Phylogeny of protein-folding trajectories reveals a unique pathway to native structure
- *Global Scientific Information and Computing Center, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8550, Japan; and ‡Graduate School of Integrated Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
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Edited by Harold A. Scheraga, Cornell University, Ithaca, NY, and approved November 11, 2004 (received for review September 22, 2004)
Abstract
To scrutinize how a protein folds at atomic resolution, we performed 200 molecular dynamics simulations (each of 50 ns) of the miniprotein Trp-cage on the computational grid. Within the trajectories, 58 folding and 31 unfolding events were identified and subjected to extensive comparison and classification. Based on an analogy with biological sequences, the folding and unfolding trajectories (arrays of sequential snapshots of structures) were aligned by dynamic programming allowing gaps. A phylogenetic tree derived from the alignments revealed four distinct groups of the trajectories, characterized by the Trp side-chain motions and the main-chain motions. It was found that only one group attained the native structure and that the other three led to pseudonative structures having the correct main-chain trace but different nonnative Trp side-chain rotamers, indicating that those four folded structures were each attained through a unique folding pathway.
Footnotes
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↵ † To whom correspondence should be addressed. E-mail: mota{at}gsic.titech.ac.jp.
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Author contributions: M.O. designed research and performed research; M.O., M.I., and A.K. analyzed data; M.O. and A.K. wrote the paper; and M.I. supervised the molecular dynamics simulation.
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This paper was submitted directly (Track II) to the PNAS office.
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Abbreviation: rmsd, rms deviation.
- Copyright © 2004, The National Academy of Sciences
