Upgrading of the general AMBER force field 2 for fluorinated alcohol biosolvents: A validation for water solutions and melittin solvation

IF 1.8 4区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Peptide Science Pub Date : 2023-09-21 DOI:10.1002/psc.3543

Michele Casoria, Marina Macchiagodena, Paolo Rovero, Claudia Andreini, Anna Maria Papini, Gianni Cardini, Marco Pagliai

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Abstract

The standard GAFF2 force field parameterization has been refined for the fluorinated alcohols 2,2,2-trifluoroethanol (TFE), 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), and 1,1,1,3,3,3-hexafluoropropan-2-one (HFA), which are commonly used to study proteins and peptides in biomimetic media. The structural and dynamic properties of both proteins and peptides are significantly influenced by the biomimetic environment created by the presence of these cosolvents in aqueous solutions. Quantum mechanical calculations on stable conformers were used to parameterize the atomic charges. Different systems, such as pure liquids, aqueous solutions, and systems formed by melittin protein and cosolvent/water solutions, have been used to validate the new models. The calculated macroscopic and structural properties are in agreement with experimental findings, supporting the validity of the newly proposed models.

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氟化醇生物溶剂的通用AMBER力场2的升级：水溶液和蜂毒肽溶剂化的验证。

已对氟化醇2,2,2-三氟乙醇（TFE）、1,1,1,3,3-六氟-2-丙醇（HFIP）和1,1,1,31,3,3-六氟丙烷-2-酮（HFA）的标准GAFF2力场参数化进行了改进，它们通常用于研究仿生介质中的蛋白质和肽。蛋白质和肽的结构和动力学性质都受到水溶液中这些共溶剂产生的仿生环境的显著影响。使用稳定构象体的量子力学计算来参数化原子电荷。不同的系统，如纯液体、水溶液，以及由蜂毒素蛋白和共溶剂/水溶液形成的系统，已被用于验证新模型。计算的宏观和结构性质与实验结果一致，支持了新提出的模型的有效性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Peptide Science 生物-分析化学

CiteScore

3.40

自引率

4.80%

发文量

审稿时长

1.7 months

期刊介绍： The official Journal of the European Peptide Society EPS The Journal of Peptide Science is a cooperative venture of John Wiley & Sons, Ltd and the European Peptide Society, undertaken for the advancement of international peptide science by the publication of original research results and reviews. The Journal of Peptide Science publishes three types of articles: Research Articles, Rapid Communications and Reviews. The scope of the Journal embraces the whole range of peptide chemistry and biology: the isolation, characterisation, synthesis properties (chemical, physical, conformational, pharmacological, endocrine and immunological) and applications of natural peptides; studies of their analogues, including peptidomimetics; peptide antibiotics and other peptide-derived complex natural products; peptide and peptide-related drug design and development; peptide materials and nanomaterials science; combinatorial peptide research; the chemical synthesis of proteins; and methodological advances in all these areas. The spectrum of interests is well illustrated by the published proceedings of the regular international Symposia of the European, American, Japanese, Australian, Chinese and Indian Peptide Societies.