Literature DB >> 12069622

Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment.

Vladimir Makarov1, B Montgomery Pettitt, Michael Feig.   

Abstract

Many theoretical, computational, and experimental techniques recently have been successfully used for description of the solvent distribution around macromolecules. In this Account, we consider recent developments in the areas of protein and nucleic acid solvation and hydration as seen by experiment, theory, and simulations. We find that in most cases not only the general phenomena of solvation but even local hydration patterns are more accurately discussed in the context of water distributions rather than individual molecules of water. While a few localized or high-residency waters are often associated with macromolecules in solution (or crystals from aqueous liquors), these are readily and accurately included in this more general description. The goal of this Account is to review the theoretical models used for the description of the interfacial solvent structure on the border near DNA and protein molecules. In particular, we hope to highlight the progress in this field over the past five years with a focus on comparison of simulation and experimental results.

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Year:  2002        PMID: 12069622     DOI: 10.1021/ar0100273

Source DB:  PubMed          Journal:  Acc Chem Res        ISSN: 0001-4842            Impact factor:   22.384


  63 in total

1.  Thermodynamics of the hydrophobicity in crystallization of insulin.

Authors:  Lisa Bergeron; Luis F Filobelo; Oleg Galkin; Peter G Vekilov
Journal:  Biophys J       Date:  2003-12       Impact factor: 4.033

2.  Modeling the hydration layer around proteins: HyPred.

Authors:  Jouko J Virtanen; Lee Makowski; Tobin R Sosnick; Karl F Freed
Journal:  Biophys J       Date:  2010-09-08       Impact factor: 4.033

3.  Molecular dynamics of a protein surface: ion-residues interactions.

Authors:  Ran Friedman; Esther Nachliel; Menachem Gutman
Journal:  Biophys J       Date:  2005-05-13       Impact factor: 4.033

4.  Light-scattering studies of protein solutions: role of hydration in weak protein-protein interactions.

Authors:  A Paliwal; D Asthagiri; D Abras; A M Lenhoff; M E Paulaitis
Journal:  Biophys J       Date:  2005-06-24       Impact factor: 4.033

5.  Role of molecular charge and hydrophilicity in regulating the kinetics of crystal growth.

Authors:  S Elhadj; J J De Yoreo; J R Hoyer; P M Dove
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-07       Impact factor: 11.205

Review 6.  Protein-solvent interactions.

Authors:  Ninad Prabhu; Kim Sharp
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

7.  Molecular dynamics simulations of Trichomonas vaginalis ferredoxin show a loop-cap transition.

Authors:  Tiffany E Weksberg; Gillian C Lynch; Kurt L Krause; B Montgomery Pettitt
Journal:  Biophys J       Date:  2007-02-26       Impact factor: 4.033

8.  Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents.

Authors:  John T King; Evan J Arthur; Charles L Brooks; Kevin J Kubarych
Journal:  J Phys Chem B       Date:  2012-05-07       Impact factor: 2.991

9.  Solvation free energies of alanine peptides: the effect of flexibility.

Authors:  Hironori Kokubo; Robert C Harris; Dilipkumar Asthagiri; B Montgomery Pettitt
Journal:  J Phys Chem B       Date:  2013-12-13       Impact factor: 2.991

10.  Multibody correlations in the hydrophobic solvation of glycine peptides.

Authors:  Robert C Harris; Justin A Drake; B Montgomery Pettitt
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

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