Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University , Grahamstown, 6140, South Africa.
Faculty of Engineering and Natural Sciences, Sabanci University , Tuzla 34956, Istanbul, Turkey.
J Chem Inf Model. 2018 Feb 26;58(2):383-404. doi: 10.1021/acs.jcim.7b00630. Epub 2018 Feb 12.
Central to Hsp90's biological function is its ability to interconvert between various conformational states. Drug targeting of Hsp90's regulatory mechanisms, including its modulation by cochaperone association, presents as an attractive therapeutic strategy for Hsp90 associated pathologies. In this study, we utilized homology modeling techniques to calculate full-length structures of human Hsp90α in closed and partially open conformations and used these structures as a basis for several molecular dynamics based analyses aimed at elucidating allosteric mechanisms and modulation sites in human Hsp90α. Atomistic simulations demonstrated that bound adenosine triphosphate (ATP) stabilizes the dimer by "tensing" each protomer, while adenosine diphosphate (ADP) and apo configurations "relax" the complex by increasing global flexibility, the former case resulting in a fully open "v-like" conformation. Dynamic residue network analysis revealed regions of the protein involved in intraprotein communication and identified several key communication hubs that correlate with known functional sites. Pairwise comparison of betweenness centrality, shortest path, and residue fluctuations revealed that a proportional relationship exists between the latter two measurables and an inverse relationship between these two and betweenness centrality. This analysis showed how protein flexibility, degree of compactness, and the distance cutoff used for network construction influence the correlations between these metrics. These findings are novel and suggest shortest path and betweenness centrality to be more relevant quantities to follow for detecting functional residues in proteins compared to residue fluctuations. Perturbation response scanning analysis identified several potential residue sites capable of modulating conformational change in favor of interstate conversion. For the ATP-bound open conformation, these sites were found to overlap with known Aha1 and client binding sites, demonstrating how naturally occurring forces associated with cofactor binding could allosterically modulate conformational dynamics.
Hsp90 生物学功能的核心是其在各种构象状态之间转换的能力。靶向 Hsp90 调节机制的药物，包括共伴侣关联的调节，为 Hsp90 相关疾病提供了一种有吸引力的治疗策略。在这项研究中，我们利用同源建模技术计算了人 Hsp90α 在闭合和部分开放构象下的全长结构，并将这些结构作为几个基于分子动力学的分析的基础，旨在阐明人 Hsp90α 的变构机制和调节位点。原子模拟表明，结合的三磷酸腺苷 (ATP) 通过“拉紧”每个原体来稳定二聚体，而二磷酸腺苷 (ADP) 和脱腺苷酸 (apo) 构型通过增加整体灵活性来“放松”复合物，前一种情况导致完全开放的“V 形”构象。动态残基网络分析揭示了蛋白质中涉及蛋白质内通讯的区域，并确定了几个与已知功能位点相关的关键通讯枢纽。成对比较介数中心度、最短路径和残基波动揭示了后两个可测量值与这两个之间以及与介数中心度之间存在比例关系。该分析表明，蛋白质灵活性、紧凑度和用于网络构建的距离截止值如何影响这些指标之间的相关性。这些发现是新颖的，表明与残基波动相比，最短路径和介数中心度是检测蛋白质中功能残基更相关的量。扰动响应扫描分析确定了几个潜在的残基位点，这些位点能够调节有利于状态间转换的构象变化。对于结合 ATP 的开放构象，这些位点与已知的 Aha1 和客户结合位点重叠，表明与辅助因子结合相关的自然力如何变构调节构象动力学。
