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Study of two bioactive peptides in vacuum and solvent by molecular modeling

Yaşar F. | Demir K.

Article | 2006 | International Journal of Modern Physics C17 ( 6 ) , pp.825 - 839

The thermodynamic and structural properties of Tyrosine-Glycine-Leusine- Phenylalanine (YGLP, in a one letter code) and Lysine-Valine-Leusine-Proline- Valine-Proline-Glutamine (KVLPVPQ) peptide sequences were studied by three-dimensional molecular modeling in vacuum and solution. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations with using ECEPP/2 force field and each simulation started from completely random initial conformation. Solvation contributions are included by a term that is proportional to solvent-accessible surface areas of peptides. In the present study, we cal . . .culated the average values of total energy, specific heat, fourth-order cumulant and end-to-end distance for two peptide sequences of milk protein as a function of temperature. With using major advantage of this simulation technique, Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of ß-turn, ?-turn and helical structures. Although structural predictions of these sequences indicate both the presence of high level of ?-turns and low level of ß-turns in vacuum and solvent, it was observed that these probabilities in vacuum were higher than the ones in solvent model. © World Scientific Publishing Company Daha fazlası Daha az

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