New implementation of and the modeling by the extended simulated annealing process to structures of T4 lysozyme mutants at the 86th residue

Abstract

The extended simulated annealing process (ESAP) is a useful method for modeling the partial structure of proteins [J. Higo et al., Biopolymers, 32, 33 (1992)]. In ESAP, a protein molecule is divided into two parts: small, flexible fragments constituting the concerned partial structure, and the remaining part, for which the structure is kept rigid during the simulation. We have improved the program of ESAP so that it can be adapted to general macromolecules. Any sidechain on the rigid part can be set to rotate. Soft repulsion between van der Waals spheres is introduced to avoid conformational trapping into local minima. This improved program was tested for modeling structural changes caused by eight kinds of amino acid mutation at the 86th residue in T4 lysozyme. For each mutant we obtained a model structure that was close to the X-ray structure. The root mean square (rms) deviations from the X-ray structure were 0.3 to 0.8 A for all heavy atoms and about 0.2 A for the main-chain atoms. We also modeled the structure of an Ile mutant, for which the X-ray structure has not yet been reported. ESAP can be used to model structural changes due to a single residue mutation in proteins. © 1996 by John Wiley & Sons, Inc.