Literature DB >> 27905589

Hydrogen-bond dynamics at the bio-water interface in hydrated proteins: a molecular-dynamics study.

Prithwish K Nandi1, Niall J English1, Zdenek Futera1, Antonio Benedetto2.   

Abstract

Water is fundamental to the biochemistry of enzymes. It is well known that without a minimum amount of water, enzymes are not biologically active. Bare minimal solvation for biological function corresponds to about a single layer of water covering enzymes' surfaces. Many contradictory studies on protein-hydration-water-coupled dynamics have been published in recent decades. Following prevailing wisdom, a dynamical crossover in hydration water (at around 220 K for hydrated lysozymes) can trigger larger-amplitude motions of the protein, activating, in turn, biological functions. Here, we present a molecular-dynamics-simulation study on a solvated model protein (hen egg-white lysozyme), in which we determine, inter alia, the relaxation dynamics of the hydrogen-bond network between the protein and its hydration water molecules on a residue-per-residue basis. Hydrogen-bond breakage/formation kinetics is rather heterogeneous in temperature dependence (due to the heterogeneity of the free-energy surface), and is driven by the magnitude of thermal motions of various different protein residues which provide enough thermal energy to overcome energy barriers to rupture their respective hydrogen bonds with water. In particular, arginine residues exhibit the highest number of such hydrogen bonds at low temperatures, losing almost completely such bonding above 230 K. This suggests that hydration water's dynamical crossover, observed experimentally for hydrated lysozymes at ∼220 K, lies not at the origin of the protein residues' larger-amplitude motions, but rather arises as a consequence thereof. This highlights the need for new experimental investigations, and new interpretations to link protein dynamics to functions, in the context of key interrelationships with the solvation layer.

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Year:  2016        PMID: 27905589     DOI: 10.1039/c6cp05601f

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  8 in total

1.  From protein and its hydration water dynamics to controlling mechano-elasticity of cellular lipid membranes and cell migration via ionic liquids.

Authors:  Antonio Benedetto
Journal:  Biophys Rev       Date:  2020-09-17

2.  From just physics to biophysics of biological systems.

Authors:  Antonio Benedetto
Journal:  Biophys Rev       Date:  2020-09-10

3.  Water-Polymer Coupling Induces a Dynamical Transition in Microgels.

Authors:  Letizia Tavagnacco; Ester Chiessi; Marco Zanatta; Andrea Orecchini; Emanuela Zaccarelli
Journal:  J Phys Chem Lett       Date:  2019-02-12       Impact factor: 6.475

4.  Why Should Metformin Not Be Given in Advanced Kidney Disease? Potential Leads from Computer Simulations.

Authors:  Visnja Kokic Males; Martina Požar
Journal:  ACS Omega       Date:  2021-06-01

Review 5.  Mechanisms of action of ionic liquids on living cells: the state of the art.

Authors:  Pallavi Kumari; Visakh V S Pillai; Antonio Benedetto
Journal:  Biophys Rev       Date:  2020-09-16

6.  Experimental demonstration of the novel "van-Hove integral method (vHI)" for measuring diffusive dynamics by elastic neutron scattering.

Authors:  Antonio Benedetto; Gordon J Kearley
Journal:  Sci Rep       Date:  2021-07-08       Impact factor: 4.379

7.  The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation.

Authors:  Hangxin Liu; Shuqing Xiang; Haomiao Zhu; Li Li
Journal:  Molecules       Date:  2021-09-05       Impact factor: 4.411

8.  Investigation of Dipolar Response of the Hydrated Hen-Egg White Lysozyme Complex under Externally Applied Electric Fields: Insights from Non-equilibrium Molecular Dynamics.

Authors:  HaoLun Wu; Mohammad Reza Ghaani; Prithwish K Nandi; Niall J English
Journal:  J Phys Chem B       Date:  2022-01-21       Impact factor: 2.991

  8 in total

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