Department of Physics, University of Houston, Houston, Texas, USA.
Biophys J. 2012 Apr 18;102(8):1934-43. doi: 10.1016/j.bpj.2012.03.025.
Toward quantitative description of protein aggregation, we develop a computationally efficient method to evaluate the potential of mean force between two folded protein molecules that allows for complete sampling of their mutual orientation. Our model is valid at moderate ionic strengths and accounts for the actual charge distribution on the surface of the molecules, the dielectric discontinuity at the protein-solvent interface, and the possibility of protonation or deprotonation of surface residues induced by the electric field due to the other protein molecule. We apply the model to the protein lysozyme, whose solutions exhibit both mesoscopic clusters of protein-rich liquid and liquid-liquid separation; the former requires that protein form complexes with typical lifetimes of approximately milliseconds. We find the electrostatic repulsion is typically lower than the prediction of the Derjaguin-Landau-Verwey-Overbeek theory. The Coulomb interaction in the lowest-energy docking configuration is nonrepulsive, despite the high positive charge on the molecules. Typical docking configurations barely involve protonation or deprotonation of surface residues. The obtained potential of mean force between folded lysozyme molecules is consistent with the location of the liquid-liquid coexistence, but produces dimers that are too short-lived for clusters to exist, suggesting lysozyme undergoes conformational changes during cluster formation.
为了定量描述蛋白质聚集，我们开发了一种计算效率高的方法来评估两个折叠蛋白质分子之间的平均力势能，该方法允许对它们的相互取向进行完全采样。我们的模型在中等离子强度下有效，并考虑了分子表面的实际电荷分布、分子-溶剂界面的介电不连续性，以及由于另一个蛋白质分子的电场导致表面残基质子化或去质子化的可能性。我们将该模型应用于溶菌酶，其溶液中既存在富含蛋白质的液相的介观聚集体，也存在液-液相分离；前者要求蛋白质与具有典型寿命约为毫秒的复合物形成。我们发现静电排斥力通常低于德热那乌-朗道-范德瓦尔斯-奥弗贝克理论的预测。尽管分子带正电荷很高，但在最低能量对接构型中的库仑相互作用是非排斥的。典型的对接构型几乎不涉及表面残基的质子化或去质子化。获得的折叠溶菌酶分子之间的平均力势能与液相共存的位置一致，但产生的二聚体寿命太短，无法形成聚集体，这表明溶菌酶在聚集体形成过程中经历构象变化。
