ReviewBiomolecules2014
Local order in the unfolded state: conformational biases and nearest neighbor interactions.
Review in Biomolecules, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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.
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Who cites it
20 citing papers in PubMed.
- Article
- What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments.Chemical science · 2024Article
- Exploring Nearest Neighbor Interactions and Their Influence on the Gibbs Energy Landscape of Unfolded Proteins and Peptides.International journal of molecular sciences · 2022Review
- Randomizing of Oligopeptide Conformations by Nearest Neighbor Interactions between Amino Acid Residues.Biomolecules · 2022Article
- Short peptides as predictors for the structure of polyarginine sequences in disordered proteins.Biophysical journal · 2021Article
- Revisiting the Formation of a Native Disulfide Bond: Consequences for Protein Regeneration and Beyond.Molecules (Basel, Switzerland) · 2020Review
- Discriminating changes in protein structure using tyrosine conjugation.Protein science : a publication of the Protein Society · 2020Article
- Glycine in Water Favors the Polyproline II State.Biomolecules · 2020Article
- Reduced alphabet of prebiotic amino acids optimally encodes the conformational space of diverse extant protein folds.BMC evolutionary biology · 2019Article
- Experimentally Derived and Computationally Optimized Backbone Conformational Statistics for Blocked Amino Acids.Journal of chemical theory and computation · 2019Article
- The Pathways of the iRFP713 Unfolding Induced by Different Denaturants.International journal of molecular sciences · 2018Article
- Using NMR Chemical Shifts to Determine Residue-Specific Secondary Structure Populations for Intrinsically Disordered Proteins.Methods in enzymology · 2018Article
- Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective.Journal of computational chemistry · 2017Article
- Using chirality to probe the conformational dynamics and assembly of intrinsically disordered amyloid proteins.Scientific reports · 2017Article
- Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins.Journal of biological physics · 2017Article
- Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Conformational analysis of short polar side-chain amino-acids through umbrella sampling and DFT calculations.Journal of molecular modeling · 2016Article
- The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design.Protein engineering, design & selection : PEDS · 2016Article
- Elastin-like polypeptides as models of intrinsically disordered proteins.FEBS letters · 2015Review
- Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.Journal of chemical theory and computation · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed.
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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.