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Computational Research in Molecular Chemistry
Simulation of the Diffusion-Controlled Reaction Between Superoxide and Superoxide Dismutase. II. Detailed ModelsS.A. Allison, R.J. Bacquet and J.A. McCammonBiopolymers, Vol. 27, Issue 2, pp. 251-269 (1988)    [PubMed 2833950]
A two-stage Brownian dynamics simulation method is used to study the diffusion-influenced bimolecular reaction between superoxide and superoxide dismutase (SOD). The crystal structure of the dimeric enzyme is used in constructing detailed topographical and electrostatic models. Several electrostatic models are considered. In the most realistic, the excluded volume of the protein, which is impermeable to penetration by mobile ions, is assigned a dielectric constant of 2 and the surrounding "solvent" is assigned a value of 78. A finite difference method is used to solve the linearized Poisson-Boltzmann equation. For native SOD, the simulations reproduce the pronounced salt dependence of the rate constant observed experimentally. This salt dependence is attributed to electrostatic interactions between enzyme and substrate that are inherently attractive and amplified by the low dielectric constant of the protein interior. The simulation method is also applied to a modified enzyme, acylated SOD.
Symposium Overview. Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and WaterGeorge L. Wilcox, Florante A. Quiocho, Cyrus Levinthal, Stephen C. Harvey, Gerald M. Maggiora and J. Andrew McCammonJournal of Computer-Aided Molecular Design, Vol. 1, No. 4, pp. 271-281 (1988)    [PubMed 3193133]
This was the first academically organized conference dealing exclusively with biological applications of supercomputers. The symposium was organized to explore in a systematic way the current state of the art in application of large scale computation to problems in physical biochemistry. The conference was held September 13-16, 1987 on the campus of the University of Minnesota in Minneapolis, Minnesota. Primary support was provided by the Minnesota Supercomputer Institute; other support came from other divisions of the University and from several corporations. Total attendance was over 140, including 24 speakers and session chairpersons.
Quantum Simulation of Ferrocytochrome cChong Zheng, Chung F. Wong, J. Andrew McCammon and Peter G. WolynesNature, Vol. 334, No. 6184, pp. 726-728 (1988)    [PubMed 2842687]
The dramatic progress in the understanding of the dynamics of biomolecules has been largely fuelled by computer simulations based on the law of classical mechanics. However in some respects biomolecules are at the borders of the domain of applicability of classical mechanics. The role of quantum mechanical effects in biomolecular structure and function is therefore worth investigating. Here we present preliminary results from a quantum simulation of a protein and contrast them with results from full classical simulations. The most significant differences are found in motions of high frequency, such as bond stretching or the torsional oscillation of groups that bear hydrogen atoms. The amplitudes of such motions are significantly increased by the penetration of atoms into classically forbidden regions. These differences will directly influence the rates of such processes as proton and electron transfer.
Ionic Strength Dependence of Enzyme-Substrate Interactions. Monte Carlo and Poisson-Boltzmann Results for Superoxide DismutaseRussell J. Bacquet, J. Andrew McCammon and Stuart A. AllisonJournal of Physical Chemistry, Vol. 92, No. 25, pp. 7134-7141 (1988)    
Monte Carlo (MC) simulations have been carried out for simplified models of the enzyme superoxide dismutase at infinite dilution in several aqueous salt solutions. Comparison is made to results obtained from numerical algorithms based on Poisson-Boltzmann (PB) theory. The impact of approximations inherent in the PB approach is found to be small. The diffusion-limited rate constant for enzyme-substrate association is computed from the MC data. The results are qualitatively in accord with experimental data. Better agreement can be obtained by using more detailed models, but this requires the use of PB rather than MC due to computational requirements. The major conclusion of this study is therefore that the approximations inherent in the PB theory are acceptable in the present application.
Computer Simulation of Proteins: Classical and Quantum DynamicsC.F. Wong and J.A. McCammonIn "Science at the John von Neumann Center, 1987," L. Anacker, Ed., John von Neumann Center, Princeton University, pp. 131-134 (1988)    
Supercomputer Simulation and Biomolecular DesignJ.A. McCammon, G. Ganti, T.P. Lybrand and C.F. WongIn "High Speed Computing, Scientific Applications and Algorithm Design," R.B. Wilhelmson, Ed., University of Illinois Press, pp. 155-161 (1988)    
Molecular Dynamics Simulation Studies of Water and Protein SolutionsC.F. Wong and J.A. McCammonIn "Science on the ETA10," L. Anacker, Ed., John Von Neumann Center, Princeton University, pp. 72-77 (1988)    
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