ArticleBiophysical journal2004
Polyproline II helix conformation in a proline-rich environment: a theoretical study.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 62 citations in OpenAlex.
- Conformational flexibility and transient structure of the proline-rich domain in p53.Biophysical journal · 2026Article
- Analysis of proteins in the light of mutations.European biophysics journal : EBJ · 2024Review
- Deducing the conformational space for an octa-proline helix.Chemical science · 2024Article
- An Unbound Proline-Rich Signaling Peptide Frequently SamplesFrontiers in molecular biosciences · 2021Article
- The polypeptide biophysics of proline/alanine-rich sequences (PAS): Recombinant biopolymers with PEG-like properties.Biopolymers · 2018Article
- Conformational ensembles explored dynamically from disordered peptides targeting chemokine receptor CXCR4.International journal of molecular sciences · 2015Article
- Krüppel-like factor 11 regulates the expression of metabolic genes via an evolutionarily conserved protein interaction domain functionally disrupted in maturity onset diabetes of the young.The Journal of biological chemistry · 2013Article
- Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.Protein science : a publication of the Protein Society · 2013Article
- Improved atomistic Monte Carlo simulations demonstrate that poly-L-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks.The journal of physical chemistry. B · 2012Article
- Isolation and identification of cryptic bioactive regions in bovine achilles tendon collagen.The protein journal · 2012Article
- A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides.Biophysical journal · 2011Article
- Relevant elements of a maize gamma-zein domain involved in protein body biogenesis.The Journal of biological chemistry · 2010Article
- UV resonance Raman investigation of the conformations and lowest energy allowed electronic excited states of tri- and tetraalanine: charge transfer transitions.The journal of physical chemistry. B · 2010Article
- Conformations and free energy landscapes of polyproline peptides.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- UV resonance raman investigation of electronic transitions in alpha-helical and polyproline II-like conformations.The journal of physical chemistry. B · 2008Article
- Exploring the impact of polyproline II (PII) conformational bias on the binding of peptides to the SEM-5 SH3 domain.Protein science : a publication of the Protein Society · 2008Article
- Predicting 13Calpha chemical shifts for validation of protein structures.Journal of biomolecular NMR · 2007Article
- The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Further evidence for the absence of polyproline II stretch in the XAO peptide.Biophysical journal · 2007Article
- Reassessing random-coil statistics in unfolded proteins.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Interest centers here on whether a polyproline II helix can propagate through adjacent non-proline residues, and on shedding light on recent experimental observations suggesting the presence of significant PP(II) structure in a short alanine-based peptide with no proline in the sequence. For this purpose, we explored the formation of polyproline II helices in proline-rich peptides with the sequences Ac-(Pro)(3)-X-(Pro)(3)-Gly-Tyr-NH(2), with X = Pro (PPP), Ala (PAP), Gln (PQP), Gly (PGP), and Val (PVP), and Ac-(Pro)(3)-Ala-Ala-(Pro)(3)-Gly-Tyr-NH(2) (PAAP), by using a theoretical approach that includes a solvent effect as well as cis <--> trans isomerization of the peptide groups and puckering conformations of the pyrrolidine ring of the proline residues. Since (13)C chemical shifts have proven to be useful for identifying secondary-structure preferences in proteins and peptides, and because values of the dihedral angles (phi,psi) are the main determinants of their magnitudes, we have, therefore, computed the Boltzmann-averaged (13)C chemical shifts for the guest residues in the PXP peptide (X = Pro, Ala, Gln, Gly, and Val) with a combination of approaches, involving molecular mechanics, statistical mechanics, and quantum mechanics. In addition, an improved procedure was used to carry out the conformational searches and to compute the solvent polarization effects faster and more accurately than in previous work. The current theoretical work and additional experimental evidence show that, in short proline-rich peptides, alanine decreases the polyproline II helix content. In particular, the theoretical evidence accumulated in this work calls into question the proposal that alanine has a strong preference to adopt conformations in the polyproline II region of the Ramachandran map.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.