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BioMed Research International
Volume 2015 (2015), Article ID 828095, 9 pages
http://dx.doi.org/10.1155/2015/828095
Research Article

A Folding Pathway Model of Mini-Protein BBA5

1Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea
2School of Liberal Arts and Sciences, Korea National University of Transportation, Chungju 380-702, Republic of Korea
3Korea Institute for Advanced Study, Seoul 130-722, Republic of Korea

Received 4 June 2015; Accepted 9 August 2015

Academic Editor: Jie-Rong Huang

Copyright © 2015 In-Ho Lee et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.