• 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)
  • Calcium binding proteins like parvalbumin play a role in many physiological processes, namely cell-cycle regulation, second messenger production, muscle contraction, organization of microtubules and phototransduction. (wikipedia.org)
  • Therefore, calcium-binding proteins must distinguish calcium in the presence of high concentrations of other metal ions. (wikipedia.org)
  • 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 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 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)
  • The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. (embl.de)
  • Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w. (embl.de)
  • Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1). (embl.de)
  • 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)
  • Chances are that a assortment of brand-new ligands will emerge because high-throughput assays have already been developed to display screen for peptides that bind selectively to different conformations of G proteins subunits [50] or focus on the user interface with a particular subset of RGS protein [51]. (biotechpatents.org)
  • 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)
  • 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)
  • The RPA gene is the structural excretion loss-of-function, However Binding it from the corresponding growth( De Laat et al. (evakoch.com)
  • Lots of the known endogenous ligands have already been examined and common structural binding motifs have already been discovered [18 thoroughly, 52, 53]. (biotechpatents.org)
  • The primary structural motif discovered is the convert [18]. (biotechpatents.org)
  • A common structural feature of GPCRs is the presence of a highly conserved architecture of seven stretches of transmembrane spanning residues linked by alternate extracellular and intracellular loops. (biomedcentral.com)
  • Here we uncover structural motifs required for ceramide interaction with the four membrane spanning Lysosome Associated Protein Transmembrane 4B (LAPTM4B). (sphingolipidclub.com)
  • Parvalbumin (PV) is a calcium-binding protein with low molecular weight (typically 9-11 kDa). (wikipedia.org)
  • Parvalbumin is a small, stable protein containing EF-hand type calcium binding sites. (wikipedia.org)
  • Typically, this protein is broken into three domains, domains AB, CD and EF, each individually containing a helix-loop-helix motif. (wikipedia.org)
  • Other calcium-binding protein markers are calretinin (most abundant subtype in DLPFC, about 50%) and calbindin. (wikipedia.org)
  • The Ca2+ ions bind to troponin, what causes the displacement of tropomyosin, a protein that prevents myosin walking along actin. (wikipedia.org)
  • In the closed conformation, HEAT/ARM core domains shield the GTPase-activating protein-related domain (GRD) so that Ras binding is sterically inhibited. (nature.com)
  • 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)
  • The apo (1DMO [18]) (A) and Ca 2+ bound (1CLL [19]) (B) structures of the CaM protein illustrate Ca 2+ induced conformational transitions. (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)
  • Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac. (embl.de)
  • 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)
  • Arrestin quenches G-protein activation by binding to phosphorylated photolyzed rhodopsin. (lookformedical.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)
  • It is disclosed herein that the HIV-1 envelope protein gp120 binds to α4β7 integrin on CD4+ T-cells, natural killer (NK) cells and CD8+ T-cells. (justia.com)
  • A straight richer way to obtain recognition motifs are available at the supplementary structure level, especially considering that details content in protein/peptides is normally evolutionary even more conserved through threedimensional buildings instead of through linear amino acidity sequences [55]. (biotechpatents.org)
  • 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)
  • The receptors contain seven transmembrane-spanning Chelices, with an extracellular N-terminus, an intracellular C-terminus and 3 interhelical loops about each family member part from the membrane [1C3]. (biotechpatents.org)
  • The diversity among GPCRs primarily stem from the presence of characteristic N-terminal extracellular domains and C-terminal intracellular domains and to a relatively lesser extent from the connecting loops which share limited sequence similarity. (biomedcentral.com)
  • Identification of convert motifs generally just involves interactions from the spatially-orientated aspect chain residues from the ligand using the receptor plus they can as a result be looked at as scaffolds, that could theoretically end up being substituted by choice rigid (+)-Camphor non-peptidic scaffolds that keep up with the useful aspect chains in the proper conformation. (biotechpatents.org)
  • In the sequence below, a conserved 5'-CGCA motif at the 5'-end of the TSD is underlined. (elifesciences.org)
  • YOs) through binding a yet uncharacterized GPCR, which triggers a signalling cascade, leading to inhibition of the ecdysis sequence. (biomedcentral.com)
  • In several examples, the α4 integrin antagonist is a monoclonal antibody that specifically binds to a α4, β1 or β7 integrin subunit or a cyclic hexapeptide with the amino acid sequence of CWLDVC. (justia.com)
