Analysis of the effect of electrostatic energy truncation in molecular dynamics simulations of immunoglobulin G light chain dimer.
Molecular dynamics (MD) simulations of immunoglobulin G (IgG) light chain dimer using particle mesh Ewald (PME) and cutoff methods of treating electrostatic interactions were performed. The results indicate that structural parameters (RMSD, radius of gyration, solvent accessible surface) are very similar for both schemes; however, PME simulation shows increased mobility of side chains. This leads to larger fluctuations in the distance between the monomers in the dimer molecule, and, as a consequence, results in decreased number of interactions across the dimer interface. The wall clock time of the simulations was also compared. It was shown that the PME method is approximately 30% faster than the cutoff method for the system studied on a single processor.
Król
Marcin
M
Department of Bioinformatics and Telemedicine Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Kraków, Poland, mykrol@cyf-kr.edu.pl
D003198:Computer Simulation; D018360:Crystallography, X-Ray; D019281:Dimerization; D006860:Hydrogen Bonding; D007074:Immunoglobulin G / Q000737:chemistry* / Q000378:metabolism*; D007147:Immunoglobulin Light Chains / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D020836:Protein Structure, Quaternary; D012492:Salts / Q000737:chemistry; D012997:Solvents; D055672:Static Electricity
D007074:Immunoglobulin G; D007147:Immunoglobulin Light Chains; D012492:Salts; D012997:Solvents