ArticlePloS one2011
Assignment of PolyProline II conformation and analysis of sequence--structure relationship.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Advances in molecular dynamics approaches for investigating cell-penetrating peptides.Biophysical reviews · 2026Review
- DSSP 4: FAIR annotation of protein secondary structure.Protein science : a publication of the Protein Society · 2025Article
- Systemic structural analysis of alterations reveals a common structural basis of driver mutations in cancer.NAR cancer · 2023Article
- Comparative molecular dynamics simulations of pathogenic and non-pathogenic huntingtin protein monomers and dimers.Frontiers in molecular biosciences · 2023Article
- Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 ofComputational and structural biotechnology journal · 2023Article
- A Perspective on the (Rise and Fall of) Protein β-Turns.International journal of molecular sciences · 2022Review
- Expanding the Disorder-Function Paradigm in the C-Terminal Tails of Erbbs.Biomolecules · 2021Review
- The Effect of Multisite Phosphorylation on the Conformational Properties of Intrinsically Disordered Proteins.International journal of molecular sciences · 2021Article
- Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity.Journal of chemical theory and computation · 2021Article
- Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison.International journal of molecular sciences · 2021Article
- Structural and dynamic characterization of the C-terminal tail of ErbB2: Disordered but not random.Biophysical journal · 2021Article
- An Unbound Proline-Rich Signaling Peptide Frequently SamplesFrontiers in molecular biosciences · 2021Article
- A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway.PLoS computational biology · 2020Article
- Sequence-Dependent Correlated Segments in the Intrinsically Disordered Region of ChiZ.Biomolecules · 2020Article
- Membrane-associated mucins of the ocular surface: New genes, new protein functions and new biological roles in human and mouse.Progress in retinal and eye research · 2020Review
- Prediction of polyproline II secondary structure propensity in proteins.Royal Society open science · 2020Article
- Position β57 of I-AScience immunology · 2019Article
- The free energy landscape of the oncogene protein E7 of human papillomavirus type 16 reveals a complex interplay between ordered and disordered regions.Scientific reports · 2019Article
- Proline 411 biases the conformation of the intrinsically disordered plant UVR8 photoreceptor C27 domain altering the functional properties of the peptide.Scientific reports · 2019Article
- Exploring Peptide⁻Solvent Interactions: A Computational Study.Molecules (Basel, Switzerland) · 2018Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSecondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely α-helices and β-sheets, apart from turns, and the rest is associated to coil. These repetitive secondary structures have specific and conserved biophysical and geometric properties. PolyProline II (PPII) helix is yet another interesting repetitive structure which is less frequent and not usually associated with stabilizing interactions. Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein-protein interactions. METHODOLOGY/PRINCIPAL
findingsA major factor that limits the study of PPII is that its assignment cannot be carried out with the most commonly used secondary structure assignment methods (SSAMs). The purpose of this work is to propose a PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment. Considering the ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most consensual rule of PPII assignment, three SSAMs that can assign PPII, were compared and analyzed. The assignment rule was defined to have a maximum coverage of all assignments made by these SSAMs. Not many constraints were added to the assignment and only PPII helices of at least 2 residues length are defined. CONCLUSIONS/SIGNIFICANCE: The simple rules designed in this study for characterizing PPII conformation, lead to the assignment of 5% of all amino as PPII. Sequence-structure relationships associated with PPII, defined by the different SSAMs, underline few striking differences. A specific study of amino acid preferences in their N and C-cap regions was carried out as their solvent accessibility and contact patterns. Thus the assignment of PPII can be coupled with DSSP and thus opens a simple way for further analysis in this field.
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