ArticleThe journal of physical chemistry. B2012
Improved atomistic Monte Carlo simulations demonstrate that poly-L-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Article
- Matrin-3 forms spherical and wormlike assemblies that are modulated by RNA binding and ALS/FTD-associated mutations.Molecular cell · 2025Article
- Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations.JACS Au · 2024Article
- Article
- Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Huntingtin fibrils with different toxicity, structure, and seeding potential can be interconverted.Nature communications · 2021Article
- Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures.APL materials · 2021Article
- An Unbound Proline-Rich Signaling Peptide Frequently SamplesFrontiers in molecular biosciences · 2021Article
- Structural Model of the Proline-Rich Domain of Huntingtin Exon-1 Fibrils.Biophysical journal · 2020Article
- Amino acid homorepeats in proteins.Nature reviews. Chemistry · 2020Review
- Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins.Biophysical journal · 2020Article
- Information theoretic measures for quantifying sequence-ensemble relationships of intrinsically disordered proteins.Protein engineering, design & selection : PEDS · 2019Article
- Article
- Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.Journal of chemical theory and computation · 2019Article
- Solution Ensemble of the C-Terminal Domain from the Transcription Factor Pdx1 Resembles an Excluded Volume Polymer.The journal of physical chemistry. B · 2019Article
- Tadpole-like Conformations of Huntingtin Exon 1 Are Characterized by Conformational Heterogeneity that Persists regardless of Polyglutamine Length.Journal of molecular biology · 2018Article
- Profilin reduces aggregation and phase separation of huntingtin N-terminal fragments by preferentially binding to soluble monomers and oligomers.The Journal of biological chemistry · 2018Article
- Monomeric Huntingtin Exon 1 Has Similar Overall Structural Features for Wild-Type and Pathological Polyglutamine Lengths.Journal of the American Chemical Society · 2017Article
- Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation.Journal of the American Chemical Society · 2016Article
- CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences.The Journal of chemical physics · 2015Article
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5 authors.
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Abstract
Poly-L-proline (PLP) polymers are useful mimics of biologically relevant proline-rich sequences. Biophysical and computational studies of PLP polymers in aqueous solutions are challenging because of the diversity of length scales and the slow time scales for conformational conversions. We describe an atomistic simulation approach that combines an improved ABSINTH implicit solvation model, with conformational sampling based on standard and novel Metropolis Monte Carlo moves. Refinements to forcefield parameters were guided by published experimental data for proline-rich systems. We assessed the validity of our simulation results through quantitative comparisons to experimental data that were not used in refining the forcefield parameters. Our analysis shows that PLP polymers form heterogeneous ensembles of conformations characterized by semirigid, rod-like segments interrupted by kinks, which result from a combination of internal cis peptide bonds, flexible backbone ψ angles, and the coupling between ring puckering and backbone degrees of freedom.
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