The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery

PLoS Comput Biol. 2014 Feb 6;10(2):e1003464. doi: 10.1371/journal.pcbi.1003464. eCollection 2014 Feb.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Cattle
  • Colchicine / metabolism
  • Computational Biology
  • Computer Simulation
  • Drug Discovery
  • Guanosine Diphosphate / metabolism
  • Microtubules / chemistry*
  • Microtubules / metabolism
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Protein Conformation
  • Protein Multimerization
  • Protein Structure, Quaternary
  • Protein Subunits
  • Thermodynamics
  • Tubulin / chemistry*
  • Tubulin / metabolism

Substances

  • Protein Subunits
