P120-Ras GTPase activating protein (RasGAP): A multi-interacting protein in downstream signaling

p120-RasGAP (Ras GTPase activating protein) plays a key role in the regulation of Ras-GTP bound by promoting GTP hydrolysis via its C-terminal catalytic domain. The p120-RasGAP N-terminal part contains two SH2, SH3, PH (pleckstrin homology) and CaLB/C2 (calcium-dependent phospholipid-binding domain) domains. These protein domains allow various functions, such as anti-/pro-apoptosis, proliferation and also cell migration depending of their distinct partners. The p120-RasGAP domain participates in protein–protein interactions with Akt, Aurora or RhoGAP to regulate functions described bellow. Here, we summarize, in angiogenesis and cancer, the various functional roles played by p120-RasGAP domains and their effector partners in downstream signaling.     

Src homology domains of v-Src stabilize an active conformation of the tyrosine kinase catalytic domain

To examine the interactions between Src homology,domains and the tyrosine kinase catalytic domain of v-Src, various combinations of domains have been expressed in bacteria as fusion proteins. Constructs containing the isolated catalytic domain, SH2 + catalytic domain, and SH3 + SH2 + catalytic domains were active in autophosphorylation assays. For the catalytic domain of v-Src, but not for v-Abl, addition of exogenous Src SH3-SH2 domains stimulated the autophosphorylation activity. In contrast to results for autophosphorylation, constructs containing Src homology domains were more active towards a synthetic peptide substrate than the isolated catalytic domain. The ability of the SH2 and SH3 domains of v-Src to stabilize an active enzyme conformation was also confirmed by refolding after denaturation in guanidinium hydrochloride. Collectively the data suggest that, in addition to their roles in intermolecular protein-protein interactions, the Src homology regions of v-Src exert a positive influence on tyrosine kinase function, potentially by maintaining an active conformation of the catalytic domain.     

Molecular Cloning and Chromosomal Localization of Human Salt-Tolerant Protein

We have isolated a novel human cDNA coding for human salt-tolerant protein (HSTP), that is a homologue of the rat salt-tolerant protein (STP) and may contribute to salt-induced hypertension by modulating renal cation transport. The nucleotide sequence (1988 bp) of the HSTP cDNA contains an open reading frame encoding a polypeptide comprising 545 amino acids, two residues fewer than the rat STP cDNA. The predicted amino acid sequence exhibits 92% identity to that of the rat protein. HSTP contains predicted coiled-coil domains and Src Homology 3 domain, and shows a high degree of identity to CIP4 (Cdc42 target protein) and human Trip 10 (thyroid-hormone receptor interacting protein). We have mapped the HSTPgene to human chromosome 19 by fluorescence in situhybridization. This revised version was published online in July 2006 with corrections to the Cover Date.     

A lack of peptide binding and decreased thermostability suggests that the CASKIN2 scaffolding protein SH3 domain may be vestigial

Background

CASKIN2 is a neuronal signaling scaffolding protein comprised of multiple ankyrin repeats, two SAM domains, and one SH3 domain. The CASKIN2 SH3 domain for an NMR structural determination because its peptide-binding cleft appeared to deviate from the repertoire of aromatic enriched amino acids that typically bind polyproline-rich sequences.

Results

The structure demonstrated that two non-canonical basic amino acids (K290/R319) in the binding cleft were accommodated well in the SH3 fold. An K290Y/R319W double mutant restoring the typical aromatic amino acids found in the binding cleft resulted in a 20 °C relative increase in the thermal stability. Considering the reduced stability, we speculated that the CASKIN2 SH3 could be a nonfunctional remnant in this scaffolding protein.

Conclusions

While the NMR structure demonstrates that the CASKIN2 SH3 domain is folded, its cleft has suffered two substitutions that prevent it from binding typical polyproline ligands. This observation led us to additionally survey and describe other SH3 domains in the Protein Data Bank that may have similarly lost their ability to promote protein-protein interactions.

