了解肽在水-乙腈混合物中的优先相互作用与蛋白质-溶剂接触表面积之间的关系。

IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Monika Phougat, Narinder Singh Sahni, Devapriya Choudhury
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引用次数: 0

摘要

极性水溶性有机溶剂(POS)对蛋白质结构、稳定性和功能活性的影响是一个非常有趣和复杂的课题。本研究通过大量分子动力学模拟,研究了半极性钝化溶剂乙腈(ACN)对阻断的 Ace-Gly-X-Gly-Nme 三肽(其中 Ace 和 Nme 分别代表乙酰基和 N-甲基酰胺基团,X 代表任何氨基酸)溶解特性的影响。在 χACN = 0.1-0.9 的范围内,对每种肽进行了五种不同浓度的 ACN 模拟。使用柯克伍德-巴夫积分法计算的优先溶解参数(Γ)用于评估多肽与水/ACN 的相互作用。此外,还采用加权沃罗诺网格划分法获得了三向数据集,其中包含肽原子与水/ACN 原子间的四种时间平均接触表面积类型。利用一种称为 N 向偏最小二乘法(NPLS)的数学技术,从接触表面积中预测肽与水/ACN 之间的优先相互作用。此外,还使用代表一系列疏水性的 10 个氨基酸子集研究了肽与溶剂相互作用的温度依赖性。在 283 至 343 K 的五个温度范围内进行了 MD 模拟,随后对数据进行了分析,重点是优先溶解和肽-溶剂接触表面积。结果表明,利用肽和溶剂成分之间的接触表面积可以成功预测水/ACN 混合物在不同 ACN 浓度和温度下的优先相互作用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Understanding the relationship between preferential interactions of peptides in water-acetonitrile mixtures with protein-solvent contact surface area

Understanding the relationship between preferential interactions of peptides in water-acetonitrile mixtures with protein-solvent contact surface area

The influence of polar, water-miscible organic solvents (POS) on protein structure, stability, and functional activity is a subject of significant interest and complexity. This study examines the effects of acetonitrile (ACN), a semipolar, aprotic solvent, on the solvation properties of blocked Ace-Gly-X-Gly-Nme tripeptides (where Ace and Nme stands for acetyl and N-methyl amide groups respectively and X is any amino acid) through extensive molecular dynamics simulations. Individual simulations were conducted for each peptide, encompassing five different ACN concentrations within the range of χACN = 0.1–0.9. The preferential solvation parameter (Γ) calculated using the Kirkwood-Buff integral method was used for the assessment of peptide interactions with water/ACN. Additionally, weighted Voronoi tessellation was applied to obtain a three-way data set containing four time-averaged contact surface area types between peptide atoms and water/ACN atoms. A mathematical technique known as N-way Partial Least Squares (NPLS) was utilized to anticipate the preferential interactions between peptides and water/ACN from the contact surface areas. Furthermore, the temperature dependency of peptide-solvent interactions was investigated using a subset of 10 amino acids representing a range of hydrophobicities. MD simulations were conducted at five temperatures, spanning from 283 to 343 K, with subsequent analysis of data focusing on both preferential solvation and peptide-solvent contact surface areas. The results demonstrate the efficacy of utilizing contact surface areas between the peptide and solvent constituents for successfully predicting preferential interactions in water/ACN mixtures across various ACN concentrations and temperatures.

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来源期刊
Journal of Computer-Aided Molecular Design
Journal of Computer-Aided Molecular Design 生物-计算机:跨学科应用
CiteScore
8.00
自引率
8.60%
发文量
56
审稿时长
3 months
期刊介绍: The Journal of Computer-Aided Molecular Design provides a form for disseminating information on both the theory and the application of computer-based methods in the analysis and design of molecules. The scope of the journal encompasses papers which report new and original research and applications in the following areas: - theoretical chemistry; - computational chemistry; - computer and molecular graphics; - molecular modeling; - protein engineering; - drug design; - expert systems; - general structure-property relationships; - molecular dynamics; - chemical database development and usage.
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