The investigation of the secondary structures of various peptide sequences of beta-casein by the multicanonical simulation method

Yasar F., Celik S., Koksel H.

PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, vol.363, no.2, pp.348-358, 2006 (SCI-Expanded) identifier identifier


The structural properties of Arginine-Glutamic acid-Leucine-Glutamic acid-Glutamic acid-Leucine-Asparagine-Valine-Proline-Glycine (RELEELNVPG, in one letter code), Glutamic acid-Glutamic acid-Glutamine-Glutamine-Glutamine-Threonine-Glutamic acid (EEQQQTE) and Glutamic acid-Aspartic acid-Glutamic acid-Leucine-Glutamine-Aspartic acid-Lysine-Isoleucine (EDELQDKI) peptide sequences of beta-casein were studied by three-dimensional molecular modeling. In this work, the three-dimensional conformations of each peptide from their primary sequences were obtained by multicanonical simulations. With using major advantage of this simulation technique, Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of beta-turn, gamma-turn and helical structures. Structural predictions of these sequences of beta-casein molecule indicate the presence of high level of helical structures and beta 111-turns. The occurrence probabilities of inverse and classical beta-turns were low. The probability of helical structure of each sequence significantly decreased when the temperature increased. Our results show these peptides have highly helical structure and better agreement with the results of spectroscopic techniques and other prediction methods. (c) 2005 Elsevier B.V. All rights reserved.