Author(s): Cowan R, Whittaker RG
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Abstract The retention times of compounds on reversed-phase high-performance liquid chromatography columns are determined by their overall hydrophobicity. This paper exploits this relationship to derive hydrophobicity indices for amino acid residues. Retention times of 20 Z-amino acids and their methyl, ethyl and benzyl esters were determined under standard conditions on reversed-phase high-performance liquid chromatography at pH 3.0 and pH 7.5. Retention times of derivatives of six of the amino acids were used to calculate amino acid residue hydrophobicity values relative to glycine and leucine by a computer-based iterative procedure that used splines to optimize the smoothness of fit. Using these derived curves, values for each derivative of the remaining 14 Z-amino acids were determined and averages calculated. The curves, generated independently for pH 3.0 and pH 7.5 were effectively identical and the determined hydrophobicity values (other than for charged residues) were also similar at the two pHs. The values obtained vary significantly from other published values. Comparisons with some of the more commonly used hydrophobicity/hydropathy tables are presented. The highest correlation was found with constants determined for water/octanol partitioning of N- and C-terminal protected amino acids.
This article was published in Pept Res
and referenced in Journal of Proteomics & Bioinformatics