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

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 mic

SUBMITTER: Ni B 

PROVIDER: S-EPMC3204157 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature