Electrostatics and diffusion of molecules in solution:
simulations with the University of Houston, Brownian Dynamics program

a Department of Chemistry: University of South Alabama, Mobile. Al 36688. USA
b Department of Chemistry and Biochemistry and Department of Pharmacology University of California San Diego,
La Jolla. CA 92093-0365. USA
c European Molecular Biology Laboratory: Meyerhofstr. 1, 69012 Heidelberg, Germany
d Bristol Myers-Squibb Pharmaceutical Research Institute, PO. Box 4000, Princeton. NJ 08543. USA
c Laboratory of Physical Chemistry. Swiss Federal Institute of Technology, ETH Zentrum, CH-8092. Zrich, Switzerland
f Department of Mathematics. University of Houston. Houston TX, 77204-3476. USA
g Center for Advanced Research in Biotechnology. National Institute of Standards and Technology. 9600 Gudelsky Dr..
Rockville. MD 20850-3479. USA

Abstract:
This paper is a follow-up to the initial communication (Comput. Phys. Commun. 62 ( 1991 ) 187-197) on the Brownian Dynamics/Electrostatics program UHBD developed at the University of Houston. The program is now capable of computing pK_as of ionizable groups in proteins, performing Brownian dynamics simulations with a flexible substrate and target, and molecular mechanics/dynamics calculations using a continuum solvent. These new capabilities and other features are discussed along with selected applications which illustrate the capabilities of the current version of UHBD.

Introduction:
Electrostatics of biomolecules and diffusion of substrates to receptors are important concepts in our description of many biophysical and biochemical processes. Computer simulations at the molecular level can aid in the interpretation of such processes and in the design of systems with prescribed transport or kinetic properties.

In this paper, we describe a computer program that has been written to conduct such simulations. The program is named UHBD, for University of Houston Brownian Dynamics. The UHBD program is capable of performing and analyzing electrostatic properties of macromolecules as well as complex diffusional receptor substrate encounters. To date, the major applications of the program have been to analyze the diffusional encounters of enzymes and their substrates and the electrostatic stability of protein-ligand complexes; all the systems considered have been diluted in the principal solute species.

Comp. Phys. Comm. (1995) 91, 57-95.

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