From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins

Abstract

An improved scheme to help in the prediction of protein structure is presented. This procedure generates improved starting conformations of a protein suitable for energy minimization. Trivariate gaussian distribution functions for the π, ψ, and χ1 dihedral angles have been derived, using conformational data from high resolution protein structures selected from the Protein Data Bank (PDB). These trivariate probability functions generate initial values for the π, ψ, and χ1 dihedral angles which reflect the experimental values found in the PDB. These starting structures speed the search of the conformational space by focusing the search mainly in the regions of native proteins. The efficiency of the new trivariate probability distributions is demonstrated by comparing the results for the α‐class polypeptide fragment, the mutant Antennapedia (C39 → S) homeodomain (2HOA), with those from two reference probability functions. The first reference probability function is a uniform or flat probability function and the second is a bivariate probability function for π and ψ. The trivariate gaussian probability functions are shown to search the conformational space more efficiently than the other two probability functions. The trivariate gaussian probability functions are also tested on the binding domain of Streptococcal protein G (2GB1), an α/β class protein. Since presently available energy functions are not accurate enough to identify the most native‐like energy‐minimized structures, three selection criteria were used to identify a native‐like structure with a 1.90‐Å rmsd from the NMR structure as the best structure for the Antennapedia fragment. Each individual selection criterion (ECEPP/3 energy, ECEPP/3 energy‐plus‐free energy of hydration, or a knowledge‐based mean field method) was unable to identify a native‐like structure, but simultaneous application of more than one selection criterion resulted in a successful identification of a native‐like structure for the Antennapedia fragment. In addition to these tests, structure predictions are made for the Antennapedia polypeptide, using a Pattern Recognition‐based Importance‐Sampling Minimization (PRISM) procedure to predict the backbone conformational state of the mutant Antennapedia homeodomain. The ten most probable backbone conformational state predictions were used with the trivariate and bivariate gaussian dihedral angle probability distributions to generate starting structures (i.e., dihedral angles) suitable for energy minimization. The final energy‐minimized structures show that neither the trivariate nor the bivariate gaussian probability distributions are able to overcome the inaccuracies in the backbone conformational state predictions to produce a native‐like structure. Until highly accurate predictions of the backbone conformational states become available, application of these dihedral angle probability distributions must be limited to problems, such as homology modeling, in which only a limited portion of the backbone (e.g., surface loops) must b...