School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
J Phys Chem B. 2023 Jul 13;127(27):6144-6153. doi: 10.1021/acs.jpcb.3c02642. Epub 2023 Jun 28.
Multiway analysis, a class of techniques developed for the purpose of studying multi-dimensional multivariate data, has been applied to study the dynamical structure of the first solvation layer of Ace-Gly-X-Gly-Nme peptides (where X is any amino acid) perturbed with the increase in concentrations of acetonitrile. Separate MD simulations of each peptide were carried out in five different concentrations of acetonitrile. Association of peptide, water, and acetonitrile atoms was quantified in terms of the relative abundance of Delaunay tetrahedra whose vertices could be centered on either the peptide, acetonitrile, or water atoms. A three-way data set comprising nine types of Delaunay tetrahedra in the first dimension, five concentrations of acetonitrile in the second dimension, and 26 different peptides in the third dimension was subjected to two different multiway methods viz., the constrained PARAFAC and the unconstrained Tucker3 analysis. The results unequivocally show that the dynamic peptide-acetonitrile-water association behavior could be solely explained by the hydrophobicity of the central amino acid. The study also demonstrates the utility of multiway analysis for the integration and interpretation of large number of separate MD simulations.
多向分析是一类旨在研究多维多元数据的技术，已被应用于研究 Ace-Gly-X-Gly-Nme 肽（其中 X 是任何氨基酸）第一层溶剂化层的动力学结构，该结构受到乙腈浓度增加的干扰。对每种肽分别进行了 5 种不同浓度乙腈的 MD 模拟。肽、水和乙腈原子的缔合程度用 Delaunay 四面体的相对丰度来量化，其顶点可以以肽、乙腈或水分子为中心。一个由三个方向组成的数据集，包括第一层的九种 Delaunay 四面体、第二层的五种乙腈浓度和第三层的 26 种不同肽，分别进行了两种不同的多向方法，即约束 PARAFAC 和非约束 Tucker3 分析。结果明确表明，动态肽-乙腈-水缔合行为可以仅用中心氨基酸的疏水性来解释。该研究还证明了多向分析在整合和解释大量单独的 MD 模拟方面的实用性。
