Tripartite motif2

Proline-rich4

Subunit4

Bind5

Ribosomal proteins2

Found in proteins involved1

Genes3

Affinity3

Regulate2

Amino acids4

Functional6

Drosophila3

Myosin3

Mutation3

Interact4

Regulatory1

Complexes1

Transcriptional6

Structures6

Coiled coil4

Zinc5

KRAB10

Genetic2

Cerevisiae1

Transmembrane2

Transcription factors1

Accessory proteins2

Homology5

Encodes1

Cytoplasmic domain2

Phosphorylation4

Mediate1

MRNA6

Roles3

Biological2

Specificity3

Mutations2

Kelch2

Isoforms1

Loops1

Tyrosine kinases2

Binding Sites1