A test of implicit solvent models on the folding simulation of the GB1 peptide.
To quantify the effects of implicit solvent model on the folding of protein, thermodynamics calculation was performed for the folding of C-terminal hairpin from B1 domain of protein G using AMBER ff96 force field and different implicit solvent models (GB(OBC) and GBn). In the multiple AMBER force fields, ff96 strongly favors the hairpin conformations whereas the other force fields (e.g., ff94 and ff99) favor the helical conformations. In recent studies ff96 was found to be better balanced for various secondary structures than other force fields. The two implicit solvent models mentioned above were shown to be the most appropriate for beta-hairpin folding [M. S. Shell et al., J. Phys. Chem. B 112, 6878 (2008)]. The free energy landscape as a function of several different reaction coordinates was studied for both solvent models. The comparison of the results from these implicit models shows that the combination of AMBER ff96 with the GB(OBC) model yields stable structures that are in better agreement with experiments and results calculated using the explicit solvent model.
Shao
Qiang
Q
Department of Chemistry, Texas A&M University, College Station, Texas 77845, USA.
Yang
Lijiang
L
Gao
Yi Qin
YQ
D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics; D013997:Time Factors
C029152:G-substrate; D009419:Nerve Tissue Proteins; D010446:Peptide Fragments; D012997:Solvents