Journal of Physical Chemistry, Vol.98, No.2, 702-711, 1994
Hierarchical Algorithm for Computer Modeling of Protein Tertiary Structure - Folding of Myoglobin to 6.2 Angstrom Resolution
We present a method for determining the tertiary structure of alpha-proteins through computer simulation. A simple model is used in which residues are described by a discrete set of phi-psi dihedral angle conformations and the extent of alpha-helical regions is assumed to be known and held fixed. The algorithm makes use of the assigned secondary structure to construct a representation of the molecule where helices and loops are described by cylinders and spheres respectively. Correspondence with the residue conformations is maintained by using loop geometries from a list of structures calculated using the allowed dihedral angles in segments of the appropriate length. The optimization consists of a Monte Carlo simulated annealing procedure combined with a genetic algorithm in which additional structures are generated by combining parts of different members of the ensemble. We present as an example the results of simulations carried out on myoglobin in which we obtain a low-energy structure with root mean square deviation of 6.2 Angstrom from the native structure. The inter-residue distance map shows that all regions of helix-helix contact are represented confirming that the overall topology of the folded structure is correct. The root mean square deviation of the helical regions alone is 4.1 Angstrom, indicating that the packing of the helices is well-reproduced by the present model.