Structural and functional features of lysine acetylation of plant and animal tubulins
Abstract
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 withmore »
- Authors:
-
- Laboratory of Structural Biology, Institute of Food Biotechnology and Genomics National Academy of Sciences of Ukraine Kyiv 04123 Ukraine
- Medway School of Pharmacy Universities of Kent and Greenwich Kent ME4 4TB UK
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1409472
- Resource Type:
- Publisher's Accepted Manuscript
- Journal Name:
- Cell Biology International
- Additional Journal Information:
- Journal Name: Cell Biology International Journal Volume: 43 Journal Issue: 9; Journal ID: ISSN 1065-6995
- Publisher:
- Wiley Blackwell (John Wiley & Sons)
- Country of Publication:
- Country unknown/Code not available
- Language:
- English
Citation Formats
Rayevsky, Alexey V., Sharifi, Mohsen, Samofalova, Dariya A., Karpov, Pavel A., and Blume, Yaroslav B. Structural and functional features of lysine acetylation of plant and animal tubulins. Country unknown/Code not available: N. p., 2017.
Web. doi:10.1002/cbin.10887.
Rayevsky, Alexey V., Sharifi, Mohsen, Samofalova, Dariya A., Karpov, Pavel A., & Blume, Yaroslav B. Structural and functional features of lysine acetylation of plant and animal tubulins. Country unknown/Code not available. https://doi.org/10.1002/cbin.10887
Rayevsky, Alexey V., Sharifi, Mohsen, Samofalova, Dariya A., Karpov, Pavel A., and Blume, Yaroslav B. Wed .
"Structural and functional features of lysine acetylation of plant and animal tubulins". Country unknown/Code not available. https://doi.org/10.1002/cbin.10887.
@article{osti_1409472,
title = {Structural and functional features of lysine acetylation of plant and animal tubulins},
author = {Rayevsky, Alexey V. and Sharifi, Mohsen and Samofalova, Dariya A. and Karpov, Pavel A. and Blume, Yaroslav B.},
abstractNote = {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).},
doi = {10.1002/cbin.10887},
journal = {Cell Biology International},
number = 9,
volume = 43,
place = {Country unknown/Code not available},
year = {Wed Nov 15 00:00:00 EST 2017},
month = {Wed Nov 15 00:00:00 EST 2017}
}
https://doi.org/10.1002/cbin.10887
Web of Science
Works referenced in this record:
Structural basis for the regulation of tubulin by vinblastine
journal, May 2005
- Gigant, Benoît; Wang, Chunguang; Ravelli, Raimond B. G.
- Nature, Vol. 435, Issue 7041
Prediction of Protein Binding Regions in Disordered Proteins
journal, May 2009
- Mészáros, Bálint; Simon, István; Dosztányi, Zsuzsanna
- PLoS Computational Biology, Vol. 5, Issue 5
Regulation of microtubule dynamics by inhibition of the tubulin deacetylase HDAC6
journal, September 2009
- Zilberman, Y.; Ballestrem, C.; Carramusa, L.
- Journal of Cell Science, Vol. 122, Issue 19
Structure of the -tubulin acetyltransferase, TAT1, and implications for tubulin-specific acetylation
journal, October 2012
- Friedmann, D. R.; Aguilar, A.; Fan, J.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 48
HDAC6 is a microtubule-associated deacetylase
journal, May 2002
- Hubbert, Charlotte; Guardiola, Amaris; Shao, Rong
- Nature, Vol. 417, Issue 6887
Post-translational modifications and multiple tubulin isoforms in Nicotiana tabacum L. cells
journal, March 1997
- Smertenko, Andrey; Blume, Yaroslav; Viklický, Vladimír
- Planta, Vol. 201, Issue 3
Detyrosination of alpha tubulin does not stabilize microtubules in vivo [published erratum appears in J Cell Biol 1990 Sep;111(3):1325-6]
journal, July 1990
- Webster, D. R.
- The Journal of Cell Biology, Vol. 111, Issue 1
Atomic resolution structure of human -tubulin acetyltransferase bound to acetyl-CoA
journal, October 2012
- Taschner, M.; Vetter, M.; Lorentzen, E.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 48
High-Resolution Model of the Microtubule
journal, January 1999
- Nogales, Eva; Whittaker, Michael; Milligan, Ronald A.
