Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.
Institute of Biotechnology, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland.
J Chem Theory Comput. 2024 Sep 10;20(17):7546-7559. doi: 10.1021/acs.jctc.4c00743. Epub 2024 Aug 26.
prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics simulations for interactions in biologically relevant systems involving water, ions, proteins, lipids, and saccharides. Recognizing the inherent limitations of nonpolarizable force fields in precisely modeling electrostatic interactions essential for various biological processes, we mitigate these shortcomings by accounting for electronic polarizability in a physically rigorous mean-field way that does not add to computational costs. With this scaling of (both integer and partial) charges within the CHARMM36 framework, prosECCo75 addresses overbinding artifacts. This improves agreement with experimental ion binding data across a broad spectrum of systems─lipid membranes, proteins (including peptides and amino acids), and saccharides─without compromising their biomolecular structures. prosECCo75 thus emerges as a computationally efficient tool providing enhanced accuracy and broader applicability in simulating the complex interplay of interactions between ions and biomolecules, pivotal for improving our understanding of many biological processes.
proSECCo75 是一个经过优化的力场,通过电荷缩放有效地纳入了电子极化。它旨在提高名义上不可极化分子动力学模拟在涉及水、离子、蛋白质、脂质和糖的生物相关系统中的相互作用的准确性。认识到不可极化力场在精确建模对各种生物过程至关重要的静电相互作用方面的固有局限性,我们通过以物理上严格的平均场方式考虑电子极化来减轻这些缺点,而不会增加计算成本。通过在 CHARMM36 框架内对(整数和部分)电荷进行这种缩放,proSECCo75 解决了过度结合的伪像问题。这提高了与广泛系统(脂质膜、蛋白质(包括肽和氨基酸)和糖)的实验离子结合数据的一致性,而不会损害它们的生物分子结构。因此,proSECCo75 成为一种计算效率高的工具,在模拟离子和生物分子之间相互作用的复杂相互作用方面提供了更高的准确性和更广泛的适用性,对于提高我们对许多生物过程的理解至关重要。