Wendoloski J J, Matthew J B
E.I. du Pont de Nemours & Co., Central Research & Development Department, Wilmington, Delaware 19880-0228.
Proteins. 1989;5(4):313-21. doi: 10.1002/prot.340050407.
Electrostatic calculations have been carried out on a number of structural conformers of tuna cytochrome c. Conformers were generated using molecular dynamics simulations with a range of solvent simulating, macroscopic dielectric formalisms, and one solvent model that explicitly included solvent water molecules. Structures generated using the lowest dielectric models were relatively tight, with side chains collapsed on the surface, while those from the higher dielectric models had more internal and external fluidity, with surface side chains exploring a fuller range of conformational space. The average structure generated with the explicitly solvated model corresponded most closely with the crystal structure. Individual pK values, overall titration curves, and electrostatic potential surfaces were calculated for average structures and structures along each simulation. Differences between structural conformers within each simulation give rise to substantial changes in calculated local electrostatic interactions, resulting in pK value fluctuations for individual sites in the protein that vary by 0.3-2.0 pK units from the calculated time average. These variations are due to the thermal side chain reorientations that produce fluctuations in charge site separations. Properties like overall titration curves and pH dependent stability are not as sensitive to side chain fluctuations within a simulation, but there are substantial effects between simulations due to marked differences in average side chain behavior. These findings underscore the importance of proper dielectric formalism in molecular dynamics simulations when used to generate alternate solution structures from a crystal structure, and suggest that conformers significantly removed from the average structure have altered electrostatic properties that may prove important in episodic protein properties such as catalysis.
已对金枪鱼细胞色素c的多个结构构象体进行了静电计算。构象体是使用分子动力学模拟生成的，采用了一系列溶剂模拟、宏观介电形式以及一种明确包含溶剂水分子的溶剂模型。使用最低介电常数模型生成的结构相对紧密，侧链折叠在表面，而使用较高介电常数模型生成的结构具有更多的内部和外部流动性，表面侧链探索更广泛的构象空间。用明确溶剂化模型生成的平均结构与晶体结构最为接近。针对平均结构以及每个模拟过程中的结构，计算了各个pK值、整体滴定曲线和静电势表面。每个模拟过程中结构构象体之间的差异导致计算出的局部静电相互作用发生显著变化，从而使蛋白质中各个位点的pK值波动，与计算出的时间平均值相差0.3 - 2.0个pK单位。这些变化是由于热诱导的侧链重新取向导致电荷位点间距发生波动。诸如整体滴定曲线和pH依赖性稳定性等性质对模拟过程中的侧链波动不太敏感，但由于平均侧链行为存在显著差异，不同模拟之间存在实质性影响。这些发现强调了在从晶体结构生成替代溶液结构的分子动力学模拟中，正确的介电形式的重要性，并表明与平均结构有显著差异的构象体具有改变的静电性质，这可能在诸如催化等蛋白质偶发性质中证明是重要的。
