Bimolecular reaction simulation using Weighted Ensemble Brownian dynamics and the University of Houston Brownian Dynamics program.
We discuss here the implementation of the Weighted Ensemble Brownian (WEB) dynamics algorithm of Huber and Kim in the University of Houston Brownian Dynamics (UHBD) suite of programs and its application to bimolecular association problems. WEB dynamics is a biased Brownian dynamics (BD) algorithm that is more efficient than the standard Northrup-Allison-McCammon (NAM) method in cases where reaction events are infrequent because of intervening free energy barriers. Test cases reported here include the Smoluchowski rate for association of spheres, the association of the enzyme copper-zinc superoxide dismutase with superoxide anion, and the binding of the superpotent sweetener N-(p-cyanophenyl)-N'-(diphenylmethyl)-guanidinium acetic acid to a monoclonal antibody fragment, NC6.8. Our results show that the WEB dynamics algorithm is a superior simulation method for enzyme-substrate reaction encounters with large free energy barriers.
Rojnuckarin
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Department of Chemical Engineering, University of Wisconsin, Madison, Wisconsin 53706, USA.
Livesay
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Subramaniam
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D000085:Acetates / Q000737:chemistry; D000465:Algorithms; D000911:Antibodies, Monoclonal / Q000737:chemistry*; D001665:Binding Sites; D001671:Biochemistry / Q000379:methods*; D003198:Computer Simulation; D019281:Dimerization; D006146:Guanidines / Q000737:chemistry; D007128:Immunoglobulin Fragments / Q000737:chemistry*; D007700:Kinetics; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D055672:Static Electricity; D013482:Superoxide Dismutase / Q000737:chemistry* / Q000378:metabolism; D013481:Superoxides / Q000737:chemistry* / Q000378:metabolism; D013549:Sweetening Agents / Q000737:chemistry; D013816:Thermodynamics
D000085:Acetates; D000911:Antibodies, Monoclonal; D006146:Guanidines; D007128:Immunoglobulin Fragments; D013549:Sweetening Agents; D013481:Superoxides; C083643:NC 174; D013482:Superoxide Dismutase