title: Theoretical investigation of the photoinitiated folding of HP-36.
abstract: A computational model was developed to examine the phototriggered folding of a caged protein, a protein modified with an organic photolabile cross-linker. Molecular dynamics simulations of the modified 36-residue fragment of subdomain B of chicken villin head piece with a photolabile linker were performed, starting from both the caged and the uncaged structures. Construction of a free-energy landscape, based on principal components as well as on radius of gyration versus root-mean-square deviation, and circular dichroism calculations were employed to characterize folding behavior and structures. The folded structures observed in the molecular dynamics trajectories were found to be similar to that of the wild-type protein, in agreement with the published experimental results. The free-energy landscapes of the modified and wild-type proteins have similar topology, suggesting common thermodynamic/kinetic behavior. The existence of small differences in the free-energy surface of the modified protein from that of the native protein, however, indicates subtle differences in the folding behavior.
authors.affiliation: Department of Applied Chemistry, Sejong University, Seoul 143-747, Korea.
authors.forename: Soonmin
authors.initials: S
authors.lastname: Jang
authors.forename: Narasimha
authors.initials: N
authors.lastname: Sreerama
authors.forename: Vivian H-C
authors.initials: VH
authors.lastname: Liao
authors.forename: S Hsiu-Feng
authors.initials: SH
authors.lastname: Lu
authors.forename: Feng-Yin
authors.initials: FY
authors.lastname: Li
authors.forename: Seokmin
authors.initials: S
authors.lastname: Shin
authors.forename: Robert W
authors.initials: RW
authors.lastname: Woody
authors.forename: Sheng Hsien
authors.initials: SH
authors.lastname: Lin
mesh_terms: D000818:Animals; D002645:Chickens; D002942:Circular Dichroism; D003432:Cross-Linking Reagents / Q000528:radiation effects; D007700:Kinetics; D008958:Models, Molecular; D008962:Models, Theoretical; D016900:Neurofilament Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D010777:Photochemistry; D017510:Protein Folding; D013816:Thermodynamics
chemical_list: D003432:Cross-Linking Reagents; D016900:Neurofilament Proteins; D010446:Peptide Fragments; C115223:villin headpiece subdomain peptide