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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

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Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations.

Parag Mukhopadhyay¹, Gérard Zuber, David N Beratan

¹Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.

Biophysical Journal

|September 23, 2008

Summary

Alanine dipeptide primarily adopts extended polyproline II (PPII) and compact alpha-right-handed (αR) conformations in water. Raman optical activity (ROA) spectroscopy combined with theory confirms these structures, excluding alpha-left-handed (αL) and beta-conformations.

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Area of Science:

Biophysical Chemistry
Computational Chemistry
Spectroscopy

Background:

Short polypeptides, like alanine dipeptide, are crucial models for understanding protein folding.
Spectroscopic studies suggest a preference for extended polyproline II (PPII) conformations in alanine-based peptides.

Purpose of the Study:

To investigate the conformational preferences of alanine dipeptide in solution.
To determine the population of alpha-helical (αR and αL) and beta-sheet (β) conformations versus PPII structures.
To validate the use of Raman optical activity (ROA) spectroscopy coupled with theoretical calculations for conformational analysis.

Main Methods:

Analysis of Raman optical activity (ROA) spectra for N-acetylalanine-N'-methylamide (Ala dipeptide) in aqueous solutions (H2O and D2O).
Density functional theory (DFT) calculations employing Monte Carlo (MC) sampling to generate diverse peptide conformations.
Comparison of experimental ROA spectra with computed spectra derived from sampled αR, αL, PPII, and β conformations.

Main Results:

Computed ROA spectra for αR and PPII conformations closely matched experimental findings.
No significant spectral similarity was observed for the computed αL and β conformations.
Explicit inclusion of solute-solvent interactions was critical for accurate spectral reproduction.

Conclusions:

Alanine dipeptide predominantly populates αR and PPII conformations in aqueous solution.
ROA spectroscopy, supported by DFT/MC simulations with explicit solvent effects, is a powerful tool for identifying dominant peptide structures.
The study refutes significant populations of αL and β-structures for alanine dipeptide under investigated conditions.