评估蛋白质周围水的长程定向排序:拔河情景的特征

IF 2.9 3区 化学 Q3 CHEMISTRY, PHYSICAL
Subhabrata Hazra, Biman Jana
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引用次数: 0

摘要

生物分子对水结构和动力学的长期扰动由于其在生物分子识别中的潜在作用而受到极大的关注。在本文中,我们研究了在生理盐环境存在和不存在的情况下,具有不同总电荷(+8,0和-8)的蛋白质周围水分子的局部和远程取向结构。在蛋白质的第一个水合层观察到大量的in取向水分子,而不管它们的总电荷。从第三水合层开始,水分子主要报告各自蛋白质的总电荷。在没有生理盐环境的情况下,这种长程排序甚至持续到第9水合层,在生理盐环境下,超过第5水合层后就消失了。蛋白质不同类型表面原子周围的长程定向排序表现出特别丰富和异质性的行为。当表面原子的电荷和蛋白质的总电荷相反时,在水分子的长程取向排序中表现出明显的拔河特征。当水在较低的距离报告表面原子的电荷时,水分子在较远的距离报告蛋白质的总电荷,交叉约为10 Å。即使在生理盐环境下,这种现象仍然存在。水介导的取向波的破坏性/建设性叠加的证据源自两个具有相似/相反总电荷的单独蛋白质,这里也证明了。这些结果对于研究蛋白质-蛋白质、蛋白质-配体、蛋白质- dna等生物分子间水介导的远距离识别现象具有重要意义。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Evaluating long-range orientational ordering of water around proteins: Signature of a tug-of-war scenario
Long-range perturbations of water structure and dynamics by the biomolecules are subject of great interests due to their potential role in biomolecular recognition. In this article, we examine the local and long-range orientational structure of water molecules surrounding the proteins with different total charges (+8, 0 and -8) both with and without the presence of physiological salt environment. A prominent population of In-oriented water molecules is observed at the first hydration shell of the proteins, irrespective of their total charges. Starting from third hydration layer, water molecules report mainly the total charge of the respective protein. This long-range ordering persists up to even ninth hydration layer without physiological salt environment and vanishes beyond the fifth hydration shell at physiological salt environment. Long-range orientational orderings around different types of surface atoms of a protein show particularly rich and heterogeneous behaviours. When the surface atom’s charge and protein’s total charge are opposite, a clear signature of tug-of-war is demonstrated in the long-range orientational ordering of water molecules. While the water reports surface atom’s charge at lower distances, water molecules at longer distances reports total charge of the protein with a crossover around 10 Å. This phenomena persist even in the presence of physiological salt environment. The evidence of destructive/constructive superposition of water-mediated orientation waves originating from two individual proteins with similar/opposite total charges is also demonstrated here. These results are important in entangling long-range water-mediated recognition phenomena among biomolecules (protein-protein, protein-ligand, protein-DNA, etc).
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来源期刊
Physical Chemistry Chemical Physics
Physical Chemistry Chemical Physics 化学-物理:原子、分子和化学物理
CiteScore
5.50
自引率
9.10%
发文量
2675
审稿时长
2.0 months
期刊介绍: Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.
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