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Populations of the Three Major Backbone Conformations in 19 Amino-Acid Dipeptides

Grdadolnik, Jože; Mohaček Grošev, Vlasta; Baldwin, Robert S.; Avbelj, Franc (2011) Populations of the Three Major Backbone Conformations in 19 Amino-Acid Dipeptides. Proceedings of the National Academy of Sciences, 108 (5). pp. 1794-1798. ISSN 1091-6490

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The amide III region of the peptide infrared and Raman spectra has been used to determine the relative populations of the 3 major backbone conformations (PII, β and αR) in 19 amino-acid dipeptides. The results provide a benchmark for force field or other methods of predicting backbone conformations in flexible peptides. There are 3 resolvable backbone bands in the amide III region. The major population is either PII or β for all dipeptides except Gly while the αR population is measurable but always minor (≤ 10%) for 18 dipeptides. (The Gly φ, ψ map is complex and so is the interpretation of the amide III bands of Gly.) There are substantial differences in the relative β and PII populations among the 19 dipeptides. The band frequencies have been assigned as PII, 1317-1306 cm-1 ; αR, 1304-1294 cm-1 ; and β, 1294-1270 cm-1. The 3 bands were measured by both attenuated total reflection spectroscopy and by Raman spectroscopy. Consistent results, both for band frequency and relative population, were obtained by both spectroscopic methods. The β and PII bands were assigned from the dependence of the 3J(HN, Hα) coupling constant (known for all 19 dipeptides) on the relative β population. The PII band assignment agrees with one made earlier from Raman optical activity data. The temperature dependences of the relative β and PII populations fit the standard model with Boltzmann-weighted energies for alanine and leucine between 30 and 60 degrees C.

Item Type: Article
Uncontrolled Keywords: vibrational spectroscopy; backbone conformations; spectral populations; aqueous solution; protein-coil-library; peptide backbone; coupling-constants; force-fields; alanine; nmr; preferences; distributions; residue; helix
Subjects: NATURAL SCIENCES > Physics
Divisions: Division of Materials Physics
Project titleProject leaderProject codeProject type
Fizika i primjena nanostruktura i volumne tvari[135746] Mile Ivanda098-0982904-2898MZOS
Depositing User: Vlasta Mohaček Grošev
Date Deposited: 08 Jan 2014 11:21
DOI: 10.1073/pnas.1017317108

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