Bacterial Mini Microtubule as a Minimal Model System for Exploring Dynamic Instability Using Molecular Dynamics Simulations

Vladimir A. Fedorov; Ekaterina G. Kholina; Nikita B. Gudimchuk; Ilya B. Kovalenko

doi:10.14529/jsfi250201

Authors

Vladimir A. Fedorov Department of Biology, Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-9397-1548
Ekaterina G. Kholina Department of Biology, Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-5918-5084
Nikita B. Gudimchuk Department of Physics, Lomonosov Moscow State University, Moscow, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia; Pskov State University, Pskov, Russia https://orcid.org/0000-0002-7283-8959
Ilya B. Kovalenko Department of Biology, Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-4949-6591

DOI:

https://doi.org/10.14529/jsfi250201

Keywords:

bacterial microtubule, Lomonosov-2, computational performance, multi-scale simulations, molecular dynamics

Abstract

Large scale computational modeling has been fruitfully applied to explore microtubules – an essential component of the cellular skeleton – for over two decades. In this paper, we describe simulations of a yet computationally unexplored minimalistic system of the bacterial mini microtubule, using the high performance resources of Lomonosov Moscow State University. We highlight similarities between the eukaryotic and bacterial microtubules at the protofilament level, the size and stability of the entire mini microtubule system and the computational benefits of using the bacterial mini microtubule as a minimal model to understand dynamic instability. Our results are discussed in the context of a bigger picture of the evolution of molecular dynamics simulations, aiming to understand microtubules, illustrating how the sophistication and scale of the computational efforts increased over the years.

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