Structures calcium binding motif helix loop helix motifs. Medical search. Frequent questions

S100A10 is a member of the S100 family of proteins containing two EF-hand calcium-binding motifs. (wikipedia.org)
As a member of the S-100 family, its structure resembles that of the S-100A1 and S-100B proteins. (wikipedia.org)
Unlike other S-100 proteins, the second EF-hand of protein p11 is incapable of binding calcium due to a series of mutations caused by deletions and substitutions. (wikipedia.org)
P11 and annexin II form a heterotetrameric protein complex that imitates the structure and function of S-100 proteins activated by the binding of calcium. (wikipedia.org)
Complexed with the annexin II, p11 binds receptor and channel proteins and guides them to the cell surface, resulting in increased membrane localization and consequent magnified functional expression of these proteins. (wikipedia.org)
In this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structural motifs may be defined and searched for in large protein structure databases, and we show that common structural motifs involved in stabilizing protein folds are present in evolutionarily and structurally unrelated proteins, also in deeply buried locations which are not obviously related to protein function. (biomedcentral.com)
The possibility to define custom motifs and search for their occurrence in other proteins permits the identification of recurrent arrangements of residues that could have structural implications. (biomedcentral.com)
The three-dimensional structure of proteins has been an extensively studied topic for several decades. (biomedcentral.com)
The main reason for our interest in general ( i.e. , sequentially non-contiguous) structural motifs, is the crucial role played by side-chains in the correct packing of proteins. (biomedcentral.com)
Calcium binding induces conformational transitions in calmodulin that make it specifically active to particular target proteins. (biomedcentral.com)
Ca 2+ binding alters CaM conformation (compare the structure of Ca 2+ -free CaM [ 18 ] in Figure 1A with that of fully Ca 2+ bound CaM [ 19 ] in Figure 1B ) and changes its affinity to target proteins. (biomedcentral.com)
The term 'motif' is also describes a consensus sequence of amino acids, i.e. a partial sequence common to a number of different proteins, which may or may not adopt similar conformations in the different proteins. (vigyansarovar.com)
These helix-turn-helix structure found in many proteins(transcription factors). (vigyansarovar.com)
Large number of prokaryotic repressors belong to the helix-turn-helix family of proteins. (vigyansarovar.com)
Unlike HTH proteins, the actual DNA-binding motif of the HLH proteins is a stretch of about 13 "basic" amino acids adjacent to the HLH whose main role is in protein dimerization. (vigyansarovar.com)
Results ISWI is certainly a RanGTP-dependent microtubule-binding proteins Previously, NLS-containing MAPs have been made by sequential purification of MAPs and importin-Cbinding protein, leading to the identification of the NLS-MAP, Xnf7 (Maresca et al. (researchensemble.com)
Even so, the bound small percentage that was eluted by high sodium still contained a sigificant number of protein (Fig. 1 A). Because ISWI is certainly a nuclear proteins that were reported to bind MTs (Trachtulcov et al. (researchensemble.com)
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 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)
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)
They share a common structure and signal through HETEROTRIMERIC G-PROTEINS. (lookformedical.com)
Eye proteins are the biological molecules that make up the various structures of the eye and are essential for its proper function. (lookformedical.com)
Since the last overview of sPLA 2 -binding proteins (sPLA 2 -BPs) 10 years ago, several important discoveries have occurred in this area. (ijbs.com)

Therefore, entire motif comprising the DNA-binding basic region and the HLH is termed bHLH . (vigyansarovar.com)
Most often, one helix is smaller in bHLH, and, because of the flexibility of the loop, helps in dimerization by folding and packing against another helix. (vigyansarovar.com)
PTF1 (Inorganic Phosphorus Starvation Induced Transcription Factor 1) is a member of bHLH (basic Helix Loop Helix) family of wheat regulating several genes during phosphorus starvation. (als-journal.com)
These transcriptional factors belong to the basic helix-loop-helix-leucine zipper (bHLH-LZ) transcription factor family and bind the E-box DNA motifs in the promoter regions of target genes to enhance transcription. (molcells.org)

Supersecondary structures or motifs, are simple and frequent combinations of the secondary structure with a specific geometric arrangement. (vigyansarovar.com)
Supersecondary structures can also be considered as an intermediate between secondary and tertiary structures. (vigyansarovar.com)
Recurring supersecondary structures characterized by 20 amino acids folding into two alpha helices connected by a non-helical "loop" segment. (lookformedical.com)

CaM-induced target dimerization has been reported as having another distinctly different binding mode. (biomedcentral.com)
The two amphipathic helices, particularly the highly conserved hydrophobic amino acids, are thought to mediate dimerization, which is a prerequisite to DNA binding. (vigyansarovar.com)
This hydrophobic region provides an area for dimerization, allowing the motifs to "zip" together. (vigyansarovar.com)

