Structural and functional features of lysine acetylation of plant and animal tubulins

Abstract

The study of the genome and the proteome of different species and representatives of distinct kingdoms, especially detection of proteome via wide-scaled analyses has various challenges and pitfalls. Attempts to combine all available information together and isolate some common features for determination of the pathway and their mechanism of action generally have a highly complicated nature. However, microtubule (MT) monomers are highly conserved protein structures, and microtubules are structurally conserved from Homo sapiens to Arabidopsis thaliana. The interaction of MT elements with microtubule-associated proteins and post-translational modifiers is fully dependent on protein interfaces, and almost all MT modifications are well described except acetylation. Crystallography and interactome data using different approaches were combined to identify conserved proteins important in acetylation of microtubules. Application of computational methods and comparative analysis of binding modes generated a robust predictive model of acetylation of the ϵ-amino group of Lys40 in α-tubulins. In turn, the model discarded some probable mechanisms of interaction between elements of interest. Reconstruction of unresolved protein structures was carried out with modeling by homology to the existing crystal structure (PDBID: 1Z2B) from B. taurus using Swiss-model server, followed by a molecular dynamics simulation. Docking of the human tubulin fragment with Lys40 into the active site of α-tubulin acetyltransferase, reproduces the binding mode of peptidomimetic from X-ray structure (PDBID: 4PK3).

Tubulin Acetylation Mediates Bisphenol A Effects on the Microtubule Arrays of Allium cepa and Triticum turgidum

“…In general, post-translational modifications of tubulin, such as acetylation, de-tyrosination, and phosphorylation, play important roles in regulating the stability and function of microtubules [41]. α-Tubulin acetylation is among the most common modifications [42] and is considered to be a marker of stable microtubules and resistant to turnover [43]; although, tubulin acetylation has been also found on dynamic microtubules [25]. It is suggested that tubulin acetylation weakens lateral interactions between protofilaments, thus “softening” microtubules and increasing their flexibility [44].…”

Editorial: Structural bioinformatics and biophysical approaches for understanding the plant responses to biotic and abiotic stresses

“…However, the underlying structural and functional relationships of these molecular mechanisms require more research. Computational and biophysical approaches are viable options for analyses of target molecules to understand their interactions and dynamics that initiate biochemical and physiological responses of plants (Wan et al, 2015;Konda et al, 2018;Moffett and Shukla, 2018;Rayevsky et al, 2019;Jha et al, 2022). These responses in turn control plant tolerance and resistance to sub-optimal environmental conditions.…”

A Journey Through Plant Cytoskeleton: Hot Spots in Signaling and Functioning

“…Besause MTs are highly conserved protein structures, the interaction of MT elements with MT‐associated proteins and post‐translational modifiers is fully dependent on protein interfaces, and almost all MT modifications are well described except acetylation. The paper of Raevsky et al () describes the application of computational methods and comparative analysis of binding modes generated a robust predictive model of acetylation of the ϵ‐amino group of Lys40 in α‐tubulins. As it was demonstrated, the surfaces and amino acid sequences of tubulin homologues from Arabidopsis thaliana are very similar to those from Homo sapiens.…”