A Folding Pathway Model of Mini-Protein BBA5

作者：Lee In Ho; Kim Seung Yeon; Lee Jooyoung^*

来源：Biomed Research International, 2015, 2015: 828095.

DOI：10.1155/2015/828095

We present the folding pathway model of mini-protein BBA5, a bundle of secondary structures, alpha-helix and beta-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 alpha-helix. The N-terminal beta-hairpin was observed to form only after alpha-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 beta beta alpha 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.

• 出版日期2015