Helix-turn-helix (HTH) consists of two α-helices that constitutes of a right-handed three helical bundle with helices α 2 and α 3 arranged perpendicular to one another joined by a short strand of amino acids (figure below). (vigyansarovar.com)
The common feature of trihelix TFs in plants is that the DNA-binding domain contains three helical structures (helix-loop-helix-loop-helix). (biomedcentral.com)

Recognition of structural motifs, by comparison, is less well developed and much less frequently used, possibly due to a lack of easily accessible and easy to use software. (biomedcentral.com)
Our purpose in this paper is to present the mechanisms and facilities whereby structural motifs can be defined and searched for using the freely available and well established modelling tool Swiss-PdbViewer [ 26 ], and to present illustrative examples of the types of information that can be obtained by doing so. (biomedcentral.com)
In particular, the facilities for defining and searching for structural motifs now available in Swiss-PdbViewer include an interactive visual interface for defining structural motifs, and a machinery that is able to quickly search very large collections of structures for such motifs. (biomedcentral.com)
In this study, we adopt a structural systems biology approach and develop a mathematical model to investigate various types of cooperative calcium-calmodulin interactions. (biomedcentral.com)
The results of our analysis reduce the gap between current understanding of intracellular calmodulin function at the structural level and physiological calcium-dependent calmodulin target activation experiments. (biomedcentral.com)
DNA binding), and others can be the part of larger structural assemblies. (vigyansarovar.com)
The RPA gene is the structural excretion loss-of-function, However Binding it from the corresponding growth( De Laat et al. (evakoch.com)

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)

The structure of p11 is classified by a pair of the helix-loop-helix motif, also known as the EF-hand-type that recognizes and binds calcium ions. (wikipedia.org)
Our model predicts that the specificity and selectivity of CaM target regulation is likely to be due to the following factors: variations in the target-specific Ca 2+ dissociation and cooperatively effected dissociation constants, and variations in the number of Ca 2+ ions required to bind CaM for target activation. (biomedcentral.com)

In general, transcription factors including this domain are dimeric, each with one helix that contains basic amino acid residues facilitate DNA binding. (vigyansarovar.com)
The motif comprises two α helices, E and F that flank a loop of 12 contiguous residues. (vigyansarovar.com)
Five of the loop residues should contain an oxygen atom and preferably be aspartate or glutamate, as they act as calcium ligands (Figure below). (vigyansarovar.com)
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)

Helix loop helix are eukaryotic homolog of the HTH motif and are characterized by two ampipathic α -helices (60-90 amino acids) connected by a loop (10-25 amino acids). (vigyansarovar.com)
The eukaryotic HLH is physically larger than the prokaryotic counterpart HTH motif. (vigyansarovar.com)
The human pathogen Mycoplasma genitalium , a member of the pneumoniae cluster of mycoplasmas, binds to eukaryotic cells by means of its adhesion complex, the Nap. (nature.com)
We determined subnanometer-resolution cryo-electron microscopy structures of eukaryotic ribosome-Sec61 complexes. (cipsm.de)

The best known canonical binding mode of CaM interaction with a target is the "wrap-around" in which both N - and C -terminal domains of CaM bind to the same target protein region. (biomedcentral.com)

Finally, to our knowledge, the presented structure-search machinery is the only one to permit arbitrary combinations of amino-acid-type constraints, secondary structure constraints, distance constraints, and sequence separation constraints. (biomedcentral.com)

Both crystal structures and the cryo-EM structure are found in a closed conformation, where the sialic acid binding site in P110 is occluded. (nature.com)
The cryo-EM structure of the endocytic receptor DEC-205. (uci.edu)
Here we describe the 3.2 Å cryo-EM structure of human DEC-205, thereby illuminating the structure of the mannose receptor protein family. (uci.edu)
We establish a pH dependant oligomerisation pathway forming tetrameric DEC-205 using solution-based techniques and ultimately solved the 4.9 Å cryo-EM structure of the DEC-205 tetramer to identify the unfurling of the second lectin ring which enables tetramer formation. (uci.edu)

Given a network motif structure representing a specific biological function in one cell type or species, this approach utilized a comparative modeling strategy to connect it with other network motifs which are evolutionarily related to each other. (biomedcentral.com)

Today, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. (biomedcentral.com)
α 3 is recognition helix that binds to DNA major groove through a series of hydrogen bonds and various Vander wall forces with exposed bases. (vigyansarovar.com)
Its major function is in DNA recognition, as α 3 helix is involved in the recognition and is known as " recognization helix " while another one stabilizes the interaction between DNA and Protein. (vigyansarovar.com)
Here we demonstrate that the sterile-alpha motif (SAM) domain of Smaug functions as an RNA-recognition domain. (embl.de)

The genes were selected on thorough literature review and on the basis of presence of more than one G-box (Binding motif of PTF1) in their promoter regions. (als-journal.com)

The p11 monomer is an asymmetric protein composed of four alpha helices. (wikipedia.org)

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)

Abnormal number or structure of chromosomes. (lookformedical.com)
2008). Both TPX2 and CDK11 are inhibited with AT7519 Pdgfb the importin-/ heterodimer in the mitotic cytoplasm and released from it when RanGTP binds to importin- around chromosomes. (researchensemble.com)

A family of G-protein-coupled receptors that was originally identified by its ability to bind N-formyl peptides such as N-FORMYLMETHIONINE LEUCYL-PHENYLALANINE. (lookformedical.com)

A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. (lookformedical.com)
Thermal stability assays show that ERKi do not destabilise ERK2 (or ERK1) in vitro, suggesting that ERK2 turnover is a cellular consequence of ERKi binding. (babraham.ac.uk)

By contrast, the cryo-ET structure shows an open conformation, where the binding site is accessible. (nature.com)

DEC-205 (CD205), a member of the macrophage mannose receptor protein family, is the prototypic endocytic receptor of dendritic cells, whose ligands include phosphorothioated cytosine-guanosine (CpG) oligonucleotides, a motif often seen in bacterial or viral DNA. (uci.edu)
Using this framework to analyze the SM (Sec1/Munc18)-SNARE ( N -ethylmaleimide-sensitive factor activating protein receptor) system in exocytic membrane fusion in yeast and neurons, we find that the SM-SNARE network motifs of yeast and neurons show distinct dynamical behaviors. (biomedcentral.com)

The dimerized form of the protein is created by packing between the H1 and H4 helices in an antiparallel arrangement with the hydrophobic regions residing in the core. (wikipedia.org)
Finally, a number of side chains form a hydrophobic core between the α helices and thus must be hydrophobic. (vigyansarovar.com)
Amphipathic α-helix - consists of hydrophobic region due to leucine and hydrophilic amino acids outside. (vigyansarovar.com)
Furthermore, the hydrophobic leucine region is absolutely required for DNA binding. (vigyansarovar.com)

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)
Descriptors are arranged in a hierarchical structure, which enables searching at various levels of specificity. (wakehealth.edu)
Structures of macromolecular drug targets, especially when bound to modulators, can reveal ligand-binding pockets and pinpoint protein-ligand interactions that influence the mechanism of action, potency, and specificity. (silverchair.com)

Recently, we determined the crystal structure of the extracellular region of P110 and demonstrated its binding to sialic acid receptors 6 . (nature.com)
The 3' replication has freely activated by RNase Z surface, a mature binding in receptors( reviewed in Maraia and Lamichhane 2011). (evakoch.com)

We identify the closed binding mode of neuronal SM (Munc18-1) and SNARE (syntaxin-1) as the key factor leading to mechanistic divergence of membrane fusion systems in yeast and neurons. (biomedcentral.com)

The four helix-loop-helix EF-hand Ca 2+ -binding sites (shown in different colours in Figure 1C ) are also capable of binding intracellular calcium's physiologically inactive competitor Mg 2+ (Figure 1D ) [ 20 , 21 ]. (biomedcentral.com)
We demonstrate here that the LRRC8C-LRRC8A(IL1 25 ) chimera comprising LRRC8C and 25 amino acids unique to the first intracellular loop (IL1) of LRRC8A has a heptameric structure like that of homologous pannexin channels. (elifesciences.org)

The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. (embl.de)

However, these channels are either non-functional or exhibit abnormal regulation and pharmacology, limiting their utility for structure-function analyses. (elifesciences.org)
Small recurring subnetworks that perform specific cellular subfunctions (termed network motifs) are largely reused to build the functional modules. (biomedcentral.com)

Leucine zipper motifs are usually found as part of a DNA-binding domain in many transcription factors , and are therefore these motifs are involved in regulating gene expression . (vigyansarovar.com)
The primary function of the TFs (Transcription Factors) is to regulate gene expression by binding to cis -element. (als-journal.com)

More than fifty years ago, Pauling and Corey described the two dominant forms of secondary structure, the α-helix and the β-sheet [ 1 ]. (biomedcentral.com)

The DEC-205 monomer forms a compact structure comprising two intercalated rings of C-type lectin-like domains, where the N-terminal cysteine-rich and fibronectin domains reside at the central intersection. (uci.edu)

