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Intrinsic amino acid side‐chain hydrophilicity/hydrophobicity coefficients determined by reversed‐phase high‐performance liquid chromatography of model peptides: Comparison with other hydrophilicity/hydrophobicity scales
Author(s) -
Mant Colin T.,
Kovacs James M.,
Kim HyunMin,
Pollock David D.,
Hodges Robert S.
Publication year - 2009
Publication title -
peptide science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.21316
Subject(s) - chemistry , side chain , amino acid , peptide , chromatography , high performance liquid chromatography , octanol , folding (dsp implementation) , partition coefficient , organic chemistry , biochemistry , polymer , electrical engineering , engineering
An accurate determination of the intrinsic hydrophilicity/hydrophobicity of amino acid side‐chains in peptides and proteins is fundamental in understanding many area of research, including protein folding and stability, peptide and protein function, protein–protein interactions and peptide/protein oligomerization, as well as the design of protocols for purification and characterization of peptides and proteins. Our definition of intrinsic hydrophilicity/hydrophobicity of side‐chains is the maximum possible hydrophilicity/hydrophobicity of side‐chains in the absence of any nearest‐neighbor effects and/or any conformational effects of the polypeptide chain that prevent full expression of side‐chain hydrophilicity/hydrophobicity. In this review, we have compared an experimentally derived intrinsic side‐chain hydrophilicity/hydrophobicity scale generated from RP‐HPLC retention behavior of de novo designed synthetic model peptides at pH 2 and pH 7 with other RP‐HPLC‐derived scales, as well as scales generated from classic experimental and calculation‐based methods of octanol/water partitioning of N α ‐acetyl‐amino‐acid amides or free energy of transfer of free amino acids. Generally poor correlation was found with previous RP‐HPLC‐derived scales, likely due to the random nature of the peptide mixtures in terms of varying peptide size, conformation and frequency of particular amino acids. In addition, generally poor correlation with the classical approaches served to underline the importance of the presence of a polypeptide backbone when generating intrinsic values. We have shown that the intrinsic scale determined here is in full agreement with the structural characteristics of amino acid side‐chains. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 573–595, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com