ArticleProceedings of the National Academy of Sciences of the United States of America2007
The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Proline-Free Local Turn via N-Oxidation: Crystallographic and Solution Evidence for a Six-Membered N-O⋯H-N Ring.Molecules (Basel, Switzerland) · 2025Article
- Exploring Nearest Neighbor Interactions and Their Influence on the Gibbs Energy Landscape of Unfolded Proteins and Peptides.International journal of molecular sciences · 2022Review
- Article
- Exploring Peptide⁻Solvent Interactions: A Computational Study.Molecules (Basel, Switzerland) · 2018Article
- Microsecond and nanosecond polyproline II helix formation in aqueous nanodrops measured by mass spectrometry.Chemical communications (Cambridge, England) · 2016Article
- Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation.The journal of physical chemistry. B · 2016Article
- Local order in the unfolded state: conformational biases and nearest neighbor interactions.Biomolecules · 2014Review
- pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study.The journal of physical chemistry. B · 2013Article
- The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.Journal of chemical theory and computation · 2013Article
- Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides.Journal of biomolecular NMR · 2012Article
- The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures.Protein engineering, design & selection : PEDS · 2010Article
- Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.The journal of physical chemistry. B · 2009Article
- Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations.Biophysical journal · 2008Article
- Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Studying the structural properties of polyalanine and polyglutamine peptides.Journal of molecular modeling · 2007Article
- Enthalpic and entropic stages in alpha-helical peptide unfolding, from laser T-jump/UV Raman spectroscopy.Journal of the American Chemical Society · 2007Article
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2 authors.
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Abstract
The solution structure of the hepta-alanine polypeptide Ac-X(2)A(7)O(2)-NH(2) (XAO) has been a matter of controversy in the current literature. On one side of the argument is a claim that the peptide adopts a mostly polyproline II (PPII) structure, with a <20% population of beta conformations at room temperature [Shi Z, Olson CA, Rose GA, Baldwin RL, Kallenbach NR (2002) Proc Natl Acad Sci USA 99:9190-9195], whereas the other side of the argument insists that the peptide exists as an ensemble of conformations, including multiple beta-turn structures [Makowska J, Rodziewicz-Motowidlo S, Baginska K, Vila JA, Liwo A, Chmurzynski L, Scheraga HA (2006) Proc Natl Acad Sci USA 103:1744-1749]. We have used an excitonic coupling model to simulate the amide I band of the FTIR, vibrational circular dichroism, and isotropic and anisotropic Raman spectra of XAO, where, for each residue, the backbone dihedral angle varphi was constrained by using the reported (3)J(CalphaHNH) values and a modified Karplus relation. The best reproduction of the experimental data could only be achieved by assuming an ensemble of conformations, which contains various beta-turn conformations ( approximately 26%), in addition to beta-strand ( approximately 23%) and PPII ( approximately 50%) conformations. PPII is the dominant conformation in segments not involved in turn formations. Most of the residues were found to sample the bridge region connecting the PPII and right-handed helix troughs in the Ramachandran plot, which is part of the very heterogeneous ensemble of conformations generally termed type IV beta-turn.
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