ArticleFrontiers in chemistry2019
Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water.
Article in Frontiers in chemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed.
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- Structural and free energy landscape analysis for the discovery of antiviral compounds targeting the cap-binding domain of influenza polymerase PB2.Scientific reports · 2024Article
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- 6-Octadecenoic and Oleic Acid in Liquid Smoke Rice Husk Showed COVID-19 Inhibitor Properties.Advances in pharmacological and pharmaceutical sciences · 2024Article
- Computational insights into the mechanisms underlying structural destabilization and recovery in trafficking-deficient hERG mutants.Frontiers in molecular biosciences · 2024Article
- Elevated concentrations cause upright alpha-synuclein conformation at lipid interfaces.Nature communications · 2023Article
- Local Xenon-Protein Interaction Produces Global Conformational Change and Allosteric Inhibition in Lysozyme.Biochemistry · 2023Article
- Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models.Journal of chemical information and modeling · 2023Article
- Generating Protein Folding Trajectories Using Contact-Map-Driven Directed Walks.Journal of chemical information and modeling · 2023Article
- Deciphering Selectivity Mechanism of BRD9 and TAF1(2) toward Inhibitors Based on Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations.Molecules (Basel, Switzerland) · 2023Article
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6 authors.
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Abstract
In this study, we examined the folding processes of eight helical proteins (2I9M, TC5B, 1WN8, 1V4Z, 1HO2, 1HLL, 2KFE, and 1YYB) at room temperature using the explicit solvent model under the AMBER14SB force field with the accelerated molecular dynamics (AMD) and traditional molecular dynamics (MD), respectively. We analyzed and compared the simulation results obtained by these two methods based on several aspects, such as root mean square deviation (RMSD), native contacts, cluster analysis, folding snapshots, free energy landscape, and the evolution of the radius of gyration, which showed that these eight proteins were successfully and consistently folded into the corresponding native structures by AMD simulations carried out at room temperature. In addition, the folding occurred in the range of 40~180 ns after starting from the linear structures of the eight proteins at 300 K. By contrast, these stable folding structures were not found when the traditional molecular dynamics (MD) simulation was used. At the same time, the influence of high temperatures (350, 400, and 450 K) is also further investigated. Study found that the simulation efficiency of AMD is higher than that of MD simulations, regardless of the temperature. Of these temperatures, 300 K is the most suitable temperature for protein folding for all systems. To further investigate the efficiency of AMD, another trajectory was simulated for eight proteins with the same linear structure but different random seeds at 300 K. Both AMD trajectories reached the correct folded structures. Our result clearly shows that AMD simulation are a highly efficient and reliable method for the study of protein folding.
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