Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure.
We have investigated the folding pathway of the 36-residue villin headpiece subdomain (HP-36) by action-derived molecular dynamics simulations. The folding is initiated by hydrophobic collapse, after which the concurrent formation of full tertiary structure and alpha-helical secondary structure is observed. The collapse is observed to be associated with a couple of specific native contacts contrary to the conventional nonspecific hydrophobic collapse model. Stable secondary structure formation after the collapse suggests that the folding of HP-36 follows neither the framework model nor the diffusion-collision model. The C-terminal helix forms first, followed by the N-terminal helix positioned in its native orientation. The short middle helix is shown to form last. Signs for multiple folding pathways are also observed.
Korea Research Institute of Standards and Science, Daejon 305-600, Korea.
In-Ho
IH
Lee
Seung-Yeon
SY
Kim
Jooyoung
J
Lee
D056004:Molecular Dynamics Simulation; D016900:Neurofilament Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
D016900:Neurofilament Proteins; D010446:Peptide Fragments; C115223:villin headpiece subdomain peptide