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Stephen D. Bond

Citation:

Yuhui Cheng, Jason K. Suen, Deqiang Zhang, Stephen D. Bond, Yongjie Zhang, Yuhua Song, Nathan A. Baker, Chandrajit L. Bajaj, Michael J. Holst and J. Andrew McCammon, Finite Element Analysis of the Time-Dependent Smoluchowski Equation for Acetylcholinesterase Reaction Rate Calculations, Biophysical Journal 92:10 (2007) 3397-3406.

Abstract:

This article describes the numerical solution of the time-dependent Smoluchowski equation to study diffusion in biomolecular systems. Specifically, finite element methods have been developed to calculate ligand binding rate constants for large biomolecules. The resulting software has been validated and applied to the mouse acetylcholinesterase monomer and several tetramers. Rates for inhibitor binding to mAChE were calculated at various ionic strengths with several different time steps. Calculated rates show very good agreement with experimental and theoretical steady-state studies. Furthermore, these finite element methods require significantly fewer computational resources than existing particle-based Brownian dynamics methods and are robust for complicated geometries. The key finding of biological importance is that the rate accelerations of the monomeric and tetrameric mAChE that result from electrostatic steering are preserved under the non-steadystate conditions that are expected to occur in physiological circumstances.

Full Text:

DOI: 10.1529/biophysj.106.102533

PMID: 17307827

Preprint:

Finite Element Analysis of the Time-Dependent Smoluchowski Equation for Acetylcholinesterase Reaction Rate Calculations (2.0M, PDF)

Bibtex:
@article{CSZB2007,
  author  = {Yuhui Cheng and Jason K. Suen and Deqiang Zhang and Stephen D.
             Bond and Yongjie Zhang and Yuhua Song and Nathan A. Baker and
             Chandrajit L. Bajaj and Michael J. Holst and J. Andrew McCammon},
  title   = {Finite Element Analysis of the Time-Dependent Smoluchowski
             Equation for Acetylcholinesterase Reaction Rate Calculations},
  journal = {Biophysical Journal},
  volume  = 92,
  number  = 10,
  year    = 2007,
  pages   = {3397--3406},
  doi     = {10.1529/biophysj.106.102533},
  pubmed  = 17307827
}

Stephen Bond