title: 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 microscopic reason behind unfolding of the protein. Implications of different truncation schemes in reaction-field simulations of biomolecules are discussed.
authors.affiliation: Department of Physics and Optical Science, University of North Carolina Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA.
authors.forename: Boris
authors.initials: B
authors.lastname: Ni
authors.forename: Andrij
authors.initials: A
authors.lastname: Baumketner
mesh_terms: D004247:DNA / Q000737:chemistry*; D006801:Humans; D006863:Hydrogen-Ion Concentration; D015847:Interleukin-4 / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D058767:Protein Unfolding; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D014867:Water / Q000737:chemistry
chemical_list: C508598:IL4 protein, human; D012997:Solvents; D014867:Water; D015847:Interleukin-4; D004247:DNA