The experimental approach of network motif identification is extensively applied for modeling specific cellular processes [ 8 ]. (biomedcentral.com)

The X-ray structure of the casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. (elifesciences.org)

b Network of hydrogen bonds in the vicinity of the oligosaccharide-binding site between P140 (blue) and P110N (yellow). (nature.com)

Knowledge of the three-dimensional structures of the carbo-hydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein-carbohydrate interactions. (iucr.org)

With numerous illustrations and tables, each of the nearly 300 sections of the Guide describes genes involved in a specific pathway, process, or structure from the molecular and cellular levels to developmental and physiological processes. (cshlpress.com)
Network motifs, recurring subnetwork patterns, provide significant insight into the biological networks which are believed to govern cellular processes. (biomedcentral.com)

This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures. (iucr.org)

Subsequently, a variety of further patterns and regularities ( e.g. , [ 2 - 4 ]) in protein structures have been found, that have proven useful in the context of protein structure determination and quality assessment of determined structures. (biomedcentral.com)

S100 calcium-binding protein A10 (S100A10), also known as p11, is a protein that is encoded by the S100A10 gene in humans and the S100a10 gene in other species. (wikipedia.org)
However, whereas studies have mainly focused on modeling or analysis of topological or kinetic features of network motifs in a single cell type or species, network motifs can be used to reflect dynamical and evolutionary adaptations to meet physiological variances over a time course. (biomedcentral.com)

Now, eight transporters were found to control the uptake and efflux of calcium. (mdpi.com)
The first difference is found in the primary structures. (iucr.org)
Recently, Np95 (also known as UHRF1 or ICBP90) has been found to interact with Dnmt1 and to bind hemimethylated DNA, indicating together with genetic studies a central role in the maintenance of DNA methylation. (cipsm.de)

Residue 6 of the loop must be a glycine because the side chain of any other residue would disturb the structure of the motif. (vigyansarovar.com)
Glycine max is a calcium-loving crop. (mdpi.com)

Here we report the crystal structure of P140 both alone and in complex with the N-terminal domain of P110. (nature.com)
a P140 contains a large N-terminal domain and a smaller C-terminal domain, which is followed in sequence by a predicted transmembrane helix. (nature.com)
This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologues. (embl.de)
These results suggest that the SAM domain might have a primary role in RNA binding. (embl.de)
In addition, the subfamilies have only one DNA-binding domain, except the GT-2 subfamily, which contains two DNA-binding domains [ 6 ]. (biomedcentral.com)
The chromo-domain binds histone H3 tails methylated on lysine 9. (cipsm.de)

Some of these motifs are associated with a particular defined function (e.g. (vigyansarovar.com)
Structure-function studies of VRAC/LRRC8 heteromeric channels are complicated by their undefined, likely variable, and experimentally uncontrollable stoichiometry. (elifesciences.org)

In agreement with this, recent findings on the structure and post-translational modifications of PP2A emphasize the importance of PP2A holoenzyme composition in its regulation and pleiotropic activities. (ac.be)
3 This article will review the recent advances in the structure and regulation of this fascinating enzyme. (ac.be)
Our findings provide new insights into VRAC/LRRC8 channel structure and suggest that lipids may play important roles in channel gating and regulation. (elifesciences.org)

a X-ray crystal structure of the P140-P110N heterodimer. (nature.com)

heme and calcium targets are leading with example unique to particles for distinctive PTEN, higher metabolism, specific mechanism, T dislocations, more protein or hydrogen. (erik-mill.de)

The precise mechanisms underlying calcium binding to calmodulin are still, however, quite poorly understood. (biomedcentral.com)
We compare the predictions of our analysis with physiological dose-response curves taken from the literature, in order to provide a quantitative comparison of the effects of different mechanisms of cooperativity on calcium-calmodulin interactions. (biomedcentral.com)

A variation of the wrap-around CaM binding interaction has been shown to occur with the brain specific PKC substrate CAP-23/NAP-22 [ 23 ]. (biomedcentral.com)
Helix-turn-helix motif are involved in many processes that includes DNA repair, RNA metabolism, and protein-protein interaction . (vigyansarovar.com)

We present a comparative network motif experimental approach, which helps to explain complex biological phenomena and increases the understanding of biological functions at the molecular level by exploring evolutionary design principles of network motifs. (biomedcentral.com)
The evolutionary dynamics of biological processes shape the network structure over large time scales. (biomedcentral.com)

Sterile alpha motif. (embl.de)

The structure of P140, for which there are no molecular models or experimental phases available, was determined by density modification techniques, starting with a mask derived from the sub-tomogram-averaged map of the whole Nap obtained by cryo-electron tomography (cryo-ET) (see Methods). (nature.com)

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