HOMOLOGY MODELING USING SIMULATED ANNEALING OF RESTRAINED MOLECULAR-DYNAMICS AND CONFORMATIONAL SEARCH CALCULATIONS WITH CONGEN - APPLICATION IN PREDICTING THE 3-DIMENSIONAL STRUCTURE OF MURINE HOMEODOMAIN MSX-1

We have developed an automatic approach for homology modeling using re strained molecular dynamics and simulated annealing procedures, togeth er with conformational search algorithms available in the molecular me chanics program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers, 2 6:137-168). The accuracy of the method is validated by ''predicting'' structures of two homeodomain proteins with known three-dimensional st ructures, and then applied to predict the three-dimensional structure of the homeodomain of the murine Msx-1 transcription factor. Regions o f the unknown protein structure that are highly homologous to the know n template structure are constrained by ''homology distance constraint s,'' whereas the conformations of nonhomologous regions of the unknown protein are defined only by the potential energy function. A full ene rgy function (excluding explicit solvent) is employed to ensure that t he calculated structures have good conformational energies and are phy sically reasonable. As in NMR structure determinations, information on the consistency of the structure prediction is obtained by superposit ion of the resulting family of protein structures. In this paper, our homology modeling algorithm is described and compared with related hom ology modeling methods using spatial constraints derived from the stru ctures of homologous proteins. The software is then used to predict th e DNA-hound structures of three homeodomain proteins from the X-ray cr ystal structure of the engrailed homeodomain protein (Kissinger CR et al., 1990, Cell 63:579-590). The resulting backbone and side-chain con formations of the modeled yeast Mat alpha 2 and D. melanogaster Antenn apedia homeodomains are excellent matches to the corresponding publish ed X-ray crystal (Wolberger C et al., 1991, Cell 67:517-528) and NMR ( Billeter M et al., 1993, J Mol Biol 234:1084-1097) structures, respect ively. Examination of these structures of Msx-1 reveals a network of h ighly conserved surface salt bridges that are proposed to play a role in regulating protein-protein interactions of homeodomains in transcri ption complexes.