ArticleProceedings of the National Academy of Sciences of the United States of America2009
Conformations and free energy landscapes of polyproline peptides.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed.
- Constant trouble with prolines-navigating a global translation dilemma.Nucleic acids research · 2026Review
- Energy landscape analysis of the development of the chromosome structure across the cell cycle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A flexible peptide linking the periplasmic and cytoplasmic domains of MxiG controls type III secretion signaling and stable sorting platform assembly inFrontiers in cellular and infection microbiology · 2025Article
- Article
- Digital Light Processing of Thermoresponsive Hydrogels from Polyproline-Based Star Polypeptides.Small (Weinheim an der Bergstrasse, Germany) · 2024Article
- Proline, a unique amino acid whose polymer, polyproline II helix, and its analogues are involved in many biological processes: a review.Amino acids · 2024Review
- Deducing the conformational space for an octa-proline helix.Chemical science · 2024Article
- SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact.Communications biology · 2022Article
- Light-Harvesting Crystals Formed from BODIPY-Proline Biohybrid Conjugates: Antenna Effects and Excitonic Coupling.The journal of physical chemistry. A · 2022Article
- An Unbound Proline-Rich Signaling Peptide Frequently SamplesFrontiers in molecular biosciences · 2021Article
- A Global Minimization Toolkit for Batch-Fitting and χBiophysical journal · 2020Article
- Simulation Study of the Plasticity of k-Turn Motif in Different Environments.Biophysical journal · 2020Article
- Investigation of theRSC advances · 2020Article
- Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers.The journal of physical chemistry. B · 2020Article
- A spin-1 representation for dual-funnel energy landscapes.The Journal of chemical physics · 2018Article
- Theoretical and NMR Conformational Studies of β-Proline Oligopeptides With Alternating Chirality of Pyrrolidine Units.Frontiers in chemistry · 2018Article
- Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats.Biophysical journal · 2017Article
- Infrared Multiple-Photon Dissociation Action Spectroscopy of the bJournal of the American Society for Mass Spectrometry · 2017Article
- Article
- Measuring the Elasticity of Poly-l-Proline Helices with Terahertz Spectroscopy.Angewandte Chemie (International ed. in English) · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The structure of the proline amino acid allows folded polyproline peptides to exist as both left- (PPII) and right-handed (PPI) helices. We have characterized the free energy landscapes of hexamer, nanomer, and tridecamer polyproline peptides in gas phase and implicit water as well as explicit hexane and 1-propanol for the nanomer. To enhance the sampling provided by regular molecular dynamics, we used the recently developed adaptively biased molecular dynamics method, which describes Landau free energy maps in terms of relevant collective variables. These maps, as a function of the collective variables of handedness, radius of gyration, and three others based on the peptide torsion angle omega, were used to determine the relative stability of the different structures, along with an estimate of the transition pathways connecting the different minima. Results show the existence of several metastable isomers and therefore provide a complementary view to experimental conclusions based on photo-induced electron transfer experiments with regard to the existence of stable heterogeneous subpopulations in PPII polyproline.
Indexed as
Identifiers
What OpenQuestion holds
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.