Over a long period of time blocked dipeptides and unblocked tripeptides have been used as model systems for obtaining conformational propensities of amino acids in unfolded peptides. Conflicting arguments have been made in favor of both types of peptides. In order to address this issue, a conformational analysis of the alanine dipeptide and of trialanine was carried out in order to elucidate the effect of terminal groups on the conformation of alanine. The Raman, IR, and vibrational circular dichroism amide I' profiles of both peptides in aqueous solution were measured. The respective conformational distributions were obtained from an analysis of these data and corresponding 3J(HNHa) constants. The conformational ensemble of alanine tripeptide was found to be nearly pH-independent at room temperature and only slightly different from that of alanine dipeptide. These results were supported with Molecular Dynamics simulations carried out with OPLS force field and a SPCE water model.

Is the amino acid dipeptide a suitable model system for investigating structural preferences in the unfolded state?

244th National Meeting (2012)

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