Abstract
Understanding the hydrophilicity/hydrophobicity of amino acid side chains in peptides/proteins is one the most important aspects of biology. Though many hydrophilicity/hydrophobicity scales have been generated, an “intrinsic” scale has yet to be achieved. “Intrinsic” implies the maximum possible hydrophilicity/hydrophobicity of side chains in the absence of nearest‐neighbor or conformational effects that would decrease the full expression of the side‐chain hydrophilicity/hydrophobicity when the side chain is in a polypeptide chain. Such a scale is the fundamental starting point for determining the parameters that affect side‐chain hydrophobicity and for quantifying such effects in peptides and proteins. A 10‐residue peptide sequence, Ac–X–G–A–K–G–A–G–V–G–L‐amide, was designed to enable the determination of the intrinsic values, where position X was substituted by all 20 naturally occurring amino acids and norvaline, norleucine, and ornithine. The coefficients were determined by reversed‐phase high‐performance liquid chromatography using six different mobile phase conditions involving different pH values (2, 5, and 7), ion‐pairing reagents, and the presence and absence of different salts. The results show that the intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides (proteins) is independent of pH, buffer conditions, or whether C~8~ or C~18~ reversed‐phase columns were used for 17 side chains (Gly, Ala, Cys, Pro, Val, nVal, Leu, nLeu, Ile, Met, Tyr, Phe, Trp, Ser, Thr, Asn, and Gln) and dependent on pH and buffer conditions, including the type of salt or ion‐pairing reagent for potentially charged side chains (Orn, Lys, His, Arg, Asp, and Glu). © 2005 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 84: 283–297, 2006
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