Recombinant human tubulin was purified following a previously described protocol31 ,56 using slightly modified buffers. Cell pellets obtained from 2 L of High Five insect cells expressing human TUBB3-TEVsite-StrepTagII, with the C-terminal StrepTagII cleavable by tobacco etch virus (TEV) protease, and TUBA1B-His, with internal 6x His-Tag (WT, αE254A, αE254N, and αE254Q) were resuspended 1:1 (vol/vol) in cold lysis buffer (80 mM PIPES, 1 mM EGTA, 1 mM MgCl2, 50 mM imidazole, 100 mM KCl, 0.2 mM GTP, 1 mM β-ME, pH 7.2) and lysed using an Emulsiflex-C5 homogenizer (Avestin). The resulting lysate was clarified by ultracentrifugation (160,000× g, 45 min, 4 °C), filtered using 0.22 µm PES syringe filters (4602, Merck) and flowed through a 5-mL HisTrap HP column (GE17-5255-01, Cytiva). The column was then first washed with 5 column volumes (CVs) of Ni-dilution buffer (80 mM PIPES, 1 mM EGTA, 6 mM MgCl2, 50 mM imidazole, 0.2 mM GTP, 1 mM β-ME, pH 7.2), then with 5 CVs of Ni wash buffer 1 (80 mM PIPES, 1 mM EGTA, 11 mM MgCl2, 0.2 mM GTP, 5 mM ATP, 1 mM β-ME, pH 7.2), then with 5 CVs of Ni wash buffer 2 (80 mM PIPES, 1 mM EGTA, 5 mM MgCl2, 0.1% (vol/vol) Tween-20, 10% (w/vol) glycerol), 0.2 mM GTP, 1 mM β-ME, pH 7.2) and finally with 5 CVs of Ni-dilution buffer. The protein was eluted with Ni-elution buffer (80 mM PIPES, 1 mM EGTA, 5 mM MgCl2, 300 mM imidazole 0.2 mM GTP, 1 mM β-ME, pH 7.2). The eluted protein was collected in a 96-well plate containing 1 volume of Strep binding buffer (80 mM PIPES, 1 mM EGTA, 5 mM MgCl2, 0.2 mM GTP, 1 mM β-ME, pH 7.2) in order to immediately dilute 4 times the imidazole present in the Ni-elution buffer. The eluted fractions corresponding to the main peak were joined, diluted 2 times with Strep binding buffer, and passed through two HiTrap SP FF columns of 1 mL (17505401, Cytiva) and one StrepTrap HP of 5 mL (28-9075-48, Cytiva) serially connected and equilibrated in Strep binding buffer. The columns were then washed with 2 CVs of Strep binding buffer, and the protein was eluted in Strep elution buffer (80 mM PIPES, 1 mM EGTA, 5 mM MgCl2, 2.5 mM
Porcine brain tubulin was purified as previously described57 (link). Briefly, tubulin was purified from brain extract by sequential cycles of polymerization of tubulin at 37 °C in high-concentration PIPES buffer supplemented with ATP, GTP, and glycerol, followed by depolymerization on ice. For long-term storage 5-ml-tubulin aliquots were frozen and stored in liquid nitrogen. Tubulin used in experiments was passed through another polymerization/depolymerization cycle and was snap-frozen and stored in 10 µl aliquots in liquid nitrogen. Tubulin was labeled with CF640R-NHS (SCJ4600044, Merck) or biotin-NHS (203112, Merck), as previously described58 (link). Briefly, NHS-fluorophores dissolved in anhydrous DMSO were added drop by drop to microtubules obtained from cycled tubulin while gently mixing. After 40 min, the labeled microtubules were depolymerized at 4 °C. The samples were then ultracentrifuged (280,000× g, 10 min, 4 °C), and the pellet was discarded. The supernatant containing labeled tubulin was aliquoted, snap-frozen, and stored in liquid nitrogen in 5 µl aliquots.
mGFP-EB3 used for TIRF microscopy experiments was purified as previously described31 . Briefly, mGFP-EB3 was expressed in E. coli BL-21 cells and purified by nickel-affinity chromatography, followed by size exclusion chromatography. Monomeric human EB3 calponin homology (CH) domain (residues 1-200) used for cryo-EM experiments was purified as previously described30 (link),32 . Briefly, EB3-CH was expressed in E. coli BL-21 cells and was purified by nickel-affinity chromatography, followed by size exclusion chromatography.