title: A Folding Pathway Model of Mini-Protein BBA5.
abstract: We present the folding pathway model of mini-protein BBA5, a bundle of secondary structures, α-helix and β-hairpin, by using action-derived molecular dynamics (ADMD) simulations. From ten independent ADMD simulations, we extracted common features of the folding pathway of BBA5, from which we found that the early stage chain compaction was followed by the formation of C-terminal α-helix. The N-terminal β-hairpin was observed to form only after α-helix was stabilized. This result is in good agreement with the experimental observation that BBA5 mutants were moderately cooperative folders, and their C-terminal helical fragments were of higher secondary structure propensity while the N-terminal hairpin fragments were of a random coil spectrum. We found that the most flexible part of BBA5 is the N-terminal four residues. Although both are made of the identical ββα motif, the secondary structure formation sequence of BBA5 is found to be different from that of FSD-1. Finally, a description of the folding pathway in terms of principal component analysis is presented to characterize the folding dynamics in reduced dimensions. With only three principal components, we were able to describe 83.4% of the pathway.
authors.affiliation: Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea.
authors.forename: In-Ho
authors.initials: IH
authors.lastname: Lee
authors.affiliation: School of Liberal Arts and Sciences, Korea National University of Transportation, Chungju 380-702, Republic of Korea.
authors.forename: Seung-Yeon
authors.initials: SY
authors.lastname: Kim
authors.affiliation: Korea Institute for Advanced Study, Seoul 130-722, Republic of Korea.
authors.forename: Jooyoung
authors.initials: J
authors.lastname: Lee
mesh_terms: D000595:Amino Acid Sequence; D004268:DNA-Binding Proteins / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D011506:Proteins; D014157:Transcription Factors