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丝氨酸蛋白酶中的长程静电作用:机器学习驱动的反应采样为酶设计提供见解。

Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design.

作者信息

Zlobin Alexander, Maslova Valentina, Beliaeva Julia, Meiler Jens, Golovin Andrey

机构信息

Institute for Drug Discovery, Leipzig University Medical School, Brüderstraße 34, Leipzig 04103, Germany.

Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory 1, building 73, Moscow 119234, Russia.

出版信息

J Chem Inf Model. 2025 Feb 24;65(4):2003-2013. doi: 10.1021/acs.jcim.4c01827. Epub 2025 Feb 10.

Abstract

Computational enzyme design is a promising technique for producing novel enzymes for industrial and clinical needs. A key challenge that this technique faces is to consistently achieve the desired activity. Fundamental studies of natural enzymes revealed critical contributions from second-shell - and even more distant - residues to their remarkable efficiency. In particular, such residues organize the internal electrostatic field to promote the reaction. Engineering such fields computationally proved to be a promising strategy, which, however, has some limitations. Charged residues necessarily form specific patterns of local interactions that may be exploited for structural integrity. As a result, it is impossible to probe the electrostatic field alone by substituting amino acids. We hypothesize that an approach that isolates the influences of residues' charges from other influences could yield deeper insights. We use molecular modeling with AI-enhanced QM/MM reaction sampling to implement such an approach and apply it to a model serine protease subtilisin. We find that the negative charge 8 Å away from the catalytic site is crucial to achieving the enzyme's catalytic efficiency, contributing more than 2 kcal/mol to lowering the barrier. In contrast, a positive charge from the second-closest charged residue opposes the efficiency of the reaction by raising the barrier by 0.8 kcal/mol. This result invites discussion into the role of this residue and trade-offs that might have taken place in the evolution of such enzymes. Our approach is transferable and can help investigate the evolution of electrostatic preorganization in other enzymes. We believe that the study and engineering of electrostatic fields in enzymes is a promising direction to advance both fundamental and applied enzymology and lead to the design of new powerful biocatalysts.

摘要

计算酶设计是一种很有前景的技术,可用于生产满足工业和临床需求的新型酶。该技术面临的一个关键挑战是始终如一地实现所需的活性。对天然酶的基础研究揭示了第二壳层甚至更远的残基对其卓越效率的关键贡献。特别是,这些残基组织内部静电场以促进反应。通过计算设计这样的电场被证明是一种很有前景的策略,然而,它也有一些局限性。带电荷的残基必然会形成特定的局部相互作用模式,这些模式可能被用于维持结构完整性。因此,不可能仅通过替换氨基酸来探测静电场。我们假设一种将残基电荷的影响与其他影响隔离开来的方法可能会产生更深入的见解。我们使用人工智能增强的量子力学/分子力学反应采样的分子建模来实施这种方法,并将其应用于模型丝氨酸蛋白酶枯草杆菌蛋白酶。我们发现,距离催化位点8 Å处的负电荷对于实现该酶的催化效率至关重要,它对降低反应势垒的贡献超过2千卡/摩尔。相比之下,距离第二近的带电荷残基的正电荷通过将势垒提高0.8千卡/摩尔来阻碍反应效率。这一结果引发了关于该残基的作用以及在这类酶的进化过程中可能发生的权衡的讨论。我们的方法具有可转移性,有助于研究其他酶中静电预组织的进化。我们相信,对酶中静电场的研究和工程设计是推进基础和应用酶学发展并设计新型强大生物催化剂的一个有前景的方向。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/34b0/11863386/02373bf895f1/ci4c01827_0001.jpg

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