Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three‐dimensional structure of murine homeodomain Msx‐1

Abstract

We have developed an automatic approach for homology modeling using restrained molecular dynamics and simulated annealing procedures, together with conformational search algorithms available in the molecular mechanics program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26137-168). The accuracy of the method is validated by "predicting" structures of two homeodomain proteins with known three-dimensional structures, and then applied to predict the three-dimensional structure of the homeodomain of the murine Msx-1 transcription factor. Regions of the unknown protein structure that are highly homologous to the known template structure are constrained by "homology distance constraints," whereas the conformations of nonhomologous regions of the unknown protein are defined only by the potential energy function. A full energy function (excluding explicit solvent) is employed to ensure that the calculated structures have good conformational energies and are physically reasonable. As in NMR structure determinations, information on the consistency of the structure prediction is obtained by superposition of the resulting family of protein structures. In this paper, our homology modeling algorithm is described and compared with related homology modeling methods using spatial constraints derived from the structures of homologous proteins. The software is then used to predict the DNA-bound structures of three homeodomain proteins from the X-ray crystal structure of the engrailed homeodomain protein (Kissinger CR et al., 1990, Cell 63:579-590). The resulting backbone and side-chain conformations of the modeled yeast MatcY2 and D. melunogaster Antennapedia homeodomains are excellent matches to the corresponding published X-ray crystal (Wolberger C et al., 1991, Cell 67517-528) and NMR , J Mol Biol234:1084-1097) structures, respectively. Examination of these structures of Msx-1 reveals a network of highly conserved surface salt bridges that are proposed to play a role in regulating protein-protein interactions of homeodomains in transcription complexes. Abbreviations: Antp, homeodomain of the D. melanogusrer Antennapedia protein; DG, distance geometry calculations using metric-mauix embedding methods; Conf. E., total conformational energy including electrostatic effects, computed from the CHARMM potential function; Mata2, homeodomain of the yeast M a t d protein; Msx-1, homeodomain of the murine Msx-1 protein; pdf, probability density function; RMSD, R M S deviation; SARMD, simulated annealing with restrained molecular dynamics; VDW E., van der Waals energy computed from the Lennard-Jones portion of the CHARMM potential function. Keywords 956Homology modeling of homeodomain Msx-1 with CONGEN 957The homeodomain is a highly conserved sequence-specific DNAbinding domain that has been found in many transcription factors. First discovered in Drosophila melanogaster, homeodomains have been found in almost every organism from nematodes to humans (Kessel & Gruss, 1990; Wang et al., 1993), and have been found to play a fu...

Disabling Receptor Ensembles with Rationally Designed Interface Peptidomimetics

“…Frameworks for the molecular models were generated by using coordinates from the template structures for manually selected matching residues of the modeled proteins. Missing coordinates for peptide segments that did not have a counterpart in the template structures were calculated by either "Regularizing Region" and "Model Side Chains" tools (for short loops) or by modeling loop conformation using a "Congen" (30,31) program (for longer loops). The final monomeric structures were then obtained by running the CHARMm energy minimization in the Residue Topology File mode.…”

Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments

“…''Homologous atoms'' are defined using alignments of amino acid residues of the template and target sequences as described elsewhere. 21 Only heavy atoms (atoms other than hydrogen) are considered in defining ''homologous atoms.'' Figure 1 displays the various sequences and alignments used in these calculations.…”

“…We employed our recently published 21 automated method of homology modeling using simulated annealing and restrained molecular dynamics calculations with the molecular mechanics program CONGEN 22,23 and the CHARMM force field. 28 This procedure generates a family of three-dimensional protein structures for a homologous protein based on the atomic coordinates of a known protein structure.…”

“…[21][22][23] Conformational energies were computed using the CHARMM force field 28 with a distance-dependent dielectric constant (⑀ ϭ r). The starting structures of the unknown protein were fully-extended conformations differing in the randomly-assigned atomic velocities and were subjected to an unrestrained adopted-basis Newton-Raphson (ABNR) minimization prior to the simulated annealing calculations in order to relieve any energetically unfavorable contacts.…”

“…20 Detailed discussions of different homology modeling methods can be found in the literature. 20,21 We have recently described an automated and objective approach for homology modeling 21 using simulated annealing with restrained molecular dynamics methods available in the molecular mechanics program CONGEN. 22,23 In these ''homology constrained'' CONGEN calculations, the relative positions of atoms of the unknown protein structure that are ''homologous'' to atoms of the known template structure are constrained by ''homology distance constraints,'' whereas the conformations of the ''non-homologous regions'' of the unknown protein are defined by the potential energy function.…”