Jump to main content
Jump to site search

Issue 43, 2012
Previous Article Next Article

Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules

Author affiliations

Abstract

The structures of biomolecules and the strengths of association between them depend critically on interactions with water molecules. Thus, understanding these interactions is a prerequisite for understanding the structure and function of all biomolecules. Inhomogeneous fluid solvation theory provides a framework to derive thermodynamic properties of individual water molecules from a statistical mechanical analysis. In this work, two biomolecules are analysed to probe the distribution and thermodynamics of surrounding water molecules. The great majority of hydration sites are predicted to contribute favourably to the total free energy with respect to bulk water, though hydration sites close to non-polar regions of the solute do not contribute significantly. Analysis of a biomolecule with a positively and negatively charged functional group predicts that a charged species perturbs the free energy of water molecules to a distance of approximately 6.0 Å. Interestingly, short simulations are found to provide converged predictions if samples are taken with sufficient frequency, a finding that has the potential to significantly reduce the required computational cost of such analysis. In addition, the predicted thermodynamic properties of hydration sites with the potential for direct hydrogen bonding interactions are found to disagree significantly for two different water models. This study provides important information on how inhomogeneous fluid solvation theory can be employed to understand the structures and intermolecular interactions of biomolecules.

Graphical abstract: Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules

Back to tab navigation

Article information


Submitted
30 Jul 2012
Accepted
25 Sep 2012
First published
26 Sep 2012

Phys. Chem. Chem. Phys., 2012,14, 15106-15117
Article type
Paper

Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules

D. J. Huggins, Phys. Chem. Chem. Phys., 2012, 14, 15106 DOI: 10.1039/C2CP42631E

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.


Social activity

Search articles by author

Spotlight

Advertisements