STUDY OF TWO BIOACTIVE PEPTIDES IN VACUUM AND SOLVENT BY MOLECULAR MODELING

F. Yaşar () and K. Demir
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F. Yaşar: Department of Physics Engineering, Hacettepe University, Ankara, Turkey
K. Demir: Department of Physics, Zonguldak Karaelmas University, Zonguldak, Turkey

International Journal of Modern Physics C (IJMPC), 2006, vol. 17, issue 06, 825-839

Abstract: The thermodynamic and structural properties of Tyrosine-Glycine-Leusine-Phenylalanine (YGLF, 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 calculated 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 β-turn, γ-turn and helical structures. Although structural predictions of these sequences indicate both the presence of high level of γ-turns and low level of β-turns in vacuum and solvent, it was observed that these probabilities in vacuum were higher than the ones in solvent model.

Keywords: Molecular modeling; multicanonical simulation; solvation models; bioactive peptides (search for similar items in EconPapers)
Date: 2006
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DOI: 10.1142/S0129183106009382

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