Literature DB >> 15869376

Modeling water, the hydrophobic effect, and ion solvation.

Ken A Dill1, Thomas M Truskett, Vojko Vlachy, Barbara Hribar-Lee.   

Abstract

Water plays a central role in the structures and properties of biomolecules--proteins, nucleic acids, and membranes--and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global properties-water's thermodynamics, phase diagram, and solvation properties, for example-and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of water-as a pure liquid and as a solvent-derive from the geometric and hydrogen bonding properties of water.

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Year:  2005        PMID: 15869376     DOI: 10.1146/annurev.biophys.34.040204.144517

Source DB:  PubMed          Journal:  Annu Rev Biophys Biomol Struct        ISSN: 1056-8700


  84 in total

1.  A Density Functional Theory Evaluation of Hydrophobic Solvation: Ne, Ar and Kr in a 50-Water Cluster. Implications for the Hydrophobic Effect.

Authors:  Nadya Kobko; Mateusz Marianski; Amparo Asensio; Robert Wieczorek; J J Dannenberg
Journal:  Comput Theor Chem       Date:  2011-11-22       Impact factor: 1.926

2.  Effects of select anions from the Hofmeister series on the gas-phase conformations of protein ions measured with traveling-wave ion mobility spectrometry/mass spectrometry.

Authors:  Samuel I Merenbloom; Tawnya G Flick; Michael P Daly; Evan R Williams
Journal:  J Am Soc Mass Spectrom       Date:  2011-09-13       Impact factor: 3.109

3.  A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

Authors:  Hui Sun; Jiayi Wen; Yanxiang Zhao; Bo Li; J Andrew McCammon
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

4.  Protein-ligand interactions: thermodynamic effects associated with increasing nonpolar surface area.

Authors:  James M Myslinski; John E DeLorbe; John H Clements; Stephen F Martin
Journal:  J Am Chem Soc       Date:  2011-10-27       Impact factor: 15.419

5.  Effects of monovalent anions on a temperature-dependent heat capacity change for Escherichia coli SSB tetramer binding to single-stranded DNA.

Authors:  Alexander G Kozlov; Timothy M Lohman
Journal:  Biochemistry       Date:  2006-04-25       Impact factor: 3.162

Review 6.  Heat capacity changes associated with nucleic acid folding.

Authors:  Peter J Mikulecky; Andrew L Feig
Journal:  Biopolymers       Date:  2006-05       Impact factor: 2.505

7.  Hydrophobicity density profiles to predict thermal stability enhancement in proteins.

Authors:  Angel Mozo-Villarías; Juan Cedano; Enrique Querol
Journal:  Protein J       Date:  2006-12       Impact factor: 2.371

8.  'Reverse' Hofmeister effects on the sol-gel transition rates for an α-helical peptide-PEG bioconjugate.

Authors:  Sean C O'Neill; Ankit D Kanthe; Jacob A Weber; Raymond S Tu
Journal:  Phys Chem Chem Phys       Date:  2018-08-01       Impact factor: 3.676

9.  Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.

Authors:  Faik N Musayev; Martino L di Salvo; Tzu-Ping Ko; Amit K Gandhi; Ashwini Goswami; Verne Schirch; Martin K Safo
Journal:  Protein Sci       Date:  2007-08-31       Impact factor: 6.725

10.  An Investigation of Ion-Pairing of Alkali Metal Halides in Aqueous Solutions Using the Electrical Conductivity and the Monte Carlo Computer Simulation Methods.

Authors:  Jure Gujt; Marija Bešter-Rogač; Barbara Hribar-Lee
Journal:  J Mol Liq       Date:  2014-02       Impact factor: 6.165

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