HOMOLOGY MODELING OF DIVERGENT PROTEINS

A method is presented for homology modeling of proteins bearing weak s equence identity to proteins of known tertiary structure. To accommoda te non-identical amino acids in the core region, the backbone of the s tructurally conserved core of the model protein is allowed to deviate from that of the template protein. We have expanded FOLDER, a distance geometry-based homology modeling method, to allow for such displaceme nts in the structurally conserved core. Models are built by rigidly co nstraining the interatomic distances within a structurally conserved s egment and by allowing the interatomic distances between these segment s to vary by a ''divergence factor''. We test this method by simulatin g models of the beta-barrel domain D1 of CD4 and a four-helix bundle p rotein cytochrome b562 using the crystal structures of Bence-Jones pro tein and cytochrome c' as templates, respectively. In both cases, prev iously published structure-based sequence alignments were used for sim ulating models. The root-mean-square (r.m.s.) deviation of the backbon e atoms in the common core between the templates and models was found to be a function of the imposed divergence factor. Our results demonst rate that this r.m.s. deviation results from the relative displacement s of structurally conserved segments to accommodate the amino acid rep lacements in the core of the model protein. To test the integrity of t he simulated structures we compared them with their respective crystal structures. The r.m.s. deviation of the backbone atoms in the core re gions of the simulated models and their respective crystal structures is similar to 1.4 Angstrom. The r.m.s. deviation for all the backbone atoms in the models, including those in the structurally variable regi ons, which are modeled de novo, is 2.4 Angstrom for CD4 and 3.2 Angstr om for cytochrome b582 when compared with their respective X-ray struc tures.