Vibrational spectroscopy and conformational structure of protonated polyalanine peptides isolated in the gas phase

Timothy D. Vaden, Tjalling S.J.A. De Boer, John P. Simons, Lavina C. Snoek, Sándor Suhai, Béla Paizs

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The conformational structures of protonated polyalanine peptides, Ala nH+, have been investigated in the gas phase for n = 3, 4, 5, and 7 using a combination of resonant-infrared multiphoton dissociation (R-IRMPD) spectroscopy in the NH and OH stretch regions and quantum chemical calculations. Agreement between theoretical IR and experimental R-IRMPD spectral features has enabled the assignment of specific hydrogen-bonded conformational motifs in the short protonated peptides and revealed their conformational evolution under elevated-temperature conditions, as a function of increasing chain length. The shortest peptide, Ala3H+, adopts a mixture of extended and cyclic chain conformations, protonated, respectively, at a backbone carbonyl or the N-terminus. The longer peptides adopt folded, cyclic, and globular charge-solvated conformations protonated at the N-terminus, consistent with previous ion-mobility studies. The longest peptide, Ala 7H+, adopts a globular conformation with the N-terminus completely charge-solvated, demonstrating the emergence of "physiologically relevant" intramolecular interactions in the peptide backbone. The computed conformational relative free energies highlight the importance of entropic contributions in these peptides.

Original languageEnglish (US)
Pages (from-to)4608-4616
Number of pages9
JournalJournal of Physical Chemistry A
Issue number20
StatePublished - May 22 2008

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry


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