Monte carlo method applied in the search for low‐energy conformations of βαβαβ structures

A Monte Carlo approach was used to find low‐energy conformations of sequentially linked βαβαβ structures to be used as initial conformations in energy minimizations. Only L ‐type amino acids were used in the study. The composition of the linked polypeptide chain was H(Val) 6 (R) 4 (Ala) 14 (R) 4 (Val) 6 (R) 4 (Ala) 14 (R) 4 (Val) 6 OH. A loop region was represented by (R) 4 , where R was either Gly or Ala. Two types of connections were considered: connections between nearest neighbor strands in the β‐sheet, and connections between β‐strands separated by one intervening β‐strand. The loop energy and the total energy of the α‐helical and β‐strand segments in the energy‐minimized structures were analyzed. The orientations of the secondary structural elements were characterized. In agreement with the handedness observed by experiment, all right‐handed crossover conformations were computed to have lower conformational energies than the corresponding left‐handed crossover conformations. The energy gaps between the corresponding loop energies also favored right‐handed conformations. Furthermore, the packing angles between the α‐helix axis and the β‐sheet axis are also in good agreement with experimental observations. Therefore the right‐handedness of the observed βαβαβ structure can be understood from the viewpoint of energetics.