We present molecular dynamics (MD) trajectories of a single ring of B-lattice microtubule ring consisting of 13 tubulin heterodimers. The data contain trajectories of this molecular system ran under various conditions (two temperature values, three ionic strength values, three values of electric field (including no field), and four electric field orientations). Our data enable us to analyze the effects of the electric field on microtubule under a variety of conditions. This data set was a basis of our in silico discovery, which demonstrates that the electric field can open microtubule lattice [1].

Biomolecular Simulation Center Department of Pharmaceutical Chemistry Faculty of Pharmacy Heliopolis University Cairo 11777 Egypt

Institute of Photonics and Electronics of the Czech Academy of Sciences Prague 18251 Czech Republic

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Průša J., Ayoub A.T., Chafai D.E., Havelka D., Cifra M. Electro-opening of a microtubule lattice in silico. Comput. Struct. Biotechnol. J. 2021;19:1488–1496. doi: 10.1016/j.csbj.2021.02.007. PubMed DOI PMC

Ayoub A.T., Klobukowski M., Tuszynski J.A. Detailed per-residue energetic analysis explains the driving force for microtubule disassembly. PLoS Comput. Biol. 2015;11(6) doi: 10.1371/journal.pcbi.1004313. Edited by James M. Briggs. PubMed DOI PMC

Tuszynski J.A., Carpenter E.J., Huzil J.T., Malinski W., Luchko T., Luduena R.F. The evolution of the structure of tubulin and its potential consequences for the role and function of microtubules in cells and embryos. Int. J. Dev. Biol. 2006;50(2–3):341–358. doi: 10.1387/ijdb.052063jt. PubMed DOI

Chafai D.E., Sulimenko V., Havelka D., Kubínová L., Dráber P., Cifra M. Reversible and irreversible modulation of tubulin self-assembly by intense nanosecond pulsed electric fields. Adv. Mater. 2019;31(39) doi: 10.1002/adma.201903636. PubMed DOI

Marracino P., Havelka D., Průša J., Liberti M., Tuszynski J., Ayoub A.T., Apollonio F., Cifra M. Tubulin response to intense nanosecond-scale electric field in molecular dynamics simulation. Sci. Rep. 2019;9(1):10477. doi: 10.1038/s41598-019-46636-4. PubMed DOI PMC

Salomon-Ferrer R., Götz A.W., Poole D., Grand S.L., Walker RC. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald. J. Chem. Theory Comput. 2013;9(9):3878–3888. doi: 10.1021/ct400314y. PubMed DOI

Le Grand S., Götz A.W., Walker R.C. SPFP: speed without compromise—a mixed precision model for GPU accelerated molecular dynamics simulations. Comput. Phys. Commun. 2013;184(2):374–380.

Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983;79(2):926–935. doi: 10.1063/1.445869. DOI

Joung I.S., Cheatham T.E. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J. Phys. Chem. B. 2008;112(30):9020–9041. doi: 10.1021/jp8001614. PubMed DOI PMC

Meagher K.L., Redman L.T., Carlson H.A. Development of polyphosphate parameters for use with the AMBER force field. J. Comput. Chem. 2003;24(9):1016–1025. doi: 10.1002/jcc.10262. PubMed DOI

Kräutler V., Van Gunsteren W.F., Hünenberger P.H. A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J. Comput. Chem. 2001;22(5):501–508. doi: 10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V. DOI