Literature DB >> 10423414

Conformational equilibria of alkanes in aqueous solution: relationship to water structure near hydrophobic solutes.

H S Ashbaugh1, S Garde, G Hummer, E W Kaler, M E Paulaitis.   

Abstract

Conformational free energies of butane, pentane, and hexane in water are calculated from molecular simulations with explicit waters and from a simple molecular theory in which the local hydration structure is estimated based on a proximity approximation. This proximity approximation uses only the two nearest carbon atoms on the alkane to predict the local water density at a given point in space. Conformational free energies of hydration are subsequently calculated using a free energy perturbation method. Quantitative agreement is found between the free energies obtained from simulations and theory. Moreover, free energy calculations using this proximity approximation are approximately four orders of magnitude faster than those based on explicit water simulations. Our results demonstrate the accuracy and utility of the proximity approximation for predicting water structure as the basis for a quantitative description of n-alkane conformational equilibria in water. In addition, the proximity approximation provides a molecular foundation for extending predictions of water structure and hydration thermodynamic properties of simple hydrophobic solutes to larger clusters or assemblies of hydrophobic solutes.

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Year:  1999        PMID: 10423414      PMCID: PMC1300360          DOI: 10.1016/S0006-3495(99)76920-1

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  24 in total

1.  Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding.

Authors: 
Journal:  Phys Rev Lett       Date:  1996-12-09       Impact factor: 9.161

2.  Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes.

Authors:  G Hummer; A E García; D M Soumpasis
Journal:  Biophys J       Date:  1995-05       Impact factor: 4.033

3.  Hydration and conformational equilibria of simple hydrophobic and amphiphilic solutes.

Authors:  H S Ashbaugh; E W Kaler; M E Paulaitis
Journal:  Biophys J       Date:  1998-08       Impact factor: 4.033

4.  Statistical mechanical treatment of the structural hydration of biological macromolecules: Results for B-DNA.

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Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1994-12

5.  Computation of the water density distribution at the ice-water interface using the potentials-of-mean-force expansion.

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Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1994-01

6.  The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins.

Authors:  G Hummer; S Garde; A E García; M E Paulaitis; L R Pratt
Journal:  Proc Natl Acad Sci U S A       Date:  1998-02-17       Impact factor: 11.205

7.  Reconstructing the protein-water interface.

Authors:  V A Makarov; B K Andrews; B M Pettitt
Journal:  Biopolymers       Date:  1998-06       Impact factor: 2.505

8.  Hydration of an alpha-helical peptide: comparison of theory and molecular dynamics simulation.

Authors:  A E García; G Hummer; D M Soumpasis
Journal:  Proteins       Date:  1997-04

Review 9.  Areas, volumes, packing and protein structure.

Authors:  F M Richards
Journal:  Annu Rev Biophys Bioeng       Date:  1977

10.  Statistical mechanics of the B----Z transition of DNA: contribution of diffuse ionic interactions.

Authors:  D M Soumpasis
Journal:  Proc Natl Acad Sci U S A       Date:  1984-08       Impact factor: 11.205

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  5 in total

1.  Recent progress in understanding hydrophobic interactions.

Authors:  Emily E Meyer; Kenneth J Rosenberg; Jacob Israelachvili
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-05       Impact factor: 11.205

2.  Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water.

Authors:  Manoj V Athawale; Gaurav Goel; Tuhin Ghosh; Thomas M Truskett; Shekhar Garde
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-10       Impact factor: 11.205

3.  Water-like solvation thermodynamics in a spherically symmetric solvent model with two characteristic lengths.

Authors:  Sergey V Buldyrev; Pradeep Kumar; Pablo G Debenedetti; Peter J Rossky; H Eugene Stanley
Journal:  Proc Natl Acad Sci U S A       Date:  2007-12-11       Impact factor: 11.205

4.  Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.

Authors:  Luke J Gosink; Christopher C Overall; Sarah M Reehl; Paul D Whitney; David L Mobley; Nathan A Baker
Journal:  J Phys Chem B       Date:  2017-01-04       Impact factor: 2.991

Review 5.  Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins.

Authors:  Robert C Harris; B Montgomery Pettitt
Journal:  J Phys Condens Matter       Date:  2016-02-02       Impact factor: 2.333

  5 in total

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