ArticleFrontiers in molecular biosciences2021
Optimizing Gō-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane.
Article in Frontiers in molecular biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 46 citations in OpenAlex.
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- Multiscale Computational Dissection of CCRL2-Mediated Chemerin Presentation.Journal of chemical information and modeling · 2025Article
- Membrane Constriction by Dynamin through GTP-Driven Conformational Changes from Coarse-Grained Molecular Dynamics Simulations.The journal of physical chemistry letters · 2025Article
- Microtubules in Martini: Parameterizing a heterogeneous elastic-network towards a mechanically accurate microtubule.PNAS nexus · 2025Article
- GōMartini 3: From large conformational changes in proteins to environmental bias corrections.Nature communications · 2025Article
- Computational analysis of the structural-functional dynamics of a Co-receptor proteoglycan.Frontiers in molecular biosciences · 2025Article
- Martini 3 OliGo̅mers: A Scalable Approach for Multimers and Fibrils in GROMACS.Journal of chemical theory and computation · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
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- The first report of the mobile colistin resistance gene,Microbiology spectrum · 2024Article
- Membrane shapers from two distinct superfamilies cooperate in the development of neuronal morphology.The Journal of cell biology · 2023Article
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- May the force be with you: The role of hyper-mechanostability of the bone sialoprotein binding protein during early stages ofFrontiers in chemistry · 2023Article
- Editorial: Recent advances in computational modelling of biomolecular complexes.Frontiers in chemistry · 2023Article
- Molecular Insight into the Self-Assembly Process of Cellulose Iβ Microfibril.International journal of molecular sciences · 2022Article
- Lactoferrin Inhibition of the Complex Formation between ACE2 Receptor and SARS CoV-2 Recognition Binding Domain.International journal of molecular sciences · 2022Article
- Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides.Molecules (Basel, Switzerland) · 2022Article
- Mapping Mechanostable Pulling Geometries of a Therapeutic Anticalin/CTLA-4 Protein Complex.Nano letters · 2022Article
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coarse-grained (CG) molecular dynamics (MD) simulations allow us to access much larger length and time scales than atomistic MD simulations, providing an attractive alternative to the conventional simulations. Based on the well-known MARTINI CG force field, the recently developed Gō-MARTINI model for proteins describes large-amplitude structural dynamics, which has not been possible with the commonly used elastic network model. Using the Gō-MARTINI model, we conduct MD simulations of the F-BAR Pacsin1 protein on lipid membrane. We observe that structural changes of the non-globular protein are largely dependent on the definition of the native contacts in the Gō model. To address this issue, we introduced a simple cutoff scheme and tuned the cutoff distance of the native contacts and the interaction strength of the Lennard-Jones potentials in the Gō-MARTINI model. With the optimized Gō-MARTINI model, we show that it reproduces structural fluctuations of the Pacsin1 dimer from atomistic simulations. We also show that two Pacsin1 dimers properly assemble through lateral interaction on the lipid membrane. Our work presents a first step towards describing membrane remodeling processes in the Gō-MARTINI CG framework by simulating a crucial step of protein assembly on the membrane.
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