Tubulin atomic models

Fig. 4. Atomic models of tubulin in straight and curved conformations. Ribbon diagrams similar to that in Figure 3, with the same color scheme. (A and B) Outside and side views of the straight heterodimer (Lowe et al., 2001). (C) Crystal structure of the...

The first structural location of the taxane binding site [42] placed it in the interprotofilament space, thus supporting the biochemical results. However, this changed when the first high resolution 3D structure of the paclitaxel-tubulin complex was solved by electron-crystallography of a two-dimensional zinc-induced tubulin polymer [5]. The fitting of this structure into a three-dimensional reconstruction of microtubules from cryoelectron microscopy allowed a pseudo atomic resolution model of microtubules [43] in which the paclitaxel binding site was placed inside the lumen of the microtubules hidden from the outer solvent. 

The atomic coordinates from these structures are nowadays the basis of the new computational and NMR spectroscopic studies aimed at the derivation of binding models of other drugs. Therefore, we will describe the main features of tubulin structures in the next section. 

With the success of EC based modeling as a method to explore atomic interactions of PTX and epoA, we began looking at other classes of compounds such as disco-dermolide (DIS), eleutherobin (ELE), and laulimalide (LAUL). Although soaking solutions of DIS, and ELE into Zn-sheets of tubulin produced stable crystals that diffract as well or better than epoA (Fig. 1), LAUL was an anomaly. 

Fig. 6 The colchicine and vinblastine sites, a Ribbon representation of RB3-SLD and of the two tubulin a 3 heterodimers. The nucleotides (GTP on a, GDP on P), colchicine (Col, yellow) and vinblastine (Vlb, cyan) are shown as ball-and-stick models. The dashed line shows the location of the RB3-SLD linker between the N-terminal cap and the C-terminal helix, which is the least ordered part of RB3-SLD. The sulfur atom of Cys 12 of the P subunit contacting vinblastine is highlighted as a yellow sphere. b,c Illustration of the interfacial interference of destabilizing molecules with MT assembly schematic representation of the (Tc)2R-vinblastine complex (b) and of a straight protofilament (c). Longitudinal MT-specific contacts (black rectangles in c) cannot be established between vinblastine- or colchicine-bound monomers...

Fig. 7 The location on tubulin of residues that modulate the sensitivity to MT-destabilizing agents and the location of exogenous inhibitor and nucleotide sites on P tubulin. The a subunit is in semitransparent pink together with a composite P-subunit color-coded as in Fig. 3a with ball-and-stick models of bound taxol (orange), colchicine (yellow) and GDP (magenta). Ball-and-stick models of vinblastine (cyan) are drawn on the two partial vinca sites on a and on P tubulin. The sulfur atom of Cys P12 is highlighted as a yellow sphere. The sites of nine amino acid substitutions [49] that both confer resistance to vinblastine and colchicine and stabilize MTs are depicted as red (on a tubulin) or green (on P tubulin) spheres. Two residues of the P H10 helix whose mutations enhance the sensitivity to colchicine site ligands and destabilize MTs [71] are also shown as blue spheres...

Conformationally restricted macrocyclic analogues of combretastatins have been evaluated as inhibitors of tubulin polymerization [103]. These compounds present a macrocyclic structure, in vhich the para positions of the aromatic moieties have been linked by a 5 - or 6-atoms chain, in order to produce a conformational restriction. This could contribute to detect the active conformation for these ligands. Such a conformational restriction and/or the steric hindrance made them less potent inhibitors than the model compound CA-4. 

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