title: The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery.
abstract: αβ-tubulin dimers need to convert between a 'bent' conformation observed for free dimers in solution and a 'straight' conformation required for incorporation into the microtubule lattice. Here, we investigate the free energy landscape of αβ-tubulin using molecular dynamics simulations, emphasizing implications for models of assembly, and modulation of the conformational landscape by colchicine, a tubulin-binding drug that inhibits microtubule polymerization. Specifically, we performed molecular dynamics, potential-of-mean force simulations to obtain the free energy profile for unpolymerized GDP-bound tubulin as a function of the ∼12° intradimer rotation differentiating the straight and bent conformers. Our results predict that the unassembled GDP-tubulin heterodimer exists in a continuum of conformations ranging between straight and bent, but, in agreement with existing structural data, suggests that an intermediate bent state has a lower free energy (by ∼1 kcal/mol) and thus dominates in solution. In agreement with predictions of the lattice model of microtubule assembly, lateral binding of two αβ-tubulins strongly shifts the conformational equilibrium towards the straight state, which is then ∼1 kcal/mol lower in free energy than the bent state. Finally, calculations of colchicine binding to a single αβ-tubulin dimer strongly shifts the equilibrium toward the bent states, and disfavors the straight state to the extent that it is no longer thermodynamically populated.
authors: Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America.
authors: Lili X
authors: LX
authors: Peng
authors: Graduate Group in Biophysics, University of California, San Francisco, San Francisco, California, United States of America.
authors: Monica T
authors: MT
authors: Hsu
authors: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America.
authors: Massimiliano
authors: M
authors: Bonomi
authors: Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America.
authors: David A
authors: DA
authors: Agard
authors: Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America ; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America.
authors: Matthew P
authors: MP
authors: Jacobson
mesh_terms: D000818:Animals; D001665:Binding Sites; D002417:Cattle; D003078:Colchicine / Q000378:metabolism; D019295:Computational Biology; D003198:Computer Simulation; D055808:Drug Discovery; D006153:Guanosine Diphosphate / Q000378:metabolism; D008870:Microtubules / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D021122:Protein Subunits; D013816:Thermodynamics; D014404:Tubulin / Q000737:chemistry* / Q000378:metabolism
chemical_list: D021122:Protein Subunits; D014404:Tubulin; D006153:Guanosine Diphosphate; D003078:Colchicine