ArticleBiophysical journal2008
Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 64 citations in OpenAlex.
- A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.Journal of molecular modeling · 2013Article
- The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.Journal of chemical theory and computation · 2013Article
- A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides.Biophysical journal · 2011Article
- Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.The journal of physical chemistry. B · 2009Article
- Optical signatures of molecular dissymmetry: combining theory with experiments to address stereochemical puzzles.Accounts of chemical research · 2009Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mounting spectroscopic evidence indicates that alanine predominantly adopts extended polyproline II (PPII) conformations in short polypeptides. Here we analyze Raman optical activity (ROA) spectra of N-acetylalanine-N'-methylamide (Ala dipeptide) in H2O and D2O using density functional theory on Monte Carlo (MC) sampled geometries to examine the propensity of Ala dipeptide to adopt compact right-handed (alpha(R)) and left-handed (alpha(L)) helical conformations. The computed ROA spectra based on MC-sampled alpha(R) and PPII peptide conformations contain all the key spectral features found in the measured spectra. However, there is no significant similarity between the measured and computed ROA spectra based on the alpha(L)- and beta-conformations sampled by the MC methods. This analysis suggests that Ala dipeptide populates the alpha(R) and PPII conformations but no substantial population of alpha(L)- or beta-structures, despite sampling alpha(L)- and beta-structures in our MC simulations. Thus, ROA spectra combined with the theoretical analysis allow us to determine the dominant populated structures. Including explicit solute-solvent interactions in the theoretical analysis is essential for the success of this approach.
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