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非标准氨基酸的 CHARMM36 加和力场。

Additive CHARMM36 Force Field for Nonstandard Amino Acids.

机构信息

Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France.

Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.

出版信息

J Chem Theory Comput. 2021 Jun 8;17(6):3554-3570. doi: 10.1021/acs.jctc.1c00254. Epub 2021 May 19.

Abstract

Nonstandard amino acids are both abundant in nature, where they play a key role in various cellular processes, and can be synthesized in laboratories, for example, for the manufacture of a range of pharmaceutical agents. In this work, we have extended the additive all-atom CHARMM36 and CHARMM General force field (CGenFF) to a large set of 333 nonstandard amino acids. These include both amino acids with nonstandard side chains, such as post-translationally modified and artificial amino acids, as well as amino acids with modified backbone groups, such as chromophores composed of several amino acids. Model compounds representative of the nonstandard amino acids were parametrized for protonation states that are likely at the physiological pH of 7 and, for some more common residues, in both d- and l-stereoisomers. Considering all protonation, tautomeric, and stereoisomeric forms, a total of 406 nonstandard amino acids were parametrized. Emphasis was placed on the quality of both intra- and intermolecular parameters. Partial charges were derived using quantum mechanical (QM) data on model compound dipole moments, electrostatic potentials, and interactions with water. Optimization of all intramolecular parameters, including torsion angle parameters, was performed against information from QM adiabatic potential energy surface (PES) scans. Special emphasis was put on the quality of terms corresponding to PES around rotatable dihedral angles. Validation of the force field was based on molecular dynamics simulations of 20 protein complexes containing different nonstandard amino acids. Overall, the presented parameters will allow for computational studies of a wide range of proteins containing nonstandard amino acids, including natural and artificial residues.

摘要

非标准氨基酸在自然界中含量丰富,它们在各种细胞过程中起着关键作用,并且可以在实验室中合成,例如用于制造一系列药物制剂。在这项工作中,我们将加和原子 CHARMM36 力场和 CHARMM 通用力场(CGenFF)扩展到了包括 333 种非标准氨基酸的大集合。这些氨基酸包括具有非标准侧链的氨基酸,例如翻译后修饰的和人工氨基酸,以及具有修饰的主链基团的氨基酸,例如由几个氨基酸组成的生色团。代表非标准氨基酸的模型化合物针对生理 pH 值为 7 时可能的质子化状态进行了参数化,对于一些更常见的残基,在 d-和 l-异构体中也进行了参数化。考虑到所有质子化、互变异构和立体异构形式,共参数化了 406 种非标准氨基酸。重点放在了内部分子和分子间参数的质量上。使用模型化合物偶极矩、静电势和与水相互作用的量子力学 (QM) 数据来推导部分电荷。对所有分子内参数(包括扭转角参数)进行了优化,优化是针对 QM 绝热势能面 (PES) 扫描的信息进行的。特别强调了对应于可旋转二面角周围 PES 的项的质量。力场的验证是基于包含不同非标准氨基酸的 20 个蛋白质复合物的分子动力学模拟。总的来说,所提出的参数将允许对包含非标准氨基酸的广泛蛋白质进行计算研究,包括天然和人工残基。

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