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Effect of atom- and group-based truncations on biomolecules simulated with reaction-field electrostatics. | LitMetric

Effect of atom- and group-based truncations on biomolecules simulated with reaction-field electrostatics.

J Mol Model

Department of Physics and Optical Science, University of North Carolina Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA.

Published: November 2011

AI Article Synopsis

Article Abstract

The performance of the reaction-field method of electrostatics is tested in molecular dynamics simulations of protein human interleukin-4 and a short DNA fragment in explicit solvent. Two truncation schemes are considered: one based on the position of atomic charges in water molecules and the other on the position of groups of charges. The group-based truncation leads to the melting of the DNA double helix. In contrast, the atom-based truncation maintains the helical structure intact. Similarly for the protein, the group-based truncation leads to an unfolding at pH 2 while the atom-based truncation produces stable trajectories at low and normal pH, in agreement with experiment. Artificial repulsion between charged residues associated with the group-based truncation is identified as the microscopic reason behind unfolding of the protein. Implications of different truncation schemes in reaction-field simulations of biomolecules are discussed.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204157PMC
http://dx.doi.org/10.1007/s00894-011-0975-xDOI Listing

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