Systematic comparison of empirical forcefields for molecular dynamic simulation of insulin.
The use of atomistic simulation methodologies based on empirical forcefields has enhanced our understanding of many physical processes governing protein structure and dynamics. However, the forcefields used in classical modeling studies are often designed for a particular class of proteins and rely on continuous improvement and validation by comparison of simulations with experimental data. We present a comprehensive comparison of five popular forcefields for simulating insulin. The effect of each forcefield on the conformational evolution and structural properties of the peptide is analyzed in detail and compared with available experimental results. In this study we observed that different forcefields favor different structural trends. However, the all-atom forcefield CHARMM27 and the united-atom forcefield GROMOS 43A1 delivered the best representation of the experimentally observed dynamic behavior of chain B of insulin.
Todorova
Nevena
N
Applied Physics, School of Applied Sciences, RMIT University, Melbourne, Victoria, Australia.
Legge
F Sue
FS
Treutlein
Herbert
H
Yarovsky
Irene
I
D007328:Insulin / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D012399:Rotation; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties
D007328:Insulin; D012997:Solvents