Anselmi Massimiliano, Calligari Paolo, Hub Jochen S, Tartaglia Marco, Bocchinfuso Gianfranco, Stella Lorenzo
Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy.
Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany.
J Chem Inf Model. 2020 Jun 22;60(6):3157-3171. doi: 10.1021/acs.jcim.0c00307. Epub 2020 May 29.
SH2 domain-containing tyrosine phosphatase 2 (SHP2), encoded by , plays a fundamental role in the modulation of several signaling pathways. Germline and somatic mutations in are associated with different rare diseases and hematologic malignancies, and recent studies have individuated SHP2 as a central node in oncogenesis and cancer drug resistance. The SHP2 structure includes two Src homology 2 domains (N-SH2 and C-SH2) followed by a catalytic protein tyrosine phosphatase (PTP) domain. Under basal conditions, the N-SH2 domain blocks the active site, inhibiting phosphatase activity. Association of the N-SH2 domain with binding partners containing short amino acid motifs comprising a phosphotyrosine residue (pY) leads to N-SH2/PTP dissociation and SHP2 activation. Considering the relevance of SHP2 in signaling and disease and the central role of the N-SH2 domain in its allosteric regulation mechanism, we performed microsecond-long molecular dynamics (MD) simulations of the N-SH2 domain complexed to 12 different peptides to define the structural and dynamical features determining the binding affinity and specificity of the domain. Phosphopeptide residues at position -2 to +5, with respect to pY, have significant interactions with the SH2 domain. In addition to the strong interaction of the pY residue with its conserved binding pocket, the complex is stabilized hydrophobically by insertion of residues +1, +3, and +5 in an apolar groove of the domain and interaction of residue -2 with both the pY and a protein surface residue. Additional interactions are provided by hydrogen bonds formed by the backbone of residues -1, +1, +2, and +4. Finally, negatively charged residues at positions +2 and +4 are involved in electrostatic interactions with two lysines (Lys89 and Lys91) specific for the SHP2 N-SH2 domain. Interestingly, the MD simulations illustrated a previously undescribed conformational flexibility of the domain, involving the core β sheet and the loop that closes the pY binding pocket.
含SH2结构域的酪氨酸磷酸酶2（SHP2）由[基因名称未给出]编码，在多种信号通路的调节中起重要作用。[基因名称未给出]中的种系和体细胞突变与不同的罕见疾病和血液系统恶性肿瘤相关，最近的研究已确定SHP2是肿瘤发生和癌症耐药性的中心节点。SHP2结构包括两个Src同源2结构域（N-SH2和C-SH2），其后是催化性蛋白酪氨酸磷酸酶（PTP）结构域。在基础条件下，N-SH2结构域会阻断活性位点，抑制磷酸酶活性。N-SH2结构域与包含由磷酸酪氨酸残基（pY）组成的短氨基酸基序的结合伴侣结合，会导致N-SH2/PTP解离并激活SHP2。考虑到SHP2在信号传导和疾病中的相关性以及N-SH2结构域在其变构调节机制中的核心作用，我们对与12种不同肽复合的N-SH2结构域进行了微秒级的分子动力学（MD）模拟，以确定决定该结构域结合亲和力和特异性的结构和动力学特征。相对于pY，-2至+5位的磷酸肽残基与SH2结构域有显著相互作用。除了pY残基与其保守结合口袋的强相互作用外，该复合物还通过+1、+3和+5位残基插入结构域的非极性凹槽以及-2位残基与pY和蛋白质表面残基的相互作用而通过疏水作用得以稳定。-1、+1、+2和+4位残基的主链形成的氢键提供了额外的相互作用。最后，+2和+4位的带负电残基与SHP2 N-SH2结构域特有的两个赖氨酸（Lys89和Lys91）发生静电相互作用。有趣的是，MD模拟显示了该结构域以前未描述的构象灵活性，涉及核心β折叠和封闭pY结合口袋的环。
