Interplay of cysteine exposure and global protein dynamics in small‐molecule recognition by a regulator of G‐protein signaling protein
Interplay of cysteine exposure and global protein dynamics in small‐molecule recognition by a regulator of G‐protein signaling protein
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DOI：
10.1002/prot.25642
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发表时间：
2018-12
期刊：
影响因子：
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通讯作者：
Mohammadjavad Mohammadi;Hossein Mohammadiarani;Vincent S. Shaw;R. Neubig;Harish Vashisth
中科院分区：
文献类型：
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作者：
Mohammadjavad Mohammadi;Hossein Mohammadiarani;Vincent S. Shaw;R. Neubig;Harish Vashisth
G蛋白信号调节因子（Regulator of G protein signaling，RGS）蛋白在G蛋白偶联受体（GPCR）信号调节中起着关键作用，因此正成为越来越重要的治疗靶点。最近发现的靶向半胱氨酸残基的噻二唑烷酮（TDZD）化合物对RGS 4蛋白显示出不同水平的特异性和效力，从而表明在结合这些化合物时该蛋白的动力学的内在差异。在这项工作中，我们使用原子分子动力学（MD）模拟研究了几种小分子抑制剂对RGS 4中扰动和动力学运动的影响。具体来说，我们研究了RGS 4的两种构象模型，其中由于侧链运动或由于邻近螺旋的灵活性，掩埋的半胱氨酸残基暴露于溶剂中。我们发现，TDZD化合物与芳香族官能团扰动RGS 4结构比化合物与脂肪族官能团。此外，具有芳香族官能团但缺乏硫原子的小分子仅短暂地存在于蛋白质中并自发地解离到溶剂中。我们使用蛋白质-蛋白质相互作用试验进一步测量了TDZD化合物对单半胱氨酸RGS 4蛋白的抑制作用，显示化合物效力的趋势与我们的模拟研究一致。在脱辅基状态和结合TDZD化合物时的RGS 4构象的热力学分析揭示了RGS 4的两种构象模型之间的联系。半胱氨酸侧链的暴露似乎促进TDZD化合物的初始结合，随后化合物迁移到一束四个螺旋中，从而引起RGS/Gα蛋白-蛋白界面的变构扰动。
Regulator of G protein signaling (RGS) proteins play a pivotal role in regulation of G protein‐coupled receptor (GPCR) signaling and are therefore becoming an increasingly important therapeutic target. Recently discovered thiadiazolidinone (TDZD) compounds that target cysteine residues have shown different levels of specificities and potencies for the RGS4 protein, thereby suggesting intrinsic differences in dynamics of this protein upon binding of these compounds. In this work, we investigated using atomistic molecular dynamics (MD) simulations the effect of binding of several small‐molecule inhibitors on perturbations and dynamical motions in RGS4. Specifically, we studied two conformational models of RGS4 in which a buried cysteine residue is solvent‐exposed due to side‐chain motions or due to flexibility in neighboring helices. We found that TDZD compounds with aromatic functional groups perturb the RGS4 structure more than compounds with aliphatic functional groups. Moreover, small‐molecules with aromatic functional groups but lacking sulfur atoms only transiently reside within the protein and spontaneously dissociate to the solvent. We further measured inhibitory effects of TDZD compounds using a protein–protein interaction assay on a single‐cysteine RGS4 protein showing trends in potencies of compounds consistent with our simulation studies. Thermodynamic analyses of RGS4 conformations in the apo‐state and on binding to TDZD compounds revealed links between both conformational models of RGS4. The exposure of cysteine side‐chains appears to facilitate initial binding of TDZD compounds followed by migration of the compound into a bundle of four helices, thereby causing allosteric perturbations in the RGS/Gα protein–protein interface.