     

Alternatingly twisted β-hairpins and nonglycine residues in the disallowed II′ region of the Ramachandran plot

The structure of the SH3 domain of α-spectrin (PDB code 1SHG) features Asn47 in the II′ area of the Ramachandran plot, which as a rule admits only glycine residues, and this phenomenon still awaits its explanation. Here, we undertook a computational study of this particular case by means of molecular dynamics and bioinformatics approaches. We found that the region of the SH3 domain in the vicinity of Asn47 remains relatively stable during denaturing molecular dynamics simulations of the entire domain and of its parts. This increased stability may be connected with the dynamic hydrogen bonding that is susceptible to targeted in silico mutations of Arg49. Bioinformatics analysis indicated that Asn47 is in the β-turn of a distinctive structural fragment we called ‘alternatingly twisted β-hairpin.’ Fragments of similar conformation are quite abundant in a nonredundant set of PDB chains and are distinguished from ordinary β-hairpins by some surplus of glycine in their β-turns, lack of certain interpeptide hydrogen bonds, and an increased chirality index. Thus, the disallowed conformation of residues other than glycine is realized in the β-turns of alternatingly twisted β-hairpins.     

Crystallographic structure of the SH3 domain of the human c-Yes tyrosine kinase: loop flexibility and amyloid aggregation

SH3 domains from the Src family of tyrosine kinases represent an interesting example of the delicate balance between promiscuity and specificity characteristic of proline-rich ligand recognition by SH3 domains. The development of inhibitors of therapeutic potential requires a good understanding of the molecular determinants of binding affinity and specificity and relies on the availability of high quality structural information. Here, we present the first high-resolution crystal structure of the SH3 domain of the c-Yes oncogen. Comparison with other SH3 domains from the Src family revealed significant deviations in the loop regions. In particular, the n-Src loop, highly flexible and partially disordered, is stabilized in an unusual conformation by the establishment of several intramolecular hydrogen bonds. Additionally, we present here the first report of amyloid aggregation by an SH3 domain from the Src family.     

Regulation of EGF-induced phospholipase C-gamma1 translocation and activation by its SH2 and PH domains

Translocation of phospholipase C-γ1 is essential for its function in response to growth factors. However, in spite of recent progress, the phospholipase C-γ1 translocation pattern and the molecular mechanism of the translocation are far from fully understood. Contradictory results were reported as to which domain, PH or SH2, controls the epidermal growth factor-induced translocation of phospholipase C-γ1. In this communication, we studied epidermal growth factor-induced translocation of phospholipase C-γ1 by using comprehensive approaches including biochemistry, indirect fluorescence and live fluorescence imaging. We provided original evidence demonstrating that: (i) endogenous phospholipase C-γ1, similar to YFP-tagged phospholipase C-γ1, translocated to endosomes following its initial translocation from cytosol to the plasma membrane in response to epidermal growth factor; (ii) phospholipase C-γ1 remained phosphorylated in endosomes, but phospholipase C-γ1 activity is not required for its translocation, which suggests a signaling role for phospholipase C-γ1 in endosomes; (iii) the PH domain was not required for the initial translocation of phospholipase C-γ1 from cytosol to the plasma membrane, but it stabilizes phospholipase C-γ1 in the membrane at a later time; (iv) the function of the phospholipase C-γ1 PH domain in stabilizing phospholipase C-γ1 membrane association is very important in maintaining the activity of phospholipase C-γ1; and (v) the role of the PH domain in phospholipase C-γ1 membrane association and activation is dependent on PI3K activity. We conclude that the phospholipase C-γ1 SH2 and PH domains coordinate to determine epidermal growth factor-induced translocation and activation of phospholipase C-γ1.     

