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J Am Chem Soc. 2002 Sep 25;124(38):11258-9.

All-atom structure prediction and folding simulations of a stable protein.

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Center for Structural Biology and Department of Chemistry, State University of New York - Stony Brook, Stony Brook, New York 11794, USA.


We present results from all-atom, fully unrestrained ab initio folding simulations for a stable protein with nontrivial secondary structure elements and a hydrophobic core. The construct, "trpcage", is a 20-residue sequence optimized by the Andersen group at University of Washington and is currently the smallest protein that displays two-state folding properties. Compared over the well-defined regions of the experimental structure, our prediction has a remarkably low 0.97 A Calpha root-mean-square-deviation (rmsd) and 1.4 A for all heavy atoms. The simulated structure family displays additional features that are suggested by experimental data, yet are not evident in the family of NMR-derived structures.

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