Yurenko Yevgen P, Muždalo Anja, Černeková Michaela, Pecina Adam, Řezáč Jan, Fanfrlík Jindřich, Žáková Lenka, Jiráček Jiří, Lepšík Martin
Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech Republic.
Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 166 28 Prague 6, Czech Republic.
J Chem Inf Model. 2025 Jun 9;65(11):5690-5705. doi: 10.1021/acs.jcim.5c00772. Epub 2025 May 16.
The quantitative characterization of residue contributions to protein-protein binding across extensive flexible interfaces poses a significant challenge for biophysical computations. It is attributable to the inherent imperfections in the experimental structures themselves, as well as to the lack of reliable computational tools for the evaluation of all types of noncovalent interactions. This study leverages recent advancements in semiempirical quantum-mechanical and implicit solvent approaches embodied in the PM6-D3H4S/COSMO2 method for the development of a hierarchical computational protocols encompassing molecular dynamics, fragmentation, and virtual glycine scan techniques for the investigation of flexible protein-protein interactions. As a model, the binding of insulin to its receptor is selected, a complex and dynamic process that has been extensively studied experimentally. The interaction energies calculated at the PM6-D3H4S/COSMO2 level in ten molecular dynamics snapshots did not correlate with molecular mechanics/generalized Born interaction energies because only the former method is able to describe nonadditive effects. This became evident by the examination of the energetics in small-model dimers featuring all the present types of noncovalent interactions with respect to DFT-D3 calculations. The virtual glycine scan has identified 15 hotspot residues on insulin and 15 on the insulin receptor, and their contributions have been quantified using PM6-D3H4S/COSMO2. The accuracy and credibility of the approach are further supported by the fact that all the insulin hotspots have previously been detected by biochemical and structural methods. The modular nature of the protocol has enabled the formulation of several variants, each tailored to specific accuracy and efficiency requirements. The developed computational strategy is firmly rooted in general biophysical chemistry and is thus offered as a general tool for the quantification of interactions across relevant flexible protein-protein interfaces.
对于生物物理计算而言，定量表征广泛柔性界面上蛋白质 - 蛋白质结合中残基的贡献是一项重大挑战。这归因于实验结构本身固有的不完美性，以及缺乏用于评估所有类型非共价相互作用的可靠计算工具。本研究利用了半经验量子力学和隐式溶剂方法的最新进展，这些进展体现在PM6 - D3H4S/COSMO2方法中，用于开发一种分层计算协议，该协议涵盖分子动力学、片段化和虚拟甘氨酸扫描技术，以研究柔性蛋白质 - 蛋白质相互作用。作为模型，选择了胰岛素与其受体的结合，这是一个已被广泛实验研究的复杂动态过程。在十个分子动力学快照中，在PM6 - D3H4S/COSMO2水平计算的相互作用能与分子力学/广义玻恩相互作用能不相关，因为只有前一种方法能够描述非加和效应。通过检查包含所有当前类型非共价相互作用的小模型二聚体相对于DFT - D3计算的能量学，这一点变得很明显。虚拟甘氨酸扫描已在胰岛素上鉴定出15个热点残基，在胰岛素受体上鉴定出15个热点残基，并使用PM6 - D3H4S/COSMO2对它们的贡献进行了量化。该方法的准确性和可信度进一步得到以下事实的支持：所有胰岛素热点先前都已通过生化和结构方法检测到。该协议的模块化性质使得能够制定几种变体，每种变体都针对特定的准确性和效率要求进行了定制。所开发的计算策略牢固地植根于一般生物物理化学，因此作为一种通用工具提供，用于量化相关柔性蛋白质 - 蛋白质界面上的相互作用。
