Department of Physics, University at Buffalo, Buffalo, New York 14260, USA.
J Chem Phys. 2010 Jan 7;132(1):014111. doi: 10.1063/1.3288503.
The accurate modeling of protein dynamics in crystalline states holds keys to the understanding of protein dynamics relevant to functions. In this study, we used coarse-grained elastic network models (ENMs) to explore the atomic fluctuations of a protein structure that interacts with its crystalline environment, and evaluated the modeling results using the anisotropic displacement parameters (ADPs) obtained from x-ray crystallography. To ensure the robustness of modeling results, we used three ENM schemes for assigning force constant combined with three boundary conditions for treating the crystalline environment. To explore the role of crystal contact interactions in the modeling of ADPs, we varied the strength of interactions between a protein structure and its environment. For a list of 83 high-resolution crystal structures, we found that the optimal modeling of ADPs, as assessed by a variety of metrics, is achieved for weak protein-environment interactions (compared to the interactions within a protein structure). As a result, the ADPs are dominated by contributions from rigid-body motions of the entire protein structure, and the internal protein dynamics is only weakly perturbed by crystal packing. Our finding of weak crystal contact interactions is also corroborated by the calculations of residue-residue contact energy within a protein structure and between protein molecules using a statistical potential.
在晶体状态下准确地模拟蛋白质动力学，是理解与功能相关的蛋白质动力学的关键。在这项研究中，我们使用粗粒弹性网络模型（ENM）来探索与晶体环境相互作用的蛋白质结构的原子波动，并使用 X 射线晶体学获得的各向异性位移参数（ADP）来评估建模结果。为了确保建模结果的稳健性，我们使用了三种结合三种边界条件的 ENM 方案来分配力常数，以处理晶体环境。为了探索晶体接触相互作用在 ADP 建模中的作用，我们改变了蛋白质结构与其环境之间的相互作用强度。对于 83 个高分辨率晶体结构列表，我们发现，通过各种指标评估，弱的蛋白质-环境相互作用（与蛋白质结构内的相互作用相比）可以实现 ADP 的最佳建模。因此，ADP 主要由整个蛋白质结构的刚体运动贡献，晶体堆积对蛋白质内部动力学的干扰较弱。我们的发现也得到了使用统计势计算蛋白质结构内和蛋白质分子之间残基-残基接触能的支持。
