Literature DB >> 23289748

Importance of protein conformational motions and electrostatic anchoring sites on the dynamics and hydrogen bond properties of hydration water.

Somedatta Pal1, Sanjoy Bandyopadhyay.   

Abstract

The microscopic dynamic properties of water molecules present in the vicinity of a protein are expected to be sensitive to its local conformational motions and the presence of polar and charged groups at the surface capable of anchoring water molecules through hydrogen bonds. In this work, we attempt to understand such sensitivity by performing detailed molecular dynamics simulations of the globular protein barstar solvated in aqueous medium. Our calculations demonstrate that enhanced confinement at the protein surface on freezing its local motions leads to increasingly restricted water mobility with long residence times around the secondary structures. It is found that the inability of the surface water molecules to bind with the protein residues by hydrogen bonds in the absence of protein-water (PW) electrostatic interactions is compensated by enhanced water-water hydrogen bonds around the protein with uniform bulklike behaviors. Importantly, it is further noticed that in contrast to the PW hydrogen bond relaxation time scale, the kinetics of the breaking and formation of such bonds are not affected on freezing the protein's conformational motions.

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Year:  2013        PMID: 23289748     DOI: 10.1021/la303959m

Source DB:  PubMed          Journal:  Langmuir        ISSN: 0743-7463            Impact factor:   3.882


  4 in total

1.  Variability of the Cyclin-Dependent Kinase 2 Flexibility Without Significant Change in the Initial Conformation of the Protein or Its Environment; a Computational Study.

Authors:  Mohammad Taghizadeh; Bahram Goliaei; Armin Madadkar-Sobhani
Journal:  Iran J Biotechnol       Date:  2016-06       Impact factor: 1.671

2.  Anomalous behavior of water inside the SecY translocon.

Authors:  Sara Capponi; Matthias Heyden; Ana-Nicoleta Bondar; Douglas J Tobias; Stephen H White
Journal:  Proc Natl Acad Sci U S A       Date:  2015-07-02       Impact factor: 11.205

3.  Detecting and Characterizing the Kinetic Activation of Thermal Networks in Proteins: Thermal Transfer from a Distal, Solvent-Exposed Loop to the Active Site in Soybean Lipoxygenase.

Authors:  Jan Paulo T Zaragoza; Andy Nguy; Natalie Minnetian; Zhenyu Deng; Anthony T Iavarone; Adam R Offenbacher; Judith P Klinman
Journal:  J Phys Chem B       Date:  2019-10-03       Impact factor: 2.991

4.  Theoretical Exploring Selective-Binding Mechanisms of JAK3 by 3D-QSAR, Molecular Dynamics Simulation and Free Energy Calculation.

Authors:  Jingyu Zhu; Qianqian Yu; Yanfei Cai; Yun Chen; Hui Liu; Wenqing Liang; Jian Jin
Journal:  Front Mol Biosci       Date:  2020-05-27
  4 in total

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