Multicanonical simulations of five tetrapeptide sequences in the central domain of HMW glutenin

Arkin H., Yasar F., ÇELİK T., Celik S., Koksel H.

INTERNATIONAL JOURNAL OF MODERN PHYSICS C, vol.11, no.8, pp.1595-1606, 2000 (SCI-Expanded) identifier identifier


The application of the multicanonical simulation method to small proteins and peptides seems to be feasible and should be undertaken. In this work, the three-dimensional structures of five common tetrapeptide sequences (QPGQ, QSGQ, YPTS, SPQQ and QPGY, in one letter code) in the repetitive central domain of HMW glutenin subunits are investigated by using the multicanonical simulation procedure. Ramachandran plots were prepared and analyzed to predict the relative occurrence probabilities of beta -turn and gamma -turn structures and helical states. Structural predictions of the five tetrapeptide sequences indicated the presence of high level of p-turns and considerable level of gamma -turns. It was also possible to distinguish different type of turns and their occurrence probabilities.