ArticleJournal of computational chemistry2017
Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides.
Article in Journal of computational chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 26 citations in OpenAlex.
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Peptide Power: Mechanistic Insights into the Effect of Mitochondria-Targeted Tetrapeptides on Membrane Electrostatics from Molecular Simulations.Molecular pharmaceutics · 2023Article
- Role of TM3 in claudin-15 strand flexibility: A molecular dynamics study.Frontiers in molecular biosciences · 2022Article
- Molecular dynamics study of membrane permeabilization by wild-type and mutant lytic peptides from the non-enveloped Flock House virus.Biochimica et biophysica acta. Biomembranes · 2020Article
- Coarse-grained (hybrid) integrative modeling of biomolecular interactions.Computational and structural biotechnology journal · 2020Review
- The acidic tail of HMGB1 regulates its secondary structure and conformational flexibility: A circular dichroism and molecular dynamics simulation study.Computational and structural biotechnology journal · 2020Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Folding a viral peptide in different membrane environments: pathway and sampling analyses.Journal of biological physics · 2018Article
- Article
- Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.Journal of chemical theory and computation · 2017Article
- Influence of membrane composition on the binding and folding of a membrane lytic peptide from the non-enveloped flock house virus.Biochimica et biophysica acta. Biomembranes · 2017Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp). Overall, we find PACE provides an improvement over MARTINI for modeling helical peptides, based on the membrane insertion energetics for WALP16 and more realistic melittin pore dynamics. Our studies on HAfp, which forms a helical hairpin structure, do not show the hairpin structure to be stable, which may point toward a deficiency in the model. © 2017 Wiley Periodicals, Inc.
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