ArticleJournal of chemical theory and computation2021
Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- How Well Do Molecular Dynamics Force Fields Model Peptides: A Systematic Benchmark across Diverse Folding Behaviors.The journal of physical chemistry. B · 2026Article
- Conformational flexibility and transient structure of the proline-rich domain in p53.Biophysical journal · 2026Article
- Physicochemical Principles Governing the Intrinsically Disordered Salivary Peptide Histatin 5: Ensemble Structure, Electrostatics, and Environmental Responsiveness.The journal of physical chemistry. B · 2026Review
- Functions of prolyl hydroxylation in elastin.The Journal of biological chemistry · 2026Article
- Unraveling the conformational landscape of amyloid precursor protein intracellular domain.Biophysical journal · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Molecular Dynamics Insights into Peptide-Based Tetrodotoxin Delivery Nanostructures.Molecules (Basel, Switzerland) · 2024Article
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Likely Overstabilization of Charge-Charge Interactions in CHARMM36m(w): A Case for a99SB-disp Water.The journal of physical chemistry. B · 2024Article
- Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes.ArXiv · 2024Article
- Deeper Insight of the Conformational Ensemble of Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2024Article
- Exploring the Functional Landscape of the p53 Regulatory Domain: The Stabilizing Role of Post-Translational Modifications.Journal of chemical theory and computation · 2024Article
- Intrinsic Conformational Dynamics of Glycine and Alanine in Polarizable Molecular Dynamics Force Fields: Comparison to Spectroscopic Data.The journal of physical chemistry. B · 2024Article
- Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives.Amino acids · 2024Review
- Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation.Journal of chemical theory and computation · 2024Article
- Interaction of a Histidine-Rich Antimicrobial Saliva Peptide with Model Cell Membranes: The Role of Histidines.Langmuir : the ACS journal of surfaces and colloids · 2023Article
- Prion Protein Octarepeat Domain Forms Transient β-Sheet Structures upon Residue-Specific Binding to Cu(II) and Zn(II) Ions.Biochemistry · 2023Article
- Comparative molecular dynamics simulations of pathogenic and non-pathogenic huntingtin protein monomers and dimers.Frontiers in molecular biosciences · 2023Article
- Self-Diffusive Properties of the Intrinsically Disordered Protein Histatin 5 and the Impact of Crowding Thereon: A Combined Neutron Spectroscopy and Molecular Dynamics Simulation Study.The journal of physical chemistry. B · 2022Article
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Corrections and comments
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Authors and funding
4 authors.
Funding
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Abstract
Five peptides previously suggested to possess polyproline II (PPII) structure have here been investigated by using atomistic molecular dynamics simulations to compare how well four different force fields known for simulating intrinsically disordered proteins relatively well (Amber ff99SB-disp, Amber ff99SB-ILDN, CHARM36IDPSFF, and CHARMM36m) can capture this secondary structure element. The results revealed that all force fields sample PPII structures but to different extents and with different propensities toward other secondary structure elements, in particular, the β-sheet and "random coils". A cluster analysis of the simulations of histatin 5 also revealed that the conformational ensembles of the force fields are quite different. We compared the simulations to circular dichroism and nuclear magnetic resonance spectroscopy experiments and conclude that further experiments and methods for interpreting them are needed to assess the accuracy of force fields in determining PPII structure.
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