Microtubules play important roles in several essential cellular processes and their functionality is influenced by complex polymerization dynamic, which is driven by conformational changes of tubulin. The presence of destabilizing drugs, such as colchicine, stabilizes curved conformation of tubulin, preventing the integration in microtubule lattice. In this study, the effect of colchicine on three different isotypes, αβIIa, αβIII and αβIVa, was evaluated through molecular dynamics simulations with focus on the relation between structural rearrangements and conformational changes. Results suggest a correlation between the motion of the β tubulin M loop and structural modifications, such as the intradimer bending and twisting angle. The presence of colchicine influences the fluctuation of this loop and each isotype responds in different ways.