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Study Of Two Bioactive Peptides In Vacuum And Solvent By Molecular Modeling

Author

Listed:
  • F. YAŞAR

    (Department of Physics Engineering, Hacettepe University, Ankara, Turkey)

  • K. DEMIR

    (Department of Physics, Zonguldak Karaelmas University, Zonguldak, Turkey)

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.

Suggested Citation

  • F. Yaşar & K. Demir, 2006. "Study Of Two Bioactive Peptides In Vacuum And Solvent By Molecular Modeling," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 17(06), pages 825-839.
    • Handle: RePEc:wsi:ijmpcx:v:17:y:2006:i:06:n:s0129183106009382
    DOI: 10.1142/S0129183106009382
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