Dipartimento di Chimica, Materiali e Ingegneria Chimica G. Natta, Politecnico di Milano, via L. Mancinelli 7, 20131 Milano, Italy.
Langmuir. 2010 Apr 20;26(8):5679-89. doi: 10.1021/la903769c.
Adsorption of human lysozyme on hydrophobic graphite is investigated through atomistic computer simulations with molecular mechanics (MM) and molecular dynamics (MD) techniques. The chosen strategy follows a simulation protocol proposed by the authors to model the initial and the final adsorption stage on a bare surface. Adopting an implicit solvent and considering 10 starting molecular orientations so that all the main sides of the protein can face the surface, we first carry out an energy minimization to investigate the initial adsorption stage, and then long MD runs of selected arrangements to follow the surface spreading of the protein maximizing its adsorption strength. The results are discussed in terms of the kinetics of surface spreading, the interaction energy, and the molecular size, considering both the footprint and the final thickness of the adsorbed protein. The structural implications of the final adsorption geometry for surface aggregation and nanoscale structural organization are also pointed out. Further MD runs are carried out in explicit water for the native structure and the most stable adsorption state to assess the local stability of the geometry obtained in implicit solvent, and to calculate the statistical distribution of the water molecules around the whole lysozyme and its backbone.
通过使用分子力学（MM）和分子动力学（MD）技术的原子级计算机模拟，研究了人溶菌酶在疏水性石墨上的吸附。所选择的策略遵循了作者提出的模拟方案，用于在裸表面上模拟初始和最终的吸附阶段。采用隐式溶剂并考虑 10 个起始分子取向，以使蛋白质的所有主要侧面都可以面对表面，我们首先进行能量最小化以研究初始吸附阶段，然后对选定的排列进行长时间的 MD 运行，以最大限度地提高其吸附强度，从而跟踪蛋白质在表面上的扩展。根据表面扩展的动力学、相互作用能和分子大小，考虑吸附蛋白质的足迹和最终厚度，讨论了结果。还指出了最终吸附几何形状对表面聚集和纳米尺度结构组织的结构影响。对天然结构和最稳定吸附状态进行进一步的显式水 MD 运行，以评估在隐式溶剂中获得的几何形状的局部稳定性，并计算整个溶菌酶及其骨架周围水分子的统计分布。
