Defining the specificity space of the human Src homology 2 domain
Defining the specificity space of the human Src homology 2 domain
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DOI：
10.1074/mcp.m700312-mcp200
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发表时间：
2008-04-01
影响因子：
7
通讯作者：
Li, Shawn S. -C.
中科院分区：
文献类型：
--
作者：
Huang, Haiming;Li, Lei;Li, Shawn S. -C.
Src同源2（SH 2）结构域是人类基因组编码的最大的相互作用模块家族，其识别酪氨酸磷酸化序列，从而在转导和控制蛋白酪氨酸激酶发出的细胞信号中起关键作用。不同的SH 2结构域选择不同的磷酸肽，并且给定的SH 2结构域的功能通常由其识别的特定基序决定。因此，破译由SH 2结构域识别的磷酸酪氨酰肽基序是理解其细胞功能的关键。在这里，我们克隆了所有120个SH 2结构域中确定的人类基因组，并确定磷酸酪氨酸肽结合特性的76 SH 2结构域通过筛选定向肽阵列库。在这76个结构域中，我们确定了43个SH 2结构域的选择性，并对另外33个SH 2结构域的结合基序进行了改进。我们鉴定了许多新的结合基序，例如BRDG 1 SH 2结构域，其特异性选择相对于Tyr（P）残基的P + 4处的大体积疏水残基。基于定向肽阵列库数据，我们开发了评分矩阵辅助配体识别（或SMALI），这是一种基于Web的程序，用于预测含SH 2蛋白的结合伴侣。当应用于SH 2D 1A/SAP（SLAM相关蛋白）时，该蛋白的突变或缺失是X连锁淋巴组织增生综合征的基础，SMALI不仅概括了已知的相互作用，而且还鉴定了许多与该疾病相关蛋白相互作用的新蛋白。SMALI还确定了BRDG 1的一些潜在相互作用物，BRDG 1是一种功能在很大程度上未知的蛋白质。肽在溶液中的结合分析表明，SMALI评分与肽与给定的SH 2结构域的结合能很好地相关。人SH 2结构域特异性空间的定义为将来探索细胞中含SH 2蛋白的功能提供了必要的分子基础和平台。
Src homology 2 (SH2) domains are the largest family of interaction modules encoded by the human genome to recognize tyrosine-phosphorylated sequences and thereby play pivotal roles in transducing and controlling cellular signals emanating from protein-tyrosine kinases. Different SH2 domains select for distinct phosphopeptides, and the function of a given SH2 domain is often dictated by the specific motifs that it recognizes. Therefore, deciphering the phosphotyrosyl peptide motif recognized by an SH2 domain is the key to understanding its cellular function. Here we cloned all 120 SH2 domains identified in the human genome and determined the phosphotyrosyl peptide binding properties of 76 SH2 domains by screening an oriented peptide array library. Of these 76, we defined the selectivity for 43 SH2 domains and refined the binding motifs for another 33 SH2 domains. We identified a number of novel binding motifs, which are exemplified by the BRDG1 SH2 domain that selects specifically for a bulky, hydrophobic residue at P + 4 relative to the Tyr(P) residue. Based on the oriented peptide array library data, we developed scoring matrix-assisted ligand identification (or SMALI), a Web-based program for predicting binding partners for SH2-containing proteins. When applied to SH2D1A/SAP (SLAM-associated protein), a protein whose mutation or deletion underlies the X-linked lymphoproliferative syndrome, SMALI not only recapitulated known interactions but also identified a number of novel interacting proteins for this disease-associated protein. SMALI also identified a number of potential interactors for BRDG1, a protein whose function is largely unknown. Peptide in-solution binding analysis demonstrated that a SMALI score correlates well with the binding energy of a peptide to a given SH2 domain. The definition of the specificity space of the human SH2 domain provides both the necessary molecular basis and a platform for future exploration of the functions for SH2-containing proteins in cells.