Literature DB >> 25127002

New insights into the role of water in biological function: studying solvated biomolecules using terahertz absorption spectroscopy in conjunction with molecular dynamics simulations.

Valeria Conti Nibali1, Martina Havenith.   

Abstract

In life science, water is the ubiquitous solvent, sometimes even called the "matrix of life". There is increasing experimental and theoretical evidence that solvation water is not a passive spectator in biomolecular processes. New experimental techniques can quantify how water interacts with biomolecules and, in doing so, differs from "bulk" water. Terahertz (THz) absorption spectroscopy has turned out to be a powerful tool to study (bio)molecular hydration. The main concepts that have been developed in the recent years to describe the underlying solute-induced sub-picosecond dynamics of the hydration shell are discussed herein. Moreover, we highlight recent findings that show the significance of hydrogen bond dynamics for the function of antifreeze proteins and for molecular recognition. In all of these examples, a gradient of water motion toward functional sites of proteins is observed, the so-called "hydration funnel". By means of molecular dynamics simulations, we provide new evidence for a specific water-protein coupling as the cause of the observed dynamical heterogeneity. The efficiency of the coupling at THz frequencies is explained in terms of a two-tier (short- and long-range) solute-solvent interaction.

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Year:  2014        PMID: 25127002     DOI: 10.1021/ja504441h

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  42 in total

1.  Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state.

Authors:  Jessica Dielmann-Gessner; Moran Grossman; Valeria Conti Nibali; Benjamin Born; Inna Solomonov; Gregg B Fields; Martina Havenith; Irit Sagi
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-25       Impact factor: 11.205

2.  Peptide-Protein Binding Investigated by Far-IR Spectroscopy and Molecular Dynamics Simulations.

Authors:  Yoann Cote; Yves Nominé; Juan Ramirez; Petra Hellwig; Roland H Stote
Journal:  Biophys J       Date:  2017-06-20       Impact factor: 4.033

3.  The Soybean Lipoxygenase-Substrate Complex: Correlation between the Properties of Tunneling-Ready States and ENDOR-Detected Structures of Ground States.

Authors:  Adam R Offenbacher; Ajay Sharma; Peter E Doan; Judith P Klinman; Brian M Hoffman
Journal:  Biochemistry       Date:  2020-02-05       Impact factor: 3.162

4.  Dynamics and mechanism of ultrafast water-protein interactions.

Authors:  Yangzhong Qin; Lijuan Wang; Dongping Zhong
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-23       Impact factor: 11.205

5.  Label-free sensing of the binding state of MUC1 peptide and anti-MUC1 aptamer solution in fluidic chip by terahertz spectroscopy.

Authors:  Xiang Zhao; Mingkun Zhang; Dongshan Wei; Yunxia Wang; Shihan Yan; Mengwan Liu; Xiang Yang; Ke Yang; Hong-Liang Cui; Weiling Fu
Journal:  Biomed Opt Express       Date:  2017-09-11       Impact factor: 3.732

Review 6.  Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry.

Authors:  Paul S Cremer; Amar H Flood; Bruce C Gibb; David L Mobley
Journal:  Nat Chem       Date:  2017-12-19       Impact factor: 24.427

7.  Water is an active matrix of life for cell and molecular biology.

Authors:  Philip Ball
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-07       Impact factor: 11.205

Review 8.  Why Proteins are Big: Length Scale Effects on Equilibria and Kinetics.

Authors:  Kenneth A Rubinson
Journal:  Protein J       Date:  2019-04       Impact factor: 2.371

9.  Pressure and Temperature Effects on the Activity and Structure of the Catalytic Domain of Human MT1-MMP.

Authors:  Elena Decaneto; Saba Suladze; Christopher Rosin; Martina Havenith; Wolfgang Lubitz; Roland Winter
Journal:  Biophys J       Date:  2015-12-01       Impact factor: 4.033

10.  Molecular Dynamics Simulations of Macromolecular Crystals.

Authors:  David S Cerutti; David A Case
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2018-11-16
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