ArticleInternational journal of molecular sciences2019
Accelerated Molecular Dynamics Applied to the Peptaibol Folding Problem.
Article in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Novel peptaibiotics identified from Trichoderma clade Viride.Natural products and bioprospecting · 2025Article
- Unlocking the power of membrane biophysics: enhancing the study of antimicrobial peptides activity and selectivity.Biophysical reviews · 2025Review
- Antimicrobial Plant Peptides: Structure, Classification, Mechanism and Therapeutic Potential.Current topics in medicinal chemistry · 2025Review
- Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations.Computational and structural biotechnology journal · 2025Article
- Evaluation of several strategies for controlling canker plant disease caused byMolecular biology research communications · 2025Review
- Conformational analysis of the IQSEC2 protein by statistical thermodynamics.Current research in structural biology · 2024Article
- The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation.The Journal of membrane biology · 2023Review
- Modeling the Effect on a Novel Fungal Peptaibol Placed in an All-Atom Bacterial Membrane Mimicking System via Accelerated Molecular Dynamics Simulations.Life (Basel, Switzerland) · 2023Article
- Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling.Journal of chemical theory and computation · 2023Article
- Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models.Journal of chemical information and modeling · 2023Article
- Structure-activity correlations for peptaibols obtained from clade Longibrachiatum ofComputational and structural biotechnology journal · 2023Article
- Peptaibols: Diversity, bioactivity, and biosynthesis.Engineering microbiology · 2022Review
- Dynorphin A induces membrane permeabilization by formation of proteolipidic pores. Insights from electrophysiology and computational simulations.Computational and structural biotechnology journal · 2022Article
- Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives.Advances and applications in bioinformatics and chemistry : AABC · 2022Review
- Plant antimicrobial peptides: structures, functions, and applications.Botanical studies · 2021Review
- Correction: Tyagi, C., et al. Accelerated Molecular Dynamics Applied to the Peptaibol Folding Problem.International journal of molecular sciences · 2021Article
- Gaussian accelerated molecular dynamics (GaMD): principles and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
The use of enhanced sampling molecular dynamics simulations to facilitate the folding of proteins is a relatively new approach which has quickly gained momentum in recent years. Accelerated molecular dynamics (aMD) can elucidate the dynamic path from the unfolded state to the near-native state, "flattened" by introducing a non-negative boost to the potential. Alamethicin F30/3 (Alm F30/3), chosen in this study, belongs to the class of peptaibols that are 7-20 residue long, non-ribosomally synthesized, amphipathic molecules that show interesting membrane perturbing activity. The recent studies undertaken on the Alm molecules and their transmembrane channels have been reviewed. Three consecutive simulations of ~900 ns each were carried out where N-terminal folding could be observed within the first 100 ns, while C-terminal folding could only be achieved almost after 800 ns. It took ~1 μs to attain the near-native conformation with stronger potential boost which may take several μs worth of classical MD to produce the same results. The Alm F30/3 hexamer channel was also simulated in an
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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.