Force field influences in beta-hairpin folding simulations.
All-atom force fields are now routinely used for more detailed understanding of protein folding mechanisms. However, it has been pointed out that use of all-atom force fields does not guarantee more accurate representations of proteins; in fact, sometimes it even leads to biased structural distributions. Indeed, several issues remain to be solved in force field developments, such as accurate treatment of implicit solvation for efficient conformational sampling and proper treatment of backbone interactions for secondary structure propensities. In this study, we first investigate the quality of several recently improved backbone interaction schemes in AMBER for folding simulations of a beta-hairpin peptide, and further study their influences on the peptide's folding mechanism. Due to the significant number of simulations needed for a thorough analysis of tested force fields, the implicit Poisson-Boltzmann solvent was used in all simulations. The chosen implicit solvent was found to be reasonable for studies of secondary structures based on a set of simulations of both alpha-helical and beta-hairpin peptides with the TIP3P explicit solvent as benchmark. Replica exchange molecular dynamics was also utilized for further efficient conformational sampling. Among the tested AMBER force fields, ff03 and a revised ff99 force field were found to produce structural and thermodynamic data in comparably good agreement with the experiment. However, detailed folding pathways, such as the order of backbone hydrogen bond zipping and the existence of intermediate states, are different between the two force fields, leading to force field-dependent folding mechanisms.
Lwin
Thu Zar
TZ
Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA.
Luo
Ray
R
D003198:Computer Simulation; D006860:Hydrogen Bonding; D018625:Microscopy, Atomic Force / Q000379:methods*; D008958:Models, Molecular; D008968:Molecular Conformation; D009419:Nerve Tissue Proteins / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012492:Salts / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
C029152:G-substrate; D009419:Nerve Tissue Proteins; D012492:Salts; D012997:Solvents