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SIRAH_Packmol_draft_v19.pdf (2.71 MB)

Wrapping up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus.

preprint
revised on 15.12.2020, 20:05 and posted on 17.12.2020, 08:50 by Martín Soñora, Leandro Martinez, Sergio Pantano, Matías R. Machado

Simulating huge biomolecular complexes of million atoms at relevant biological timescales is becoming accessible to the broad scientific community. That proves to be crucial for urgent responses against emergent diseases in real time. Yet, there are still issues to sort regarding the system setup so that Molecular Dynamics (MD) simulations can be run in a simple and standard way. Here, we introduce an optimized pipeline for building and simulating enveloped virus-like particles (VLP). First, the membrane packing problem is tackled with new features and optimized options in PACKMOL. This allows preparing accurate membrane models of thousands of lipids in the context of a VLP within a few hours using a single CPU. Then, the assembly of the VLP system is done within the multiscale framework of the coarse-grained SIRAH force field. Finally, the equilibration protocol provides a system ready for production MD simulations within a few days on broadly accessible GPU resources. The pipeline is applied to study the Zika Virus as a test case for large biomolecular systems. The VLP stabilizes at approximately 0.5 microseconds of MD simulation, reproducing correlations greater than 0.90 against experimental density maps from cryo-electron microscopy. Detailed structural analysis of the protein envelope also shows very good agreement in root mean square deviations and B-factors with the experimental data. The level of details attained shows for the first time a possible role of anionic phospholipids in stabilizing the envelope. Combining an efficient and reliable setup procedure with an accurate coarse-grained force field provides a valuable pipeline for simulating arbitrary viral systems or sub-cellular compartments, paving the way towards whole-cell simulations.

Funding

HPC facility of LNCC - Santos Dumont, Petropolis, Brazil, grant VICBF1

FOCEM (MERCOSUR Structural Convergence Fund), COF 03/11.

History

Email Address of Submitting Author

mmachado@pasteur.edu.uy

Institution

Institut Pasteur de Montevideo

Country

Uruguay

ORCID For Submitting Author

0000-0002-9971-4710

Declaration of Conflict of Interest

No conflict to declare

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