Ocalize acetyl-K40 a-tubulin in a wide variety of animal cells and has been shown to be sensitive to the addition (via MEC-17) or removal (via HDAC6 or SIRT-2) of the acetyl group specifically at K40 [8,23,24,26]. Thus, we tested whether the Fab fragment differs from the whole antibody in its ability to distinguish MedChemExpress 1485-00-3 between acetylated and deacetylated microtubules. To do this, we immunolabeled taxol-stabilized microtubules polymerized from acetylated or deacetylated tubulins with the monoclonal 6-11B-1 and polyclonal anti-acetyl-K40 antibodies. To preclude any effects on antigen recognition by fixation [19,31], antibodies were added either without fixation (“live”) or after paraformaldehyde fixation (“PFA fixed”) of the microtubules. The monoclonal 6-11B-1 antibody stained both acetylated and deacetylated microtubules regardless of fixation conditions (Figure 4A). In contrast, the polyclonal anti-acetyl-K40 antibody stained acetylated but not deacetylated microtubules (Figure 4B). These results indicate that the monoclonal 6-11B-1 antibody recognizes both acetylated and deacetylated K40 residues within the LIMKI 3 microtubule polymer. To further examine the binding specificities of the monoclonal and polyclonal antibodies, we compared their abilities to recognize acetylated, deacetylated and unacetylated (never modified) atubulin subunits in cellular microtubules. Both antibodies failed to label any microtubule structures in PtK2 cells (Figure S4A), indicating that neither antibody recognizes unacetylated K40 residues. Both antibodies labeled highly acetylated microtubulesinduced by expression of MEC-17 in PtK2 and COS-7 cells (Figure S4B), indicating that both antibodies recognize K40acetylated microtubules in cells. However, differences were observed in the abilities of the antibodies to recognize deacetylated microtubules in cells. Whereas the polyclonal anti-acetyl-K40 antibody failed to label microtubule structures in cells expressing moderate levels of the K40-deacetyases HDAC6 or SIRT2 (Figure 5B), the monoclonal 6-11B-1 antibody still recognized a large number of cytoplasmic microtubules in expressing cells (Figure 5A; see also Figure S5). Expression of HDAC6 or SIRT2 enzymes does not create an eptiope for 6-11B-1 labeling as the antibody failed to label unacetylated microtubules in PtK2 cells that had been “deacetylated” by expression the deacetylase enzymes (Figure S6). Taken together, the results of Figures 2, 4 and 5 demonstrate that the difference between the antibodies is in binding to deacetylated a-tubulin subunits within microtubules.DiscussionThese results provide the first definitive demonstration that the K40 acetylation site of a-tubulin is located in the microtubule lumen. This result has important implications for the targeting of the K40 residue by cytoplasmic acetyltransferase and deacetylase enzymes. Since acetylation occurs after polymerization of microtubules in cells [32,33], our findings indicate that K40-modifying enzymes must access K40 residues present in the microtubule lumen rather than targeting the K40-containing loop from the outside of the microtubule. How do acetyltransferase and deacetylase enzymes access K40 residues in the lumen of the microtubule? One possibility is 
that the enzymes copolymerize with tubulins and thus reside in the interior of the microtubules. Indeed, cellular microtubules have been found to contain electron scattering material within their lumens [34]. A second possibility is t.Ocalize acetyl-K40 a-tubulin in a wide variety of animal cells and has been shown to be sensitive to the addition (via MEC-17) or removal (via HDAC6 or SIRT-2) of the acetyl group specifically at K40 [8,23,24,26]. Thus, we tested whether the Fab fragment differs from the whole antibody in its ability to distinguish between acetylated and deacetylated microtubules. To do this, we immunolabeled taxol-stabilized microtubules polymerized from acetylated or deacetylated tubulins with the monoclonal 6-11B-1 and polyclonal anti-acetyl-K40 antibodies. To preclude any effects on antigen recognition by fixation [19,31], antibodies were added either without fixation (“live”) or after paraformaldehyde fixation (“PFA fixed”) of the microtubules. The monoclonal 6-11B-1 antibody stained both acetylated and deacetylated microtubules regardless of fixation conditions (Figure 4A). In contrast, the polyclonal anti-acetyl-K40 antibody stained acetylated but not deacetylated microtubules (Figure 4B). These results indicate 
that the monoclonal 6-11B-1 antibody recognizes both acetylated and deacetylated K40 residues within the microtubule polymer. To further examine the binding specificities of the monoclonal and polyclonal antibodies, we compared their abilities to recognize acetylated, deacetylated and unacetylated (never modified) atubulin subunits in cellular microtubules. Both antibodies failed to label any microtubule structures in PtK2 cells (Figure S4A), indicating that neither antibody recognizes unacetylated K40 residues. Both antibodies labeled highly acetylated microtubulesinduced by expression of MEC-17 in PtK2 and COS-7 cells (Figure S4B), indicating that both antibodies recognize K40acetylated microtubules in cells. However, differences were observed in the abilities of the antibodies to recognize deacetylated microtubules in cells. Whereas the polyclonal anti-acetyl-K40 antibody failed to label microtubule structures in cells expressing moderate levels of the K40-deacetyases HDAC6 or SIRT2 (Figure 5B), the monoclonal 6-11B-1 antibody still recognized a large number of cytoplasmic microtubules in expressing cells (Figure 5A; see also Figure S5). Expression of HDAC6 or SIRT2 enzymes does not create an eptiope for 6-11B-1 labeling as the antibody failed to label unacetylated microtubules in PtK2 cells that had been “deacetylated” by expression the deacetylase enzymes (Figure S6). Taken together, the results of Figures 2, 4 and 5 demonstrate that the difference between the antibodies is in binding to deacetylated a-tubulin subunits within microtubules.DiscussionThese results provide the first definitive demonstration that the K40 acetylation site of a-tubulin is located in the microtubule lumen. This result has important implications for the targeting of the K40 residue by cytoplasmic acetyltransferase and deacetylase enzymes. Since acetylation occurs after polymerization of microtubules in cells [32,33], our findings indicate that K40-modifying enzymes must access K40 residues present in the microtubule lumen rather than targeting the K40-containing loop from the outside of the microtubule. How do acetyltransferase and deacetylase enzymes access K40 residues in the lumen of the microtubule? One possibility is that the enzymes copolymerize with tubulins and thus reside in the interior of the microtubules. Indeed, cellular microtubules have been found to contain electron scattering material within their lumens [34]. A second possibility is t.