Lattice protein folding with two and four-body statistical potentials.
The cooperative folding of proteins implies a description by multibody potentials. Such multibody potentials can be generalized from common two-body statistical potentials through a relation to probability distributions of residue clusters via the Boltzmann condition. In this exploratory study, we compare a four-body statistical potential, defined by the Delaunay tessellation of protein structures, to the Miyazawa-Jernigan (MJ) potential for protein structure prediction, using a lattice chain growth algorithm. We use the four-body potential as a discriminatory function for conformational ensembles generated with the MJ potential and examine performance on a set of 22 proteins of 30-76 residues in length. We find that the four-body potential yields comparable results to the two-body MJ potential, namely, an average coordinate root-mean-square deviation (cRMSD) value of 8 A for the lowest energy configurations of all-alpha proteins, and somewhat poorer cRMSD values for other protein classes. For both two and four-body potentials, superpositions of some predicted and native structures show a rough overall agreement. Formulating the four-body potential using larger data sets and direct, but costly, generation of conformational ensembles with multibody potentials may offer further improvements. Proteins 2001;43:161-174.
Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and the Howard Hughes Medical Institute, 251 Mercer Street, New York, NY 10012, USA.
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D000465:Algorithms; D003198:Computer Simulation; D008433:Mathematics; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D011487:Protein Conformation; D017510:Protein Folding; D013329:Structure-Activity Relationship; D013816:Thermodynamics