References
- Desai A., Mitchison T.J. Microtubule polymerization dynamics. Annu. Rev. Cell. Dev. Biol. 1997;13:83–117. doi: 10.1146/annurev.cellbio.13.1.83
- Gudimchuk N.B., McIntosh J.R. Regulation of Microtubule Dynamics, Mechanics and Function through the Growing Tip. Nat. Rev. Mol. Cell Biol. 2021;22:777–795. doi: 10.1038/s41580-021-00399-x
- Mitchison T., Kirschner M. Dynamic Instability of Microtubule Growth. Nature. 1984;312:237–242. doi: 10.1038/312237a0
- Weisenberg R.C., Deery W.J., Dickinson P.J. Tubulin-Nucleotide Interactions during the Polymerization and Depolymerization of Microtubules. Biochemistry. 1976;15:4248–4254. doi: 10.1021/bi00664a018
- Drechsel D.N., Kirschner M.W. The Minimum GTP Cap Required to Stabilize Microtubules. Current Biology. 1994;4:1053–1061. doi: 10.1016/S0960-9822(00)00243-8
- Roostalu J., Thomas C., Cade N.I., Kunzelmann S., Taylor I.A., Surrey T. The Speed of GTP Hydrolysis Determines GTP Cap Size and Controls Microtubule Stability. Elife. 2020;9. doi: 10.7554/eLife.51992
- LaFrance B.J., Roostalu J., Henkin G., Greber B.J., Zhang R., Normanno D., McCollum C.O., Surrey T., Nogales E. Structural Transitions in the GTP Cap Visualized by Cryo-Electron Microscopy of Catalytically Inactive Microtubules. Proceedings of the National Academy of Sciences. 2022;119. doi: 10.1073/pnas.2114994119
- Alushin G.M., Lander G.C., Kellogg E.H., Zhang R., Baker D., Nogales E. High-Resolution Microtubule Structures Reveal the Structural Transitions in Αβ-Tubulin upon GTP Hydrolysis. Cell. 2014;157:1117–1129. doi: 10.1016/j.cell.2014.03.053
- Müller-Reichert T., Chrétien D., Severin F., Hyman A.A. Structural Changes at Microtubule Ends Accompanying GTP Hydrolysis: Information from a Slowly Hydrolyzable Analogue of GTP, Guanylyl (α,β)Methylenediphosphonate. Proceedings of the National Academy of Sciences. 1998;95:3661–3666. doi: 10.1073/pnas.95.7.3661
- Fedorov V.A., Orekhov P.S., Kholina E.G., Zhmurov A.A., Ataullakhanov F.I., Kovalenko I.B., Gudimchuk N.B. Mechanical Properties of Tubulin Intra- and Inter-Dimer Interfaces and Their Implications for Microtubule Dynamic Instability. PLoS Comput. Biol. 2019;15. doi: 10.1371/journal.pcbi.1007327
- Webb B., Sali A. Comparative Protein Structure Modeling Using MODELLER. Curr. Protoc. Bioinformatics. 2016;54. doi: 10.1002/cpbi.3
- Olsson M.H.M., Søndergaard C.R., Rostkowski M., Jensen J.H. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. J. Chem. Theory Comput. 2011;7:525–537. doi: 10.1021/ct100578z
- Morozenko A., Stuchebrukhov A.A. Dowser++, a New Method of Hydrating Protein Structures. Proteins: Structure, Function, and Bioinformatics. 2016;84:1347–1357. doi: 10.1002/prot.25081
- Huang J., Rauscher S., Nawrocki G., Ran T., Feig M., de Groot B.L., Grubmüller H., MacKerell A.D. CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins. Nat. Methods. 2017;14:71–73. doi: 10.1038/nmeth.4067
- Abraham M.J., Murtola T., Schulz R., Páll S., Smith J.C., Hess B., Lindahl E. GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers. SoftwareX. 2015;1–2:19–25. doi: 10.1016/j.softx.2015.06.001
- Parrinello M., Rahman A. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method. J. Appl. Phys. 1981;52:7182–7190. doi: 10.1063/1.328693
- Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. A Smooth Particle Mesh Ewald Method. J. Chem. Phys. 1995;103:8577–8593. doi: 10.1063/1.470117
- Fedorov V., Kholina E., Gudimchuk N., Kovalenko I. High-Performance Computing of Microtubule Protofilament Dynamics by Means of All-Atom Molecular Modeling. Supercomput. Front. Innov. 2023;10:62–68. doi: 10.14529/jsfi230406
- The PyMOL Molecular Graphics System, Version 2.5 Schrödinger, LLC. https://www.pymol.org (accessed 20.11.2024).
- Grafmüller A., Voth G.A. Intrinsic Bending of Microtubule Protofilaments. Structure. 2011;19:409–417. doi: 10.1016/j.str.2010.12.020
|
|
|
