Calculation of Electrostatic Potential Field of Coronavirus S Proteins for Brownian Dynamics Simulations

Ekaterina P. Vasyuchenko; Vladimir A. Fedorov; Ekaterina G. Kholina; Sergei S. Khruschev; Ilya B. Kovalenko; Marina G. Strakhovskaya

doi:10.14529/jsfi220304

Authors

Ekaterina P. Vasyuchenko Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
Vladimir A. Fedorov Lomonosov Moscow State University, Moscow, Russian Federation https://orcid.org/0000-0002-9397-1548
Ekaterina G. Kholina Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-5918-5084
Sergei S. Khruschev Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-4714-6221
Ilya B. Kovalenko Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-4949-6591
Marina G. Strakhovskaya Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-4571-0431

DOI:

https://doi.org/10.14529/jsfi220304

Keywords:

Brownian dynamics, coarse grain, spike protein, SARS-CoV-2, SARS-CoV, MERS-CoV, phthalocyanine, photosensitizer

Abstract

The Brownian dynamics method can give insight into the initial stages of the interaction of antiviral drug molecules with the structural components of bacteria or viruses. RAM of conventional personal computer allows calculation of Brownian dynamics of interaction of antiviral drugs with individual coronavirus S protein. However, scaling up this approach for modeling the interaction of antiviral drugs with the whole virion consisting of thousands of proteins and lipids is difficult due to high requirements for computing resources. In the case of the Brownian dynamics method, the main amount of RAM in the calculations is occupied by an array of values of the virion electrostatic potential field. When the system is increased from one S protein to the whole virion, the volume of data increases significantly. The standard protocol for calculating Brownian dynamics uses a three-dimensional grid with a spatial step of 1Å to calculate the electrostatic potential field. In this work, we consider the possibility of increasing the grid spacing parameter for calculating the electrostatic potential field of individual coronavirus S proteins. In this case, the amount of RAM occupied by the electrostatic potential field is reduced, which makes it possible to use personal computers for calculations. We performed Brownian dynamics simulations of interaction of an antiviral photosensitizer molecule with S proteins of three coronaviruses SARS-CoV, MERS-CoV, and SARS-CoV-2, and demonstrated that reduction of detalization of electrostatic potential field does not influence the results of Brownian dynamics much.

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