Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States.
Division of Biotechnology , Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen 91052 , Germany.
J Chem Theory Comput. 2018 May 8;14(5):2784-2796. doi: 10.1021/acs.jctc.8b00097. Epub 2018 Apr 18.
Water is essential in many biological processes, and the hydration structure plays a critical role in facilitating protein folding, dynamics, and ligand binding. A variety of biophysical spectroscopic techniques have been used to probe the water solvating proteins, often complemented with molecular dynamics (MD) simulations to resolve the spatial and dynamic features of the hydration shell, but comparing relative water structure is challenging. In this study 1 μs MD simulations were performed to identify and characterize hydration sites around HIV-1 protease bound to an inhibitor, darunavir (DRV). The water density, hydration site occupancy, extent and anisotropy of fluctuations, coordinated water molecules, and hydrogen bonds were characterized and compared to the properties of bulk water. The water density of the principal hydration shell was found to be higher than bulk, dependent on the topology and physiochemical identity of the biomolecular surface. The dynamics of water molecules occupying principal hydration sites was highly dependent on the number of water-water interactions and inversely correlated with hydrogen bonds to the protein-inhibitor complex. While many waters were conserved following the symmetry of homodimeric HIV protease, the asymmetry induced by DRV resulted in asymmetric lower-occupancy hydration sites at the concave surface of the active site. Key interactions between water molecules and the protease, that stabilize the protein in the inhibited form, were altered in a drug resistant variant of the protease indicating that modulation of solvent-solute interactions might play a key role in conveying drug resistance. Our analysis provides insights into the interplay between an enzyme inhibitor complex and the hydration shell and has implications in elucidating water structure in a variety of biological processes and applications including ligand binding, inhibitor design, and resistance.
水在许多生物过程中是必不可少的，而水合结构在促进蛋白质折叠、动力学和配体结合方面起着至关重要的作用。已经使用了各种生物物理光谱技术来探测水溶剂化蛋白质，通常与分子动力学（MD）模拟相结合，以解析水合壳的空间和动态特征，但比较相对水结构具有挑战性。在这项研究中，进行了 1 μs 的 MD 模拟，以识别和表征与抑制剂达芦那韦（DRV）结合的 HIV-1 蛋白酶周围的水合位点。水密度、水合位点占有率、波动的程度和各向异性、配位水分子和氢键的特征，并与体相水的性质进行了比较。发现主要水合壳的水密度高于体相，这取决于生物分子表面的拓扑结构和物理化学性质。占据主要水合位点的水分子的动力学高度依赖于水分子之间的相互作用数量，并与蛋白质-抑制剂复合物的氢键呈反比。虽然许多水分子在 HIV 蛋白酶同源二聚体的对称性下得到了保留，但 DRV 引起的不对称性导致活性位点凹面处的低占有率水合位点不对称。水分子与蛋白酶之间的关键相互作用稳定了抑制剂形式的蛋白质，在蛋白酶的耐药变体中发生了改变，这表明溶剂-溶质相互作用的调节可能在传递耐药性方面发挥关键作用。我们的分析提供了对酶抑制剂复合物和水合壳之间相互作用的深入了解，并对阐明各种生物学过程和应用中的水结构具有启示作用，包括配体结合、抑制剂设计和耐药性。
