ArticleBiophysical journal2011
A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Conformational flexibility and transient structure of the proline-rich domain in p53.Biophysical journal · 2026Article
- Proline, a unique amino acid whose polymer, polyproline II helix, and its analogues are involved in many biological processes: a review.Amino acids · 2024Review
- An Expanded Polyproline Domain Maintains Mutant Huntingtin SolubleFrontiers in molecular neuroscience · 2021Article
- Temperature effect on the SARS-CoV-2: A molecular dynamics study of the spike homotrimeric glycoprotein.Computational and structural biotechnology journal · 2021Article
- Non-natural 3-Arylmorpholino-β-amino Acid as a PPII Helix Inducer.Organic letters · 2020Article
- Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats.Biophysical journal · 2017Article
- Conformational behavior of polyalanine peptides with and without protecting groups of varying chain lengths: population of PP-II structure!Journal of molecular modeling · 2015Article
- Tunable control of polyproline helix (PPII) structure via aromatic electronic effects: an electronic switch of polyproline helix.Biochemistry · 2014Article
- Local order in the unfolded state: conformational biases and nearest neighbor interactions.Biomolecules · 2014Review
- Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.Journal of chemical theory and computation · 2014Article
- Posttranslational modification of CENP-A influences the conformation of centromeric chromatin.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations.The journal of physical chemistry letters · 2013Article
- Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.Protein science : a publication of the Protein Society · 2013Article
- Temperature and urea have opposing impacts on polyproline II conformational bias.Biochemistry · 2013Article
- Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study.Nucleic acids research · 2013Article
- Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases?PLoS computational biology · 2012Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
There has been considerable debate about the intrinsic PPII propensity of amino-acid residues in denatured polypeptides. Experimentally, the propensity scale is based on the behavior of guest amino-acid residues placed in the middle of polyproline hosts. We have used classical molecular dynamics simulations, with state-of-the-art force fields to carry out a comprehensive analysis of the conformational equilibria of the proline-based host oligopeptides with single guests. The tracked structural characteristics include the PPII content, the cis/trans isomerization of the prolyl bonds, the puckering of the pyrrolidine rings of the proline residues, and the secondary structural motifs. We find no evidence for an intrinsic PPII propensity in any of the guest amino acids other than proline. Instead, the PPII content as derived from experiments may be explained in terms of: 1), a local correlation between the dihedral angles of the guest amino acid and the proline residue immediately preceding it; and 2), a nonlocal correlation between the cis/trans states of the peptide bonds. In terms of the latter, we find that the presence of a guest (other than proline, tyrosine, or tryptophan) increases the trans content of most of the prolyl bonds, which results in an effective increase of the peptide PPII content. With respect to the local dihedral correlations, we find that these are well described in terms of the so-called odds-ratio statistic. Expressed in terms of free energy language, the PPII content based on the odds-ratio of the relevant residues correlate well with the experimentally measured PPII content.
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