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Quantitation of the nearest-neighbour effects of amino acid side-chains that restrict conformational freedom of the polypeptide chain using reversed-phase liquid chromatography of synthetic model peptides with l- and d-amino acid substitutions
Side-chain backbone interactions (or “effects”) between nearest neighbours may severely restrict the conformations accessible to a polypeptide chain and thus represent the first step in protein folding. We have quantified nearest-neighbour effects ( i to i + 1) in peptides through reversed-phase liq...
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Published in: | Journal of Chromatography A 2006-08, Vol.1123 (2), p.212-224 |
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Main Authors: | , , , , |
Format: | Article |
Language: | English |
Subjects: | |
Citations: | Items that this one cites Items that cite this one |
Online Access: | Get full text |
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Summary: | Side-chain backbone interactions (or “effects”) between nearest neighbours may severely restrict the conformations accessible to a polypeptide chain and thus represent the first step in protein folding. We have quantified nearest-neighbour effects (
i to
i
+
1) in peptides through reversed-phase liquid chromatography (RP-HPLC) of model synthetic peptides, where
l- and
d-amino acids were substituted at the N-terminal end of the peptide sequence, adjacent to a
l-Leu residue. These nearest-neighbour effects (expressed as the difference in retention times of
l- and
d-peptide diastereomers at pHs 2 and 7) were frequently dramatic, depending on the type of side-chain adjacent to the
l-Leu residue, albeit such effects were independent of mobile phase conditions. No nearest-neighbour effects were observed when residue
i is adjacent to a Gly residue. Calculation of minimum energy conformations of selected peptides supported the view that, whether a
l- or
d-amino acid is substituted adjacent to
l-Leu, its orientation relative to this bulky Leu side-chain represents the most energetically favourable configuration. We believe that such energetically favourable, and different, configurations of
l- and
d-peptide diastereomers affect their respective interactions with a hydrophobic stationary phase, which are thus quantified by different RP-HPLC retention times. Side-chain hydrophilicity/hydrophobicity coefficients were generated in the presence of these nearest-neighbour effects and, despite the relative difference in such coefficients generated from peptides substituted with
l- or
d-amino acids, the relative difference in hydrophilicity/hydrophobicity between different amino acids in the
l- or
d-series is maintained. Overall, our results demonstrate that such nearest-neighbour effects can clearly restrict conformational space of an amino acid side-chain in a polypeptide chain. |
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ISSN: | 0021-9673 |
DOI: | 10.1016/j.chroma.2006.04.092 |