Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds.
We report direct folding of a 17-residue helix protein (pdb:2I9M) by standard molecular dynamics simulation (single trajectory) at room temperature with implicit solvent. Starting from a fully extended structure, 2I9M successfully folds into the native conformation within 16 ns using adaptive hydrogen bond-specific charges to take into account the electrostatic polarization effect. Cluster analysis shows that conformations in the native state cluster have the highest population (78.4%) among all sampled conformations. Folding snapshots and the secondary structure analysis demonstrate that the folding of 2I9M begins at terminals and progresses toward the center. A plot of the free energy landscape indicates that there is no significant free energy barrier during folding, which explains the observed fast folding speed. For comparison, exactly the same molecular dynamics simulation but carried out under existing AMBER charges failed to fold 2I9M into native-like structures. The current study demonstrates that electrostatic polarization of intraprotein hydrogen bonding, which stabilizes the helix, is critical to the successful folding of 2I9m.
Duan
Li L
LL
College of Physics and Electronics, Shandong Normal University, Jinan 250014, China.
Mei
Ye
Y
Zhang
Dawei
D
Zhang
Qing G
QG
Zhang
John Z H
JZ
D016000:Cluster Analysis; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D013696:Temperature; D013816:Thermodynamics
D011506:Proteins