WW and SH3 domains, two different scaffolds to recognize proline-rich ligands

WW domains are small protein modules composed of approximately 40 amino acids. These domains fold as a stable, triple stranded beta-sheet and recognize proline-containing ligands. WW domains are found in many different signaling and structural proteins, often localized in the cytoplasm as well as in the cell nucleus. Based on analyses of seven structures of WW domains, we discuss their diverse binding preferences and sequence conservation patterns. While modeling WW domains for which structures have not been determined we uncovered a case of potential molecular and functional convergence between WW and SH3 domains. The binding surface of the modeled WW domain of Npw38 protein shows a remarkable similarity to the SH3 domain of Sem5 protein, confirming biochemical data on similar binding predilections of both domains.     

Alternate Binding Modes for a Ubiquitin-SH3 Domain Interaction Studied by NMR Spectroscopy

Surfaces of many binding domains are plastic, enabling them to interact with multiple targets. An understanding of how they bind and recognize their partners is therefore predicated on characterizing such dynamic interfaces. Yet, these interfaces are difficult to study by standard biophysical techniques that often ‘freeze’ out conformations or that produce data averaged over an ensemble of conformers. In this study, we used NMR spectroscopy to study the interaction between the C-terminal SH3 domain of CIN85 and ubiquitin that involves the ‘classical’ binding sites of these proteins. Notably, chemical shift titration data of one target with another and relaxation dispersion data that report on millisecond time scale exchange processes are both well fit to a simple binding model in which free protein is in equilibrium with a single bound conformation. However, dissociation constants and chemical shift differences between free and bound states measured from both classes of experiment are in disagreement. It is shown that the data can be reconciled by considering three-state binding models involving two distinct bound conformations. By combining titration and dispersion data, kinetic and thermodynamic parameters of the three-state binding reaction are obtained along with chemical shifts for each state. A picture emerges in which one bound conformer has increased entropy and enthalpy relative to the second and chemical shifts similar to that of the free state, suggesting a less packed interface. This study provides an example of the interplay between entropy and enthalpy to fine-tune molecular interactions involving the same binding surfaces.     

The SH3 domain of postsynaptic density 95 mediates inflammatory pain through phosphatidylinositol‐3‐kinase recruitment

Sensitization to inflammatory pain is a pathological form of neuronal plasticity that is poorly understood and treated. Here we examine the role of the SH3 domain of postsynaptic density 95 (PSD95) by using mice that carry a single amino‐acid substitution in the polyproline‐binding site. Testing multiple forms of plasticity we found sensitization to inflammation was specifically attenuated. The inflammatory response required recruitment of phosphatidylinositol‐3‐kinase‐C2α to the SH3‐binding site of PSD95. In wild‐type mice, wortmannin or peptide competition attenuated the sensitization. These results show that different types of behavioural plasticity are mediated by specific domains of PSD95 and suggest novel therapeutic avenues for reducing inflammatory pain.     

Induction of cytochrome c release and apoptosis by Hck-SH3 domain-mediated signalling requires caspase-3

The function of key components of signal transduction, the Src family tyrosine kinases is dependent on catalytic activity as well as on intermolecular interaction achieved by their SH2 and SH3 modular domains. We have analyzed the effect of overexpression of the hematopoietic cell kinase (Hck) and its N-terminal unique and SH3 domains on cell survival. Overexpression of the N-terminal unique and SH3 domains (Hck-USH3) induced about 25% of expressing Cos-1 cells to undergo apoptosis 30 hrs after transfection. The full length p59 and p56 forms and the unique domain alone induced low levels of cell death. The unique and SH3 domain of a closely related kinase, Lyn did not induce apoptosis. Overexpression of a mutant USH3 domain (Gly Ala), that disrupts membrane localization, did not induce high level of apoptosis. Cells overexpressing Hck-USH3 showed activation of caspase-3 and release of cytochrome c from mitochondria into cytosol. Caspase-3 defective MCF-7 cells were resistant to apoptosis and cytochrome c release induced by Hck-USH3, which were restored by introducing the caspase-3 gene. These results suggest that Hck SH3 domain mediated signalling at the plasma membrane triggers a pathway leading to caspase-3 dependent cyto- chrome c release and apoptosis.     

