Computer Science

Observation of two families of folding pathways of BBL

Document Type

Article

Abstract

BBL is an independent folding domain of a large multienzyme complex, 2-oxoglutarate dehydrogenase. The folding mechanism of BBL is under debate between the views of noncooperative downhill-type and classical two-state. Extensive replica exchange molecular dynamics simulations of BBL in explicit solvent have shown some non-two-state behaviors despite no definitive evidence of downhill folding. In this work, we postprocess the replica exchange data using our roadmapbased MaxFlux reaction path algorithm to reveal atomically detailed folding pathways. A connected graph is used to organize and visualize the folding pathways initiated from random coils. High structural and transition heterogeneity is seen in the early stage of folding. Two main parallel folding pathways emerge in the later stage; one path shows that tertiary contact and helix formation develop at different stages of folding, whereas the other path exhibits concurrence of secondary and tertiary structure formation to some extent. Because the native state of BBL is sensitive to experimental conditions, we speculate that the relative predominance of the two pathways may vary with the protein construct and solvent conditions, possibly leading to the seeming discrepancy of experimental results. Our roadmap-based reaction path algorithm is a general tool to extract path information from replica exchange. © 2011 by the Biophysical Society.

Publication Title

Biophysical Journal

Publication Date

2011

Volume

100

Issue

10

First Page

2457

Last Page

2465

ISSN

0006-3495

DOI

10.1016/j.bpj.2011.03.058

APA Citation

Fan, J., Duan, M., Li, D. W., Wu, H., Yang, H., Han, L., & Huo, S. (2011). Observation of two families of folding pathways of BBL. Biophysical journal, 100(10), 2457-2465.

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