Literature DB >> 19425247

Hydration water dynamics near biological interfaces.

Margaret E Johnson1, Cecile Malardier-Jugroot, Rajesh K Murarka, Teresa Head-Gordon.   

Abstract

We performed classical molecular dynamics simulations using both fixed-charge and polarizable water and protein force fields to contrast the hydration dynamics near hydrophilic and amphiphilic peptides as a function of temperature. The high peptide concentrations we use serve as a model for the surface of folded proteins where hydration layers around each residue overlap significantly. Through simulation we determine that there are notable differences in the water dynamics analyzed from the outer and inner hydration layer regions of the amphiphilic peptide solution that explains the experimentally observed presence of two translational relaxations, while the hydrophilic peptide solution shows only a single non-Arrhenius translational process with no distinction between hydration layers. Given that water dynamics for the amphiphilic peptide system reproduces all known rotational and translational hydration dynamical anomalies exhibited by hydration water near protein surfaces, our analysis provides strong evidence that dynamical signatures near biological interfaces arises because of frustration in the hydration dynamics induced by chemical heterogeneity, as opposed to just topological roughness, of the protein surface.

Entities:  

Mesh:

Substances:

Year:  2009        PMID: 19425247     DOI: 10.1021/jp806183v

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  10 in total

1.  The influence of hydrogen bonding on partition coefficients.

Authors:  Nádia Melo Borges; Peter W Kenny; Carlos A Montanari; Igor M Prokopczyk; Jean F R Ribeiro; Josmar R Rocha; Geraldo Rodrigues Sartori
Journal:  J Comput Aided Mol Des       Date:  2017-01-04       Impact factor: 3.686

2.  Site-specific hydration dynamics in the nonpolar core of a molten globule by dynamic nuclear polarization of water.

Authors:  Brandon D Armstrong; Jennifer Choi; Carlos López; Darryl A Wesener; Wayne Hubbell; Silvia Cavagnero; Songi Han
Journal:  J Am Chem Soc       Date:  2011-03-28       Impact factor: 15.419

3.  Current status of the AMOEBA polarizable force field.

Authors:  Jay W Ponder; Chuanjie Wu; Pengyu Ren; Vijay S Pande; John D Chodera; Michael J Schnieders; Imran Haque; David L Mobley; Daniel S Lambrecht; Robert A DiStasio; Martin Head-Gordon; Gary N I Clark; Margaret E Johnson; Teresa Head-Gordon
Journal:  J Phys Chem B       Date:  2010-03-04       Impact factor: 2.991

4.  Amide Spectral Fingerprints are Hydrogen Bonding-Mediated.

Authors:  Sara Gómez; Cettina Bottari; Franco Egidi; Tommaso Giovannini; Barbara Rossi; Chiara Cappelli
Journal:  J Phys Chem Lett       Date:  2022-06-30       Impact factor: 6.888

Review 5.  New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.

Authors:  Jejoong Yoo; Aleksei Aksimentiev
Journal:  Phys Chem Chem Phys       Date:  2018-03-28       Impact factor: 3.676

6.  Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion.

Authors:  Dominik Budday; Sigrid Leyendecker; Henry van den Bedem
Journal:  J Chem Inf Model       Date:  2018-10-09       Impact factor: 4.956

7.  Thermodynamics and Free Energy Landscape of BAR-Domain Dimerization from Molecular Simulations.

Authors:  Adip Jhaveri; Dhruw Maisuria; Matthew Varga; Dariush Mohammadyani; Margaret E Johnson
Journal:  J Phys Chem B       Date:  2021-04-07       Impact factor: 2.991

Review 8.  The "autothixotropic" phenomenon of water and its role in proton transfer.

Authors:  Nada Verdel; Igor Jerman; Peter Bukovec
Journal:  Int J Mol Sci       Date:  2011-10-31       Impact factor: 5.923

9.  Direct observation of the dynamics of single metal ions at the interface with solids in aqueous solutions.

Authors:  Maria Ricci; William Trewby; Clodomiro Cafolla; Kislon Voïtchovsky
Journal:  Sci Rep       Date:  2017-02-23       Impact factor: 4.379

10.  Exploring the behaviour of water in glycerol solutions by using delayed luminescence.

Authors:  Rosaria Grasso; Francesco Musumeci; Marisa Gulino; Agata Scordino
Journal:  PLoS One       Date:  2018-01-29       Impact factor: 3.240

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.