Convergence analysis of molecular dynamics trajectories of intrinsically disordered protein regions using the C-terminal fragments of the proteins $\alpha$-tubulin and FtsZ as an example

Volkhin I.A., Fedorov V.A., Orekhov P.S., Gudimchuk N.B., Kovalenko I.B.
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Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins represent extremely important yet challenging-to-study regions of the proteome. All-atom molecular dynamics, widely used for sampling the configurational space of proteins, requires substantial computational resources, especially for disordered protein regions due to the large number of accessible conformations. In this work, we propose a method for estimating the convergence time of molecular dynamics trajectories, based on calculating the overlap integral between ensembles in principal component space. Simulations of 3 $\mu$s are sufficient for convergence of a short fragment of $\alpha$-tubulin but insufficient for an extended region of FtsZ, indicating the need for substantially longer simulation times or enhanced sampling methods to obtain a statistically reliable conformational ensemble for extended disordered protein fragments of this type. The method we propose can be used to determine the convergence of ensembles of intrinsically disordered protein regions obtained by all-atom molecular dynamics.

Keywords: intrinsically disordered regions (IDR), molecular dynamics, tubulin, FtsZ
Citation in English: Volkhin I.A., Fedorov V.A., Orekhov P.S., Gudimchuk N.B., Kovalenko I.B. Convergence analysis of molecular dynamics trajectories of intrinsically disordered protein regions using the C-terminal fragments of the proteins $\alpha$-tubulin and FtsZ as an example // Computer Research and Modeling, 2026, vol. 18, no. 5, pp. 1329-1346
Citation in English: Volkhin I.A., Fedorov V.A., Orekhov P.S., Gudimchuk N.B., Kovalenko I.B. Convergence analysis of molecular dynamics trajectories of intrinsically disordered protein regions using the C-terminal fragments of the proteins $\alpha$-tubulin and FtsZ as an example // Computer Research and Modeling, 2026, vol. 18, no. 5, pp. 1329-1346
DOI: 10.20537/2076-7633-2026-18-5-1329-1346
URL: http://crm-en.ics.org.ru/journal/article/3783/
Creative Commons License This work is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.

Copyright © 2026 Volkhin I.A., Fedorov V.A., Orekhov P.S., Gudimchuk N.B., Kovalenko I.B.

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