COMPARATIVE PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS. Andrej Sali, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA; e-mail sali@rockvax.rockefeller.edu

Our approach to comparative protein modeling based on satisfaction of spatial restraints will be described and evaluated. In addition, the method will be illustrated by a combined modeling and site-directed mutagenesis study of heparin binding sites on mouse mast cell proteases. In the first stage of the method, the alignment between the sequence to be modelled and related template structures is obtained. In the second stage, restraints on various distances, angles, and dihedral angles in the sequence are derived from its alignment with the template structures. The restraints are expressed in the most general form as conditional probability density functions. Their form depends on tabulated correlations between sequence and structure as found in a database of 105 family alignments containing 416 homologous structures. And finally, the 3D model is obtained by minimizing violations of homology-derived and energy restraints, using conjugate gradients and molecular dynamics procedures. The derivation and satisfaction of spatial restraints have been implemented in the MODELLER program that is available by ftp from guitar.rockefeller.edu.