Proline rich peptide sequences are very important recognition elements that have a significant bias toward the all-trans-polyproline type II (PII) conformation. Our gas-phase quantum mechanics calculations at the B3LYP/6-31G* level of theory are in good agreement with previous experimental and theoretical studies. They show that all-trans-proline conformations are energetically more favorable than all-cis-polyprolines (PI, polyproline type I). Estimates of the solvent effects show that the condensed phase can make the PI form more populated in the correct environment. Our survey of proline oligomers in the Protein Data Bank confirmed that the predominant conformations from our calculations are seen experimentally. More importantly, we propose two new secondary structures for polyprolines, namely polyproline type III and type IV (PIII and PIV). PIII is a right-handed, “square helix” from trans-proline oligomers. PIV is a â-sheet form of cis-prolines. As suggested by its calculated IR spectra, the PIII form shares characteristics of both the PI and PII forms: it has trans-amide rotamers similar to PII and forms a right-handed helix like PI. We propose that the high-energy PIII form could exist as a conformational intermediate between PI and PII. These new forms also show that the handedness of polyproline helices depends not only on the peptide rotamers (cis or trans) but also on the values of the ã torsions. Changing the ã torsion from approximately 140° to approximately -30° causes the trans oligomers to flip from a typical left-handed PII to a right-handed helix. Likewise, as the ã torsion of the cis-proline oligomers changes from roughly 165° to -30°, the conformation changes from a characteristic right-handed PI to a â-sheet.
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