快速构建蛋白质结构域克隆库的方法

对蛋白质组学的研究有许多不同的切入方法 .从研究的生物学意义和可行性考虑 ,提出从蛋白结构域入手进行蛋白质组学研究 .SH2 (Srchomology 2 )结构域是细胞信号转导中重要的元件之一 ,人SH2结构域共有约 12 0种 ,对其进行研究将深刻揭示细胞信号转导的规律 .为了得到人所有的SH2结构域序列及克隆 ,首先在公共数据库里检索出了人所有的SH2结构域序列 ,利用国际上现有的共享资源IMAGE(IntegratedMolecularAnalysisofGenomesandTheirExpression)克隆为PCR模板 ,解决了从cDNA文库中难以克隆低丰度结构域的问题 .利用有方向性的TOPO克隆技术提高克隆效率 ,从而快速高效地构建了包括 6 0个SH2结构域的克隆库 .克隆库可以方便地转换到GATEWAY系统具有各种用途的载体上 ,为SH2结构域的蛋白质组学研究奠定了坚实的基础     

The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases

Tyrosine kinases were first discovered as the protein products of viral oncogenes. We now know that this large family of metazoan enzymes includes nearly one hundred structurally diverse members. Tyrosine kinases are broadly classified into two groups: the transmembrane receptor tyrosine kinases, which sense extracellular stimuli, and the cytoplasmic tyrosine kinases, which contain modular ligand-binding domains and propagate intracellular signals. Several families of cytoplasmic tyrosine kinases have in common a core architecture, the “Src module,” composed of a Src-homology 3 (SH3) domain, a Src-homology 2 (SH2) domain, and a kinase domain. Each of these families is defined by additional elaborations on this core architecture. Structural, functional, and evolutionary studies have revealed a unifying set of principles underlying the activity and regulation of tyrosine kinases built on the Src module. The discovery of these conserved properties has shaped our knowledge of the workings of protein kinases in general, and it has had important implications for our understanding of kinase dysregulation in disease and the development of effective kinase-targeted therapies.     

CIN85 associates with TNF receptor 1 via Src and modulates TNF-alpha-induced apoptosis

CIN85 is a multidomain protein that associates with receptors carrying tyrosine kinase domains. Here we report that it is also a component of the signaling complex associated with tumor necrosis factor receptor 1 (TNFR1), which lacks a tyrosine kinase domain. This was established by showing that CIN85 was co-precipitated with TNFR1, TRADD, cIAP-1 and TARF1/2, but not with FADD, RIP, caspase-8 or TRAF6. However, CIN85 did not bind directly to the cytoplasmic domain of TNFR1 (TNFR1-CYT) but to Src family kinases, Cbl and the p85alpha subunit of phosphatidylinositol 3-kinase (PI3-K p85alpha). Src bound directly to TNFR1-CYT, but Cbl and PI3-K p85alpha did not. A human cell line ectopically expressing CIN85 was 10 times more susceptible to TNF-alpha-induced apoptosis than control cells, which expressed identical levels of TNFR1 on their surface. However, the susceptibility of these two cell lines to CD95-induced apoptosis was the same. The three SH3 domains of CIN85 were essential for this increased susceptibility to apoptosis and its proline-rich regions were also required for maximal effect. TNF-alpha treatment recruited CIN85 to the TNFR1 signaling complex. Taken together, these results indicate that CIN85 associates with TNFR1 via Src and modulates TNF-alpha-induced apoptosis.     

Endophilin B1 基因及蛋白的生物信息学分析

目的:利用生物信息学方法分析人Endophilin B1基因以及蛋白的结构,为进一步研究其功能和参与的调控机制提供一定的理论依据。方法:通过GenBank搜索Endophilin B1基因及蛋白序列,采用生物信息学方法分析该基因在不同物种中的差异,分析该蛋白的亚细胞定位,二级结构,功能域以及抗原表位。结果:该基因编码一个长度为365个氨基酸的蛋白,具有两个BAR和SH3两个功能域。Endophilin B1蛋白理论分子量为40796.3,理论等电点为5.78。二级结构中α螺旋(H)占56.44%,β折叠(E)占5.48%,无规卷曲占38.08%。Endophilin B1蛋白含有4个可能的N连接糖基化位点,5个潜在的酪蛋白激酶II磷酸化位点,7个豆蔻酰基化位点,3个PKC磷酸化位点以及2个酪氨酸激酶磷酸化位点。并进一步利用DNAstar软件分析了了该蛋白的抗原表位。结论:利用生物信息学预测出的结构和功能信息,能为Endophin B1蛋白的相关研究提供一定的信息基础。     

