A use of Ramachandran potentials in protein solution structure determinations

Abstract

A strategy is developed to use database-derived phi-psi constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived phi-psi constraints are enforced for all amino acids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the phi-psi values for each residue are examined. In the second and final run, the database-derived phi-psi constraints are enforced only for those residues which in the first run have ended in one and the same favored phi-psi region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints.