Protein structure prediction by global optimization of a potential energy function

Protein structure prediction by global optimization of a potential energy function

^*Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; ^†Faculty of Chemistry, University of Gdanśk, Sobieskiego 18, 80-952 Gdanśk, Poland; and ^‡Cornell Theory Center, Ithaca, NY 14853-3801

Contributed by H. A. Scheraga

Abstract

An approach based exclusively on finding the global minimum of an appropriate potential energy function has been used to predict the unknown structures of five globular proteins with sizes ranging from 89 to 140 amino acid residues. Comparison of the computed lowest-energy structures of two of them (HDEA and MarA) with the crystal structures, released by the Protein Data Bank after the predictions were made, shows that large fragments (61 residues) of both proteins were predicted with rms deviations of 4.2 and 6.0 Å for the C^α atoms, for HDEA and MarA, respectively. This represents 80% and 53% of the observed structures of HDEA and MarA, respectively. Similar rms deviations were obtained for ∼60-residue fragments of the other three proteins. These results constitute an important step toward the prediction of protein structure based solely on global optimization of a potential energy function for a given amino acid sequence.

Footnotes

↵ § To whom reprint requests should be addressed. e-mail: has5{at}cornell.edu.
↵ ¶ Bystroff, C., Simons, K. & Baker, D. Third Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Dec. 13–17, 1998, Pacific Grove, CA, p. 23.
↵ ‖ Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction, Dec. 13–17, 1998, Pacific Grove, CA. http://predictioncenter.llnl.gov/casp3/Casp3.html.
ABBREVIATIONS:

UNRES,

united-residue force field;

CSA,

conformational space annealing;

rmsd,

rms deviation;

PDB,

Protein Data Bank