Conformational properties of the Pro-Gly motif in the D-Ala-l-Pro-Gly-D-Ala model peptide explored by a statistical analysis of the NMR, Raman, and Raman optical activity spectra

The Journal of Organic Chemistry
Milos BudesínskýPetr Bour

Abstract

The Pro-Gly sequence in designed peptides and proteins is often used to mimic natural beta-hairpin turns. Shorter peptides containing this moiety, however, adopt multiple conformations, and their propensity to form the turn is not obvious. In this study, conformational flexibility of Pro-Gly was investigated with the aid of NMR, Raman scattering, and Raman optical activity (ROA). The spectra of a model tetrapeptide NH3+-D-Ala-L-Pro-Gly-D-Ala-CO2- were analyzed on the basis of statistical methods and density functional computations. Other peptide derivatives were adopted as supporting theoretical and experimental models. The results suggest that the loop conformation of the Pro-Gly core is not inherently stable in vacuum. On the other hand, in aqueous environment the propensity to form the beta-hairpin loops is an intrinsic property of the Pro-Gly sequence. It was observed also in a shorter Ac-D-Pro-Gly-NH-Me dipeptide. The attached alanine residues in the tetrapeptide stabilize the structure only partially. Thus an inclusion of the solvent in the calculations is important for correct description of peptide folding in the aqueous environment. The agreement of the optical spectra with the experiment was determined from overlaps b...Continue Reading

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Citations

Mar 15, 2012·Analytical and Bioanalytical Chemistry·Shigeki Yamamoto
Aug 7, 2010·The Journal of Chemical Physics·Václav Parchanský, Petr Bour
Sep 15, 2009·Chirality·Kenneth Ruud, Andreas J Thorvaldsen
Sep 30, 2010·Journal of Peptide Science : an Official Publication of the European Peptide Society·Katja Gehenn, Jennifer Reed
Nov 17, 2012·Journal of Molecular Biology·Robin RoychaudhuriDavid B Teplow
Sep 26, 2008·Journal of Computational Chemistry·Jakub KaminskýPetr Bour
Apr 18, 2009·Magnetic Resonance in Chemistry : MRC·Marcelo A Muñoz, Pedro Joseph-Nathan
Jul 7, 2009·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Vincent Liégeois
Jul 30, 2010·Physical Chemistry Chemical Physics : PCCP·Shigeki YamamotoPetr Bour
Mar 9, 2011·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Shigeki YamamotoPetr Bouř
Mar 25, 2009·The Journal of Physical Chemistry. a·Jakub KaminskýPetr Bour
Jun 17, 2009·The Journal of Physical Chemistry. a·Jirí SebekPetr Bour
Jun 29, 2010·The Journal of Physical Chemistry. a·Jana HudecováPetr Bour
Nov 9, 2011·The Journal of Physical Chemistry. B·Václav ProfantPetr Bouř
Mar 29, 2012·The Journal of Physical Chemistry. B·Maciej KamińskiMagdalena Pecul
Jan 24, 2012·Analytical Chemistry·Shigeki YamamotoPetr Bouř
Jun 14, 2011·Journal of Chemical Theory and Computation·Noah S BielerMarkus Reiher

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