Document Detail


BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from brownian dynamics simulations.
MedLine Citation:
PMID:  23039617     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
A method developed by Northrup et al. [J. Chem. Phys. 80, 1517 (1984)] for calculating protein-ligand binding rate constants (k(a)) from brownian dynamics (BD) simulations has been widely used for rigid molecules. Application to flexible molecules is limited by the formidable computational cost to treat conformational fluctuations during the long BD simulations necessary for k(a) calculation. Here, we propose a new method called BDflex for k(a) calculation that circumvents this problem. The basic idea is to separate the whole space into an outer region and an inner region, and formulate k(a) as the product of k(E) and η(d), which are obtained by separately solving exterior and interior problems. k(E) is the diffusion-controlled rate constant for the ligand in the outer region to reach the dividing surface between the outer and inner regions; in this exterior problem conformational fluctuations can be neglected. η(d) is the probability that the ligand, starting from the dividing surface, will react at the binding site rather than escape to infinity. The crucial step in reducing the determination of η(d) to a problem confined to the inner region is a radiation boundary condition imposed on the dividing surface; the reactivity on this boundary is proportional to k(E). By confining the ligand to the inner region and imposing the radiation boundary condition, we avoid multiple-crossing of the dividing surface before reaction at the binding site and hence dramatically cut down the total simulation time, making the treatment of conformational fluctuations affordable. BDflex is expected to have wide applications in problems where conformational fluctuations of the molecules are crucial for productive ligand binding, such as in cases where transient widening of a bottleneck allows the ligand to access the binding pocket, or the binding site is properly formed only after ligand entrance induces the closure of a lid.
Authors:
Nicholas Greives; Huan-Xiang Zhou
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural    
Journal Detail:
Title:  The Journal of chemical physics     Volume:  137     ISSN:  1089-7690     ISO Abbreviation:  J Chem Phys     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-10-08     Completed Date:  2013-02-20     Revised Date:  2013-10-17    
Medline Journal Info:
Nlm Unique ID:  0375360     Medline TA:  J Chem Phys     Country:  United States    
Other Details:
Languages:  eng     Pagination:  135105     Citation Subset:  IM    
Affiliation:
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.
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MeSH Terms
Descriptor/Qualifier:
Binding Sites
Kinetics
Ligands
Molecular Dynamics Simulation*
Pliability
Proteins / chemistry*
Grant Support
ID/Acronym/Agency:
GM58187/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Ligands; 0/Proteins
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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