Literature DB >> 10920003

Bimolecular reaction simulation using Weighted Ensemble Brownian dynamics and the University of Houston Brownian Dynamics program.

A Rojnuckarin1, D R Livesay, S Subramaniam.   

Abstract

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.

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Year:  2000        PMID： 10920003      PMCID： PMC1300969          DOI： 10.1016/S0006-3495(00)76327-2

Source DB:  PubMed          Journal:  Biophys J        ISSN： 0006-3495            Impact factor:   4.033


  21 in total

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Authors:  G A Huber; S Kim
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Authors:  A Rojnuckarin; S Kim; S Subramaniam
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Authors:  C L Fisher; D E Cabelli; R A Hallewell; P Beroza; T P Lo; E D Getzoff; J A Tainer
Journal:  Proteins       Date:  1997-09

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Authors:  S A Allison; R J Bacquet; J A McCammon
Journal:  Biopolymers       Date:  1988-02       Impact factor: 2.505

6.  Computer modeling of electrostatic steering and orientational effects in antibody-antigen association.

Authors:  R E Kozack; M J d'Mello; S Subramaniam
Journal:  Biophys J       Date:  1995-03       Impact factor: 4.033

7.  Simulation of enzyme-substrate encounter with gated active sites.

Authors:  R C Wade; B A Luty; E Demchuk; J D Madura; M E Davis; J M Briggs; J A McCammon
Journal:  Nat Struct Biol       Date:  1994-01

Review 8.  Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications.

Authors:  J G Garcia de la Torre; V A Bloomfield
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9.  Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase.

Authors:  J A Tainer; E D Getzoff; K M Beem; J S Richardson; D C Richardson
Journal:  J Mol Biol       Date:  1982-09-15       Impact factor: 5.469

10.  Structural analyses of various Cu2+, Zn2+-superoxide dismutases by differential scanning calorimetry and Raman spectroscopy.

Authors:  J R Lepock; L D Arnold; B H Torrie; B Andrews; J Kruuv
Journal:  Arch Biochem Biophys       Date:  1985-08-15       Impact factor: 4.013
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  16 in total

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7.  A Multiscale Computational Model for Simulating the Kinetics of Protein Complex Assembly.

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Journal:  Methods Mol Biol       Date:  2018

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Review 9.  Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.

Authors:  Daniel M Zuckerman; Lillian T Chong
Journal:  Annu Rev Biophys       Date:  2017-03-01       Impact factor: 12.981

10.  Predicting pathological von Willebrand factor unraveling in elongational flow.

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