ArticleProtein science : a publication of the Protein Society2008
Exploring the impact of polyproline II (PII) conformational bias on the binding of peptides to the SEM-5 SH3 domain.
Article in Protein science : a publication of the Protein Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins.The Journal of biological chemistry · 2021Article
- Conserved allosteric ensembles in disordered proteins using TROSY/anti-TROSY RBiophysical journal · 2021Article
- Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins.Molecules (Basel, Switzerland) · 2021Review
- Impact of Heat on Coil Hydrodynamic Size Yields the Energetics of Denatured State Conformational Bias.The journal of physical chemistry. B · 2019Article
- Sequence Reversal Prevents Chain Collapse and Yields Heat-Sensitive Intrinsic Disorder.Biophysical journal · 2018Article
- Intrinsic α helix propensities compact hydrodynamic radii in intrinsically disordered proteins.Proteins · 2017Article
- Phosphorylation Increases Persistence Length and End-to-End Distance of a Segment of Tau Protein.Biophysical journal · 2016Article
- Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities.PLoS computational biology · 2016Article
- 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
- Conformational heterogeneity within the LID domain mediates substrate binding to Escherichia coli adenylate kinase: function follows fluctuations.Topics in current chemistry · 2013Review
- Strategies for the thermodynamic characterization of linked binding/local folding reactions within the native state application to the LID domain of adenylate kinase from Escherichia coli.Methods in enzymology · 2011Article
- Characterizing the role of ensemble modulation in mutation-induced changes in binding affinity.Journal of the American Chemical Society · 2009Article
- Denatured-state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding.Journal of molecular biology · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The left-handed polyproline II helical structure (P(II)) is observed to be a dominant conformation in the disordered states of protein and small polypeptide chains, even when no prolines are present in the sequence. Recently, in work by Ferreon and Hilser, the energetics associated with Ala and Gly substitutions at a surface exposed proline site were determined calorimetrically by measuring the binding energetics of Sos peptide variants to the C-terminal Src Homology 3 domain of SEM-5. The results were interpreted as a significant conformational bias toward the bound conformation (i.e., P(II)), even when the ligand is unbound. That study was not able to determine, however, whether the conformational bias of the peptides could be explained in terms other than that of a P(II) preference. Here, we test, using a computer algorithm based on the hard sphere collision (HSC) model, the notion of whether a bias in the unbound states of the peptide ligands is specific for the P(II) conformation, or if a bias to any other region of (phi, psi) space can also result in the same observed binding energetics. The results of these computer simulations indicate that, of the regions of (phi, psi) modeled for bias in the small peptides, only the bias to the P(II) conformation, and at rates of bias similar to the experimentally observed rates, quantitatively reproduced the experimental binding energetics.
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.