Molecular dynamics simulation of human interleukin-4: Comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability

Abstract

The human protein interleukin-4 (IL-4) has been simulated at two different pH values 2 and 6, with different amounts of counterions present in the aqueous solution, and with two different force-field parameter sets using molecular dynamics simulation with the aim of validation of force field and simulation set-up by comparison to experimental nuclear magnetic resonance data, such as proton-proton nuclear Overhauser effect (NOE) distance bounds, 3J(HN,HCa) coupling constants and backbone N-H order parameters. Thirteen simulations varying in the length from 3 to 7 ns are compared. At pH 6 both force-field parameter sets used do largely reproduce the NOE's and order parameters, the GROMOS 45A3 set slightly better than the GROMOS 53A6 set. 3J values predicted from the simulation agree less well with experimental values. At pH 2 the protein unfolds, unless counterions are explicitly present in the system, but even then the agreement with experiment is worse than at pH 6. When simulating a highly charged protein, such as IL-4 at pH 2, the inclusion of counterions in the simulation seems mandatory.