Physical Virology is a relatively new discipline aimed to unravel the physical forces that rule the assembly and destabilization of viral particles. Computational approaches can provide structural and dynamical insights into those processes. However, the computational cost of simulating entire viral particles constituted by millions of atoms is prohibitive without the use of supercomputer resources. We have developed a plug&play coarse-grained force field for biomolecules including topologies and interaction parameters for proteins, lipids, nucleic acids and aqueous solvent named SIRAH (Southamerican Initiative for a Rapid and Accurate Hamiltonian). Our force field grants over 2 orders of magnitude speed up, making the simulation of viruses affordable to desktop computers.
We used this force field to characterize the dynamics of Zika virus, revealing unforeseen protein-lipid interactions that contribute to store significant tensile energy in the viral membrane, proposing it as an important factor in the spring-loaded configuration of the mature virion.
 
References
[1] Soñora M, Martínez L, Pantano S, Machado MR, Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. JCIM, 2021, 61:408
[2] Machado M, Gonzalez HC, Pantano S. MD Simulations of Virus-Like Particles with Supra CG solvation affordable to desktop computers. JCTC. 2017, 13: 5106.
[3] Soñora M, Barrera EE, Zonta F, Pantano S, The stressed life of a lipid in the Zika Virus membrane, BBA – Membranes, 2022, 1864 (1), 183804.