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Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus
Martín Soñora1, Leandro Martínez2, Sergio Pantano1
1Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay.
Journal of Chemical Information and Modeling
|January 8, 2021
Summary
We developed an optimized pipeline for simulating large biomolecular systems like enveloped virus-like particles (VLPs). This method simplifies setup and enables accurate simulations, aiding in understanding emergent diseases and viral structures.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Simulating large biomolecular complexes at biologically relevant timescales is crucial for understanding emergent diseases.
- Current methods for setting up molecular dynamics (MD) simulations of complex systems like virus-like particles (VLPs) can be challenging and time-consuming.
- There is a need for standardized and efficient pipelines to facilitate these simulations for the broader scientific community.
Purpose of the Study:
- To introduce an optimized pipeline for building and simulating enveloped virus-like particles (VLPs).
- To address challenges in system setup for molecular dynamics (MD) simulations of large biomolecular complexes.
- To enable rapid and accurate simulation of viral systems for disease research.
Main Methods:
- Utilized PACKMOL with new features for efficient membrane packing of thousands of lipids around a VLP.
- Employed the coarse-grained SIRAH force field within a multiscale framework for VLP system assembly.
- Developed an equilibration protocol suitable for broadly accessible GPU resources, enabling production MD simulations.
Main Results:
- The pipeline successfully simulated the Zika virus VLP, achieving stabilization around 0.5 μs.
- Simulation results showed high correlation (>0.90) with experimental cryo-electron microscopy density maps.
- Detailed structural analysis revealed good agreement with experimental data and suggested a role for anionic phospholipids in envelope stabilization.
Conclusions:
- The developed pipeline provides an efficient and reliable method for simulating enveloped VLPs and other large biomolecular systems.
- This approach facilitates the study of viral structures and dynamics, contributing to real-time responses against emergent diseases.
- The pipeline's success paves the way for simulating more complex systems, potentially leading to whole-cell simulations.
