درجه بندي اسيدهاي آمينه از نقطه نظر ميزان آب گريزي آنها

A Hydrophobicity Scale for the Amino Acids

Introduction: The hydrophobic interaction is a major driving force behind many effects and phenomena in biological systems many hydrophobicity scales have already been proposed and have been used to predict the topography of proteins. Objective: In the present work based on some theoretical considerations a new hydrophobic scale for the amino acids is proposed. Materials and Methods: From the empirically justified assumptions that hydrophobicity of the amino acid residues as part of a polypeptide chain is dependent on the surface area and the electro negativity content of the residues, an equation which relates the hydrophobicity to the surface area; and the number, and electro negativity of oxygen and nitrogen of the residue is proposed. from this equation a new hyrophobicity scale for the amino acids is obtained. Using this scale and a sliding window averaging method hrdrophobicity plots for the human melatonin Mella receptor and prion protein (the eause of mad cow disease) are drawn; and the intrarnembrane structure of melatonin mel., receptor and hydrophobic core ofthe second half ofthe prion protein are determined and compared with those from literatures. Results: the proposed hydrophobicity scale in this work is in good agreement with that of Engelmann and coworkers. The intramembrane structure of melatonin Mella receptor and the structure of the hydrophobic core of the prion protein predicted in this article are in good agreement with those proposed in the literatures. Conelusion: the proposed hydrophobicity scale in this work is suitable for predicting the topography of the tran membrane and globular proteins.