P. Das, M. Moll, H. Stamati, L. E. Kavraki, and C. Clementi, “Low-dimensional Free-energy Landscapes of Protein-Folding Reactions by Nonlinear Dimensionality Reduction,” Proceedings of the National Academy of Sciences, vol. 103, no. 26, pp. 9885–9890, Jun. 2006.
The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the “simple” case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular dynamics simulations. The folding free-energy landscape projected on the few relevant coordinates emerging from the dimensionality reduction can correctly identify the transition-state ensemble of the reaction. The first embedding dimension efficiently captures the evolution of the folding process along the main folding route. These results clearly show that the proposed method can efficiently find a low-dimensional representation of a complex process such as protein folding.