Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer.
The present study tests performance of different solvation models applied to molecular dynamics simulation of a large, dimeric protein molecule. Analytical Continuum Electrostatics (ACE) with two different parameter sets, older V98 and new V01, and Effective Energy Function (EEF) are employed in molecular dynamics simulation of immunoglobulin G (IgG) light chain dimer and variable domain of IgG light chain. Results are compared with explicit solvent and distance dependent dielectric constant (DDE) calculations. The overall analysis shows that the EEF method yields results comparable to explicit solvent simulations; however, the stability of simulations is lower. On the other hand, the ACE_V98 model does not seem to achieve the accuracy or stability expected in nanosecond timescale MD simulation for the studied systems. The ACE_V01 model greatly improves stability of the calculation; nonetheless, changes in radius of gyration and solvent accessible surface of the studied systems may indicate that the parameter set still needs to be improved if the method is supposed to be used for simulations of large, polymeric proteins. Additionally, electrostatic contribution to the solvation free energy calculated in the ACE model is compared with a numerical treatment of the dielectric continuum model. Wall clock time of all simulations is compared. It shows that EEF calculation is six times faster than corresponding ACE and 50 times faster than explicit solvent simulations.
Król
Marcin
M
Department of Biostatistics and Medical Informatics Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Kraków, Poland. mykrol@cyf-kr.edu.pl
D003198:Computer Simulation; D006860:Hydrogen Bonding; D007074:Immunoglobulin G; D007147:Immunoglobulin Light Chains; D007135:Immunoglobulin Variable Region / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D012997:Solvents; D055672:Static Electricity; D013997:Time Factors
D007074:Immunoglobulin G; D007147:Immunoglobulin Light Chains; D007135:Immunoglobulin Variable Region; D012997:Solvents