Evaluation of configurational entropy methods from peptide folding-unfolding simulation.
A 4-micros molecular dynamics simulation of the second beta-hairpin of the B1 domain of streptococcal protein G is used to characterize the free energy surface and to evaluate different configurational entropy estimators. From the equilibrium folding-unfolding trajectory, 200 000 conformers are clustered according to their root-mean-square deviation (RMSD). The height of the free energy barrier between pairs of clusters is found to be significantly correlated with their pairwise RMSD. Relative free energies and relative configurational entropies of the clusters are determined by explicit evaluation of the partition functions of the different clusters. These entropies are used to evaluate different entropy estimators for the largest 20 clusters as well as a subensemble comprising exclusively extended conformers. It is found that the quasi-harmonic entropy estimator operating in dihedral angle space performs better than the one using Cartesian coordinates. A recent generalization of the quasi-harmonic approach that computes Shannon entropies of probability distributions obtained by projecting the conformers along the eigenvectors of the covariance matrix performs similarly well. For the best entropy estimators, a linear correlation coefficient between 0.92 and 0.97 is found. Unexpectedly, when correlations between dihedral angles are neglected, the agreement with the reference entropies improved.
Li
Da-Wei
DW
Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610, USA.
Khanlarzadeh
Mina
M
Wang
Jinbu
J
Huo
Shuanghong
S
Brüschweiler
Rafael
R
D019277:Entropy; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding
D010455:Peptides