The SH3 domain of a M7 interacts with its C-terminal proline-rich region

Myosins play essential roles in migration, cytokinesis, endocytosis, and adhesion. They are composed of a large N-terminal motor domain with ATPase and actin binding sites and C-terminal neck and tail regions, whose functional roles and structural context in the protein are less well characterized. The tail regions of myosins I, IV, VII, XII, and XV each contain a putative SH3 domain that may be involved in protein-protein interactions. SH3 domains are reported to bind proline-rich motifs, especially "PxxP" sequences, and such interactions serve regulatory functions. The activity of Src, PI3, and Itk kinases, for example, is regulated by intramolecular interactions between their SH3 domain and internal proline-rich sequences. Here, we use NMR spectroscopy to reveal the structure of a protein construct from Dictyostelium myosin VII (DdM7) spanning A1620-T1706, which contains its SH3 domain and adjacent proline-rich region. The SH3 domain forms the signature beta-barrel architecture found in other SH3 domains, with conserved tryptophan and tyrosine residues forming a hydrophobic pocket known to bind "PxxP" motifs. In addition, acidic residues in the RT or n-Src loops are available to interact with the basic anchoring residues that are typically found in ligands or proteins that bind SH3 domains. The DdM7 SH3 differs in the hydrophobicity of the second pocket formed by the 3(10) helix and following beta-strand, which contains polar rather than hydrophobic side chains. Most unusual, however, is that this domain binds its adjacent proline-rich region at a surface remote from the region previously identified to bind "PxxP" motifs. The interaction may affect the orientation of the tail without sacrificing the availability of the canonical "PxxP"-binding surface.     

人EEN蛋白的结构预测和功能分析

采用基于神经网络的算法预测了我们自行克隆的新的白血病相关蛋白ＥＥＮ（ｅｘｔｒａ ｅｌｅｖｅｎｎｉｎｅｔｅｅｎ, ＥＥＮ）全长分子的二级结构,结果表明：ＥＥＮ 蛋白可能有三个结构域,Ｎ 端由三段α螺旋和短β折叠组成,中间为四段α螺旋组成的四螺旋结构,Ｃ端为ＳＨ３结构域,类似于在受体酪氨酸激酶信号传导途径中起重要作用的ＳＥＭ－５／ＧＲＢ２ Ｃ端ＳＨ３结构域;利用同源蛋白结构模拟的方法,模拟了ＥＥＮ ＳＨ３结构域的三维结构,结果表明：ＥＥＮ ＳＨ３结构域与ＳＥＭ－５／ＧＲＢ２ ＳＨ３结构域具有相近的结构,构成脯氨酸结合区的氨基酸非常保守．上述结果提示：ＥＥＮ 蛋白可能为新的信号蛋白,可能涉及新的信号传导途径或新的信号传导旁路,ＳＨ３结构域是其功能区域．     

The SH3 domain of nebulin binds selectively to type II peptides: theoretical prediction and experimental validation

