论文标题
蛋白质在表面存在下的蛋白质模拟：远距离静电和平均场流体动力学
Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-range Electrostatics and Mean-field Hydrodynamics
论文作者
论文摘要
大分子扩散和吸附在狭窄环境中的模拟可以为许多生物物理过程提供有价值的机械见解。为了在相关时间尺度上以原子细节进行建模溶质，可以在刚体溶质的近似值中进行布朗动力学模拟。这允许相互作用的溶质电势网格的先例，从而允许对力的计算有效计算。但是，仅凭基于网格的方法，流体动力和远程静电相互作用不能完全处理。在这里，我们开发了对流体动力和静电相互作用的处理，以通过对基于网格的基于网格和远距离相互作用进行建模，包括表面的存在。我们描述了它的应用，以模拟特征良好的蛋白质蛋白质蛋白蛋白溶菌酶和类似硅胶状的表面的自我关联和多种分子吸附。我们发现，计算模型可以恢复吸附过程的许多实验性可观察物，并为其决定因素提供见解。计算模型是在扩散关联（SDA）软件包的模拟中实现的。
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian Dynamics simulations can be carried out with the approximation of rigid body solutes moving through a continuum solvent. This allows the precomputation of interaction potential grids for the solutes, thereby allowing the computationally efficient calculation of forces. However, hydrodynamic and long-range electrostatic interactions cannot be fully treated with grid-based approaches alone. Here, we develop a treatment of both hydrodynamic and electrostatic interactions to include the presence of surfaces by modeling grid-based and long-range interactions. We describe its application to simulate the self-association and many-molecule adsorption of the well-characterized protein Hen Egg-White Lysozyme to mica-like and silica-like surfaces. We find that the computational model can recover a number of experimental observables of the adsorption process and provide insights into their determinants. The computational model is implemented in the Simulation of Diffusional Association (SDA) software package.