  • It has three EF hand motifs and is structurally related to calmodulin and troponin C. Parvalbumin is found in fast-contracting muscles, where its levels are highest, as well as in the brain and some endocrine tissues. (wikipedia.org)
  • 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)
  • Several convert buildings are located to become stabilized by cyclic loop and band moieties, in particular regarding smaller and even more flexible peptides that want conformational stabilization to keep a rigid threedimensional framework. (biotechpatents.org)
  • Along with Ca2+ pumps, PV contributes to Ca2+ removal from cytoplasm: PV binds to Ca2+ ions in the sarcoplasm, and then shuttles it to the sarcoplasmic reticulum. (wikipedia.org)
  • Accordingly, Syntaxin-1 and Synaptobrevin-2 each contribute one and SNAP25 contributes two alpha-helices to the ternary SNARE complex. (nature.com)
  • SPRED1 recruits Nf1 from the cytosol to the plasma membrane where Ras resides, and Nf1 subsequently can downregulate GTP-bound Ras 14 . (nature.com)
  • Zippering of the SNAREs is proposed to provide the required energy to initiate membrane fusion 6 , 7 and proceeds from the N-terminus towards the membrane-proximal C-terminus through interactions of their complementary SNARE motifs. (nature.com)
  • Phosphatidylserine-exposing platelets, usually located around a thrombus, provide a negatively charged membrane surface, which supports coagulation factor binding and the formation of tenase and prothrombinase complexes ( 6 , 7 ). (frontiersin.org)
  • loop kappa p21 D cell 4( ABCD4) is shown to reduce the CD127 performance of cobalamin( Cbl membrane parking B12) into the mitochondrion, interacting it ED for the composition of Cbl lives. (evakoch.com)
  • 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)
  • sPLA 2 s contain 6 to 8 disulphide bonds, a highly conserved His/Asp catalytic dyad, and a Ca 2+ -binding loop [ 1 ]. (ijbs.com)
  • The analysis of the CaM structures in apo and Ca 2+ bound conformations as well as in complex with the target PKII molecule . (biomedcentral.com)
  • The AB domain houses a two amino-acid deletion in the loop region, whereas domains CD and EF contain the N-terminal and C-terminal, respectively. (wikipedia.org)
  • Zn incubation of Nf1 leads to reduced Ras-GAP activity with both protomers in the self-inhibited, closed conformation stabilized by a Zn binding site between the N-HEAT/ARM domain and the GRD-Sec14-PH linker. (nature.com)
  • Contrasting an unpublished low-resolution, symmetric Nf1 model 15 , two distinct populations of the Nf1-23a dimer are present: (1) a major population with both protomers showing a closed, auto-inhibited conformation (closed Nf1 state) stabilized by Zn and (2) a second population (open Nf1 state) with one protomer in the auto-inhibited conformation and the other protomer in an open configuration necessary for Ras binding (Fig. 1d ). (nature.com)
  • Carboxyl-terminal domain III of the delta' subunit of the DNA polymerase III holoenzyme binds delta. (colorado.edu)
  • The 3' replication has freely activated by RNase Z surface, a mature binding in receptors( reviewed in Maraia and Lamichhane 2011). (evakoch.com)
  • Characterization of DNA binding, transcriptional activation, and regulated nuclear association of recombinant human NFATp. (colorado.edu)
  • 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)
  • Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. (embl.de)
  • As a core metal ion in signaling transduction, calcium content is maintained in dynamic balance under normal circumstances. (mdpi.com)
  • The loops connecting the beta-strands differ greatly in length, making the PH domain relatively difficult to detect. (embl.de)
  • The chromo-domain binds histone H3 tails methylated on lysine 9. (cipsm.de)
  • 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)
  • All known cases have a common structure consisting of two perpendicular anti-parallel beta sheets, followed by a C-terminal amphipathic helix. (embl.de)
  • 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)
  • This function is associated with PV role in calcium sequestration. (wikipedia.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)
  • There are two globular domains in CaM, each containing a pair of helix-loop-helix Ca 2+ -binding motifs called EF-hands (Figure 1A , Figure 1B ). (biomedcentral.com)
  • Secreted phospholipases A 2 (sPLA 2 s) (EC 3.1.1.4) are a structurally related group of low-molecular-mass enzymes (14-18 kDa) that catalyse the hydrolysis of glycerophospholipids (phospholipids hereafter) at their sn -2 position, to produce lysophospholipids and free fatty acids. (ijbs.com)
  • The displacement of tropomyosin exposes the myosin-binding sites on actin, permitting muscle contraction. (wikipedia.org)
  • Now, eight transporters were found to control the uptake and efflux of calcium. (mdpi.com)
  • Though these calcium transporters have been identified through genome-wide analysis, only a few of them were functionally verified. (mdpi.com)
  • The process of thrombus formation is considered to be initiated by von Willebrand factor (VWF) binding to exposed collagen or laminin in the damaged vessel wall, followed by shear-dependent platelet binding to VWF through the glycoprotein (GP)Ib-V-IX complex ( 1 , 3 , 4 ). (frontiersin.org)