Simulated annealing approach to the study of protein structures

One of the most difficult problems in predicting the three dimensional structure of proteins is how to deal with the local minimum problem. In many cases of practical interest this problem has been reduced to how to select an appropriate set of starting conformations for carrying out energy minimizations. How these starting conformations are selected, however, is often based on the physical intuition of the person doing the calculations, and hence it is hard to avoid bearing some sort of arbitrariness. To improve such a situation, we introduced the simulated annealing Monte Carlo algorithm to locate the optimal starting conformations for energy minimizations. The method developed here is valid for both single and multiple polypeptide chain systems. The annealing process can be conducted with respect to either the internal dihedral angles of a polypeptide chain or the external rotations and translations of various constituent polypeptide chains, and hence is particularly useful for studying the packing arrangements of secondary structures in proteins, such as helix/helix packing, helix/sheet packing and sheet/sheet packing. It was shown via a number of comparative calculations that the final structures obtained through the annealing process not only had lower energies than the corresponding energy-minimized structures reported previously, but also assumed the forms closer to the observations in proteins. All these results indicate that a better result can be obtained in search of low-energy structures of proteins by incorporating the simulated annealing approach.(ABSTRACT TRUNCATED AT 250 WORDS)