Literature DB >> 29166083

Water structure around hydrophobic amino acid side chain analogs using different water models.

Timir Hajari1, Sanjoy Bandyopadhyay1.   

Abstract

The water structure around hydrophobic groups governs various biochemical processes. There is an ongoing debate on whether water molecules near hydrophobic groups are more ordered with greater participation in water-water hydrogen bonding with respect to water in the pure bulk state. The water structure around six different hydrophobic amino acid side chain analog molecules has been studied in pure water using molecular dynamics simulations. The analysis of water tetrahedral order parameter and the number of hydrogen bonds formed by the individual water molecules in the first hydration shell of the hydrophobic analogs provide evidence that both ordering and hydrogen bonds involving water molecules are to some extent reduced in the hydrophobic hydration shell. It is revealed that the water tetrahedrality in the outer part of the first hydrophobic hydration shell is equivalent to bulk water for all the water models except for the TIP4P-2005 model which shows marginally higher tetrahedrality. However, irrespective of the model employed, water tetrahedrality has always been found to be reduced in the inner part of the first hydration shell, which eventually makes the overall water tetrahedrality in the first hydrophobic hydration shell marginally lower than that observed for pure bulk water. Importantly, it is noticed that the decrease in water structuring exhibits solute size dependencies. Around a small solute like methane, the water tetrahedral ordering or hydrogen bonding propensity is quite similar to that of the bulk state. The effect, reduction in water structuring, is however more pronounced for relatively larger solutes.

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Year:  2017        PMID: 29166083     DOI: 10.1063/1.4985671

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  5 in total

1.  What is the hydrophobic interaction contribution to the stabilization of micro-hydrated complexes of trimethylamine oxide (TMAO)? A joint DFT-D, QTAIM, and MESP study.

Authors:  Imene Derbali; Emilie-Laure Zins; Mohammad Esmaïl Alikhani
Journal:  J Mol Model       Date:  2019-11-26       Impact factor: 1.810

2.  The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study.

Authors:  Chi-Jui Feng; Andrei Tokmakoff
Journal:  J Chem Phys       Date:  2017-08-28       Impact factor: 3.488

3.  Insignificant Effect of Temperature on the Structure and Angular Jumps of Water near a Hydrophobic Cation.

Authors:  Adyasa Priyadarsini; Bhabani S Mallik
Journal:  ACS Omega       Date:  2021-03-19

4.  Uncovering the molecular mechanism for dual effect of ATP on phase separation in FUS solution.

Authors:  Chun-Lai Ren; Yue Shan; Pengfei Zhang; Hong-Ming Ding; Yu-Qiang Ma
Journal:  Sci Adv       Date:  2022-09-14       Impact factor: 14.957

5.  Univ-flu: A structure-based model of influenza A virus hemagglutinin for universal antigenic prediction.

Authors:  Jingxuan Qiu; Xinxin Tian; Yaxing Liu; Tianyu Lu; Hailong Wang; Zhuochen Shi; Sihao Lu; Dongpo Xu; Tianyi Qiu
Journal:  Comput Struct Biotechnol J       Date:  2022-08-28       Impact factor: 6.155

  5 in total

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