Nebulin, a giant modular protein from muscle, is thought to act as a molecular ruler in sarcomere assembly. The C terminus of nebulin, located in the sarcomere Z-disk, comprises an SH3 domain, a module well known for its role in protein/protein interactions. SH3 domains are known to recognize proline-rich ligands, which have been classified as type I or type II, depending on their relative orientation with respect to the SH3 domain in the complex formed. Type I ligands are bound with their N terminus at the RT loop of the SH3 domain, while type II ligands are bound with their C terminus at the RT loop. Many SH3 domains can bind peptides of either class. Despite the potential importance of the SH3 domain for the function of nebulin as an integral part of a complex network of interactions, no in vivo partner has been identified so far. We have adopted an integrated approach, which combines bioinformatic tools with experimental validation to identify possible partners of nebulin SH3. Using the program SPOT, we performed an exhaustive screening of the muscle sequence databases. This search identified a number of potential nebulin SH3 partners, which were then tested experimentally for their binding affinity. Synthetic peptides were studied by both fluorescence and NMR spectroscopy. Our results show that nebulin SH3 domain binds selectively to type II peptides. The affinity for a type II peptide, 12 residues long, spanning the sequence of a stretch of titin known to colocalise with nebulin in the Z-disk is in the submicromolar range (0.7 microM). This affinity is among the highest found for SH3/peptide complexes, suggesting that the identified stretch could have significance in vivo. The strategy outlined here is of more general applicability and may provide a valuable tool to identify potential partners of SH3 domains and of other peptide-binding modules.     

The Tyrosine Kinase c-Src Specifically Binds to the Active Integrin αIIbβ3 to Initiate Outside-in Signaling in Platelets

It is currently believed that inactive tyrosine kinase c-Src in platelets binds to the cytoplasmic tail of the β3 integrin subunit via its SH3 domain. Although a recent NMR study supports this contention, it is likely that such binding would be precluded in inactive c-Src because an auto-inhibitory linker physically occludes the β3 tail binding site. Accordingly, we have re-examined c-Src binding to β3 by immunoprecipitation as well as NMR spectroscopy. In unstimulated platelets, we detected little to no interaction between c-Src and β3. Following platelet activation, however, c-Src was co-immunoprecipitated with β3 in a time-dependent manner and underwent progressive activation as well. We then measured chemical shift perturbations in the ¹⁵N-labeled SH3 domain induced by the C-terminal β3 tail peptide NITYRGT and found that the peptide interacted with the SH3 domain RT-loop and surrounding residues. A control peptide whose last three residues where replaced with those of the β1 cytoplasmic tail induced only small chemical shift perturbations on the opposite face of the SH3 domain. Next, to mimic inactive c-Src, we found that the canonical polyproline peptide RPLPPLP prevented binding of the β3 peptide to the RT- loop. Under these conditions, the β3 peptide induced chemical shift perturbations similar to the negative control. We conclude that the primary interaction of c-Src with the β3 tail occurs in its activated state and at a site that overlaps with PPII binding site in its SH3 domain. Interactions of inactive c-Src with β3 are weak and insensitive to β3 tail mutations.     

金黄色葡萄球菌噬菌体vB_Sau_P68的基因组分析和裂解酶

【背景】金黄色葡萄球菌是常见的人畜共患条件致病菌,随着多耐药菌株分离率的增长,研发与抗生素作用模式不同的抗菌剂迫在眉睫。【目的】分离高效且特异性强的金黄色葡萄球菌噬菌体,对其进行功能注释,并对其编码的裂解酶进行功能验证。【方法】通过对噬菌体全基因组序列进行分析找到裂解酶基因,利用原核表达系统对其编码的2个裂解酶蛋白进行克隆,用SDS-PAGE与蛋白免疫印迹法(Western blotting)鉴定目的蛋白是否表达,并采用单斑法验证其裂解活性。【结果】本研究的噬菌体为一株新的金黄色葡萄球菌噬菌体,命名为vB＿Sau＿P68,该基因组全长为139 409 bp,GC含量为31.0%,编码220个开放阅读框(open reading frame,ORF),透射电镜观察具有正二十面体头部和收缩性尾部,形态学分类属于肌尾噬菌体。该噬菌体编码2个裂解酶基因,分别具有CHAP催化结构域与SH3＿5结合结构域,SDS-PAGE与Western blotting表明Lys161能够表达且有裂解活性,Lys163则无法外源表达。对Lys161序列进行分析,该裂解酶无信号肽,无跨膜区域,以无规则卷曲为主。【...