Molecular dynamics of tubulin protofilaments and the effect of taxol on their bending deformation

Fedorov V.A., Kholina E.G., Kovalenko I.B.
 pdf (1812K)

Despite the widespread use of cancer chemotherapy drugs, the molecular mechanisms of action of many of them remain unclear. Some of these drugs, such as taxol, are known to affect the dynamics of microtubule assembly and stop the process of cell division in prophase-prometaphase. Recently, new spatial structures of microtubules and individual tubulin oligomers have emerged associated with various regulatory proteins and cancer chemotherapy drugs. However, knowledge of the spatial structure in itself does not provide information about the mechanism of action of drugs.

In this work, we applied the molecular dynamics method to study the behavior of taxol-bound tubulin oligomers and used our previously developed method for analyzing the conformation of tubulin protofilaments, based on the calculation of modified Euler angles. Recent structures of microtubule fragments have demonstrated that tubulin protofilaments bend not in the radial direction, as many researchers assume, but at an angle of approximately 45◦ from the radial direction. However, in the presence of taxol, the bending direction shifts closer to the radial direction. There was no significant difference between the mean bending and torsion angles of the studied tubulin structures when bound to the various natural regulatory ligands, guanosine triphosphate and guanosine diphosphate. The intra-dimer bending angle was found to be greater than the interdimer bending angle in all analyzed trajectories. This indicates that the bulk of the deformation energy is stored within the dimeric tubulin subunits and not between them. Analysis of the structures of the latest generation of tubulins indicated that the presence of taxol in the tubulin beta subunit pocket allosterically reduces the torsional rigidity of the tubulin oligomer, which could explain the underlying mechanism of taxol’s effect on microtubule dynamics. Indeed, a decrease in torsional rigidity makes it possible to maintain lateral connections between protofilaments, and therefore should lead to the stabilization of microtubules, which is what is observed in experiments. The results of the work shed light on the phenomenon of dynamic instability of microtubules and allow to come closer to understanding the molecular mechanisms of cell division.

Keywords: tubulin, taxol, microtubules, dynamic instability, Euler angles, molecular modeling
Citation in English: Fedorov V.A., Kholina E.G., Kovalenko I.B. Molecular dynamics of tubulin protofilaments and the effect of taxol on their bending deformation // Computer Research and Modeling, 2024, vol. 16, no. 2, pp. 503-512
Citation in English: Fedorov V.A., Kholina E.G., Kovalenko I.B. Molecular dynamics of tubulin protofilaments and the effect of taxol on their bending deformation // Computer Research and Modeling, 2024, vol. 16, no. 2, pp. 503-512
DOI: 10.20537/2076-7633-2024-16-2-503-512
URL: http://crm-en.ics.org.ru/journal/article/3468/
Creative Commons License This work is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.

Indexed in Scopus

Full-text version of the journal is also available on the web site of the scientific electronic library eLIBRARY.RU

The journal is included in the Russian Science Citation Index

The journal is included in the RSCI

International Interdisciplinary Conference "Mathematics. Computing. Education"

Copyright © 2009–2024 Institute of Computer Science