"Entropy Loss of Hydroxyl Groups of Balanol upon Binding to Protein Kinase A" by Chung F. Wong

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Entropy Loss of Hydroxyl Groups of Balanol upon Binding to Protein Kinase A

Journal of Chemical Education (2002)

Chung F. Wong, University of California, San Diego
J. Andrew McCammon, University of California, San Diego
Gergely Gidofalvi, University of Chicago

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Abstract

This article describes a short project for an undergraduate to learn several techniques for computer-aided drug design. The project involves estimating the loss of the rotational entropy of the hydroxyl groups of balanol upon its binding to the enzyme protein kinase A (PKA), as the entropy loss can significantly influence PKA balanol binding affinity. This work employs semiempirical quantum mechanical techniques for estimating the potential energy curves for the rotation of the hydroxyl groups of balanol in vacuum and in PKA, and solves the Poisson equation to correct the potential energy curves for hydration effects. Statistical mechanical principles are then applied to estimate the desired entropy loss from the potential energy curves. The analysis examines the influence of hydration effects on the rotational preference of the hydroxyl groups and the significance of the rotational entropy in determining binding affinity.

Disciplines

Analytical Chemistry

Publication Date

January 9, 2002

DOI

10.1021/ed079p1122

Citation Information

Chung F. Wong, J. Andrew McCammon and Gergely Gidofalvi. "Entropy Loss of Hydroxyl Groups of Balanol upon Binding to Protein Kinase A" Journal of Chemical Education Vol. 79 Iss. 9 (2002) p. 1122 - 1126
Available at: http://works.bepress.com/chung-wong/46/