Kaushik Shivansh, Chang Chia-En A
Department of Chemistry, University of Chemistry, Riverside, CA, United States.
Front Mol Biosci. 2021 May 10;8:659687. doi: 10.3389/fmolb.2021.659687. eCollection 2021.
Ligand-protein association is the first and critical step for many biological and chemical processes. This study investigated the molecular association processes under different environments. In biology, cells have different compartments where ligand-protein binding may occur on a membrane. In experiments involving ligand-protein binding, such as the surface plasmon resonance and continuous flow biosynthesis, a substrate flow and surface are required in experimental settings. As compared with a simple binding condition, which includes only the ligand, protein, and solvent, the association rate and processes may be affected by additional ligand transporting forces and other intermolecular interactions between the ligand and environmental objects. We evaluated these environmental factors by using a ligand xk263 binding to HIV protease (HIVp) with atomistic details. Using Brownian dynamics simulations, we modeled xk263 and HIVp association time and probability when a system has xk263 diffusion flux and a non-polar self-assembled monolayer surface. We also examined different protein orientations and accessible surfaces for xk263. To allow xk263 to access to the dimer interface of immobilized HIVp, we simulated the system by placing the protein 20Å above the surface because immobilizing HIVp on a surface prevented xk263 from contacting with the interface. The non-specific interactions increased the binding probability while the association time remained unchanged. When the xk263 diffusion flux increased, the effective xk263 concentration around HIVp, xk263-HIVp association time and binding probability decreased non-linearly regardless of interacting with the self-assembled monolayer surface or not. The work sheds light on the effects of the solvent flow and surface environment on ligand-protein associations and provides a perspective on experimental design.
配体与蛋白质的结合是许多生物和化学过程的第一步也是关键步骤。本研究调查了不同环境下的分子结合过程。在生物学中，细胞有不同的区室，配体与蛋白质的结合可能发生在膜上。在涉及配体与蛋白质结合的实验中，如表面等离子体共振和连续流生物合成，实验设置中需要底物流动和表面。与仅包括配体、蛋白质和溶剂的简单结合条件相比，结合速率和过程可能会受到额外的配体传输力以及配体与环境物体之间的其他分子间相互作用的影响。我们通过使用具有原子细节的配体xk263与HIV蛋白酶（HIVp）结合来评估这些环境因素。利用布朗动力学模拟，我们对系统存在xk263扩散通量和非极性自组装单分子层表面时xk263与HIVp的结合时间和概率进行了建模。我们还研究了xk263的不同蛋白质取向和可及表面。为了使xk263能够接触到固定化HIVp的二聚体界面，我们通过将蛋白质放置在表面上方20Å处来模拟系统，因为将HIVp固定在表面会阻止xk263与界面接触。非特异性相互作用增加了结合概率，而结合时间保持不变。当xk263扩散通量增加时，无论是否与自组装单分子层表面相互作用，HIVp周围的有效xk263浓度、xk263与HIVp的结合时间和结合概率均呈非线性下降。这项工作揭示了溶剂流动和表面环境对配体与蛋白质结合的影响，并为实验设计提供了一个视角。
