Document Detail


A computational framework for mechanical response of macromolecules: application to the salt concentration dependence of DNA bendability.
MedLine Citation:
PMID:  19413960     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
A computational framework is presented for studying the mechanical response of macromolecules. The method combines a continuum mechanics (CM) model for the mechanical properties of the macromolecule with a continuum electrostatic (CE) treatment of solvation. The molecules are represented by their shape and key physicochemical characteristics such as the distribution of materials properties and charge. As a test case, we apply the model to the effect of added salt on the bending of DNA. With a simple representation of DNA, the CM/CE framework using a Debye-Hückel model leads to results that are in good agreement with both analytical theories and recent experiments, including a modified Odijk-Skolnick-Fixman theory that takes the finite length of DNA into consideration. Calculations using a more sophisticated CE model (Poisson-Boltzmann), however, suffer from convergence problems, highlighting the importance of balancing numerical accuracy in the CM and CE models when dealing with very large systems, particularly those with a high degree of symmetry.
Authors:
Liang Ma; Arun Yethiraj; Xi Chen; Qiang Cui
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Biophysical journal     Volume:  96     ISSN:  1542-0086     ISO Abbreviation:  Biophys. J.     Publication Date:  2009 May 
Date Detail:
Created Date:  2009-05-05     Completed Date:  2009-07-16     Revised Date:  2013-06-02    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  United States    
Other Details:
Languages:  eng     Pagination:  3543-54     Citation Subset:  IM    
Affiliation:
Graduate Program in Biophysics, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Computer Simulation
DNA / chemistry*
Elasticity
Models, Molecular*
Monte Carlo Method
Nucleic Acid Conformation*
Salts / chemistry*
Sodium Chloride / chemistry
Static Electricity
Grant Support
ID/Acronym/Agency:
R01-GM071428/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Salts; 7647-14-5/Sodium Chloride; 9007-49-2/DNA
Comments/Corrections

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


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