European Molecular Biology Laboratory, 69012 Heidelberg, Germany
We have investigated the use of mean-force potentials (MFPs) for predicting protein tertiary structure. As a simple test case, we chose to work with leucine zipper (LZ) homodimers for which accurate 3D prediction from the sequence alone is already possible using molecular dynamics (MD) and other methods (Nilges & Brunger, 1993). The backbone coordinates of LZs can be described using the coiled coil equations, first derived by Crick in 1952. Assuming the standard alpha-helical parameters, the coiled coil equations have just three free parameters. Using Sippl's mean-force potentials (1990), we have developed an exhaustive grid search strategy for finding the optimal coiled coil parameters for a given sequence. The method was applied to three LZ sequences: GCN4, Jun, and Max. In each case, the search produced a lowest-energy structure very close to the experimentally determined structure. In the case of GCN4, a fine-grid search resulted in a predicted structure 0.7 Angstroms backbone RMSD away from the crystal structure. Three main conclusions can be drawn from these results. Firstly, as a method for predicting the 3D structure of LZs, our method achieves the same or better accuracy as the previous MD methods, and is much faster. Secondly, the results show that, at least for one class of folds, MFPs give a global minimum very close to the native structure. Thirdly, even though the MFPs were derived from a subset of the PDB from which multimers were excluded (and hence only strictly valid for intramolecular interactions), these potentials were able to identify the correct dimer structure. This suggests that the rules embodied in the MFPs are also valid for intermolecular interactions. These conclusions support the utility of MFPs in predicting tertiary structure.
References
Sippl, M. J. (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins, J. Mol. Biol. 231:859-883
Nilges, M. & Brunger, A. T. (1993) Successful prediction of the coiled coil geometry of the GCN4 leucine zipper domain by simulated annealing: comparison to the X-ray structure. Proteins. 15:133-146