Model for the Yeast Cofactor A–β-Tubulin Complex Based on Computational Docking and Mutagensis

Virtually every biological process involves protein–protein contact but relatively few protein–protein complexes have been solved by X-ray crystallography. As more individual protein structures become available, computational methods are likely to play increasingly important roles in defining these interactions. Tubulin folding and dimer formation are complex processes requiring a variety of protein cofactors. One of these is cofactor A, which interacts with β-tubulin prior to assembly of the α-tubulin–β-tubulin heterodimer. In the yeast Saccharomyces cerevisiae, β-tubulin is encoded by TUB2 and cofactor A by RBL2. We have used computational docking and site-directed mutagenesis to generate a model of the Rbl2–Tub2 complex from the solved structures of these two proteins. Residues in the N termini and the loops of the Rbl2 homodimer appear to mediate binding to β-tubulin. These interact with β-tubulin residues in the region that contains helices H9 and H10. Rbl2 and α-tubulin share overlapping binding sites on the β-tubulin molecule providing a structural explanation for the mutually exclusive binding of Rbl2 and α-tubulin to β-tubulin.