Long-range electrostatic interactions in molecular dynamics: an endothelin-1 case study.
An extensive conformational search in explicit solvent was performed in order to compare the influence of different long-range electrostatic interaction treatments in molecular dynamics. The short peptide endothelin-1 was selected as the subject of molecular dynamics studies that started from both X-ray and NMR obtained structures. Electrostatic interactions were treated using two of the most common methods--residue-based cutoff and particle mesh Ewald (PME). Analyses of free energy calculations (MM-PBSA method used), secondary structure elements and hydrogen bonds were performed, and there suggested that there is no unambiguous conclusion about which of the two methods of long-range electrostatics treatment should be used in MD simulations in this case. The most reliable data was provided by a trajectory that started with the NMR structure and used the cutoff method to treat electrostatic interactions. This leads to a recommendation that the choice of electrostatics treatment should be made carefully and not automatically by choosing the PME method simply because it is the most widely used.
Fadrná
Eva
E
National Centre for Biomolecular Research, Department of Organic Chemistry, Faculty of Science, Masaryk University, Kotlárská 2, 611 37 Brno, Czech Republic. evaf@chemi.muni.cz
Hladecková
Klára
K
Koca
Jaroslav
J
D019332:Endothelin-1 / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D055672:Static Electricity
D019332:Endothelin-1; D010446:Peptide Fragments