Solvation model effects on two specific peptides of milk protein


YAŞAR F. , DEMİR K.

CHINESE JOURNAL OF PHYSICS, cilt.45, ss.622-636, 2007 (SCI İndekslerine Giren Dergi) identifier identifier

  • Cilt numarası: 45 Konu: 6
  • Basım Tarihi: 2007
  • Dergi Adı: CHINESE JOURNAL OF PHYSICS
  • Sayfa Sayıları: ss.622-636

Özet

The equilibrium thermodynamic properties of two bioactive peptide sequences which have great effects on blood pressure were studied by three-dimensional molecular modeling in an aqueous solution. Our first peptide, Tyrosine-Glycine-Leucine-Phenylalanine (YGLF, in a one letter code), is found in the primary structure of bovine milk whey protein alpha-LA (residue 50-53). The other peptide, Lysine-Valine-Leusine-Proline-Valine-Proline-Glutamine (KVLPVPQ) takes in the beta-casein (beta-CN) (residue 169-175) part of milk. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations with the use of an ECEPP/2 force field, and the solvation contributions are included by a term that is proportional to the solvent accessible surface area of the peptide. Each simulation was started from a completely random initial conformation. No a-priori information about the ground-state was used in the simulations. In the present study, in order to determine the solvation model dependency of the thermodynamic properties, we calculated the average values of the total energy, specific heat, fourth-order cumulant, and end-to-end distance for these peptide sequences of milk protein as a function of temperature in two solvation models. We observed that the specific heat of each peptide shows a different behavior in the solvation models, which have one or two peaks as a function of temperature. That is why we have also investigated the structural properties to gain insight into the relation of these peaks with the structural transitions. Our results indicate that the calculated thermodynamic and structural properties of each peptide really depend on the chosen solvent model.