- Cell, Vol. 96, Issue 1
Microtubules acquire resistance from mechanical breakage through intralumenal acetylation
journal, April 2017
- Xu, Zhenjie; Schaedel, Laura; Portran, Didier
- Science, Vol. 356, Issue 6335
Alpha-tubulin acetylase activity in isolated Chlamydomonas flagella
journal, December 1985
- Greer, K.
- The Journal of Cell Biology, Vol. 101, Issue 6
A Bacterial Acetyltransferase Destroys Plant Microtubule Networks and Blocks Secretion
journal, February 2012
- Lee, Amy Huei-Yi; Hurley, Brenden; Felsensteiner, Corinna
- PLoS Pathogens, Vol. 8, Issue 2
Structure of the GCN5 histone acetyltransferase bound to a bisubstrate inhibitor
journal, October 2002
- Poux, A. N.; Cebrat, M.; Kim, C. M.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 22
Post-translational modifications regulate microtubule function
journal, December 2003
- Westermann, Stefan; Weber, Klaus
- Nature Reviews Molecular Cell Biology, Vol. 4, Issue 12
Tubulin Acetyltransferase αTAT1 Destabilizes Microtubules Independently of Its Acetylation Activity
journal, December 2012
- Kalebic, Nereo; Martinez, Concepcion; Perlas, Emerald
- Molecular and Cellular Biology, Vol. 33, Issue 6
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
journal, April 2014
- Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew
- Nucleic Acids Research, Vol. 42, Issue W1
Low resolution structure of microtubules in solution
journal, July 1992
- Andreu, J. M.; Bordas, J.; Diaz, J. F.
- Journal of Molecular Biology, Vol. 226, Issue 1
Conformational changes in tubulin in GMPCPP and GDP-taxol microtubules observed by cryoelectron microscopy
journal, July 2012
- Yajima, Hiroaki; Ogura, Toshihiko; Nitta, Ryo
- The Journal of Cell Biology, Vol. 198, Issue 3
HDAC6 deacetylation of tubulin modulates dynamics of cellular adhesions
journal, March 2007
- Tran, A. D. -A.; Marmo, T. P.; Salam, A. A.
- Journal of Cell Science, Vol. 120, Issue 8
Inhibition of HDAC6 Deacetylase Activity Increases Its Binding with Microtubules and Suppresses Microtubule Dynamic Instability in MCF-7 Cells
journal, June 2013
- Asthana, Jayant; Kapoor, Sonia; Mohan, Renu
- Journal of Biological Chemistry, Vol. 288, Issue 31
Effects of tubulin acetylation and tubulin acetyltransferase binding on microtubule structure
journal, January 2014
- Howes, Stuart C.; Alushin, Gregory M.; Shida, Toshinobu
- Molecular Biology of the Cell, Vol. 25, Issue 2
Elongator Controls the Migration and Differentiation of Cortical Neurons through Acetylation of α-Tubulin
journal, February 2009
- Creppe, Catherine; Malinouskaya, Lina; Volvert, Marie-Laure
- Cell, Vol. 136, Issue 3
Tubulin acetylation protects long-lived microtubules against mechanical ageing
journal, February 2017
- Portran, Didier; Schaedel, Laura; Xu, Zhenjie
- Nature Cell Biology, Vol. 19, Issue 4
Multiple tubulins: evolutionary aspects and biological implications
journal, June 2013
- Breviario, Diego; Gianì, Silvia; Morello, Laura
- The Plant Journal, Vol. 75, Issue 2
Molecular Basis for Age-Dependent Microtubule Acetylation by Tubulin Acetyltransferase
journal, June 2014
- Szyk, Agnieszka; Deaconescu, Alexandra M.; Spector, Jeffrey
- Cell, Vol. 157, Issue 6
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
journal, February 2003
- Dominguez, Cyril; Boelens, Rolf; Bonvin, Alexandre M. J. J.
- Journal of the American Chemical Society, Vol. 125, Issue 7
MEC-17 is an α-tubulin acetyltransferase
journal, September 2010
- Akella, Jyothi S.; Wloga, Dorota; Kim, Jihyun
- Nature, Vol. 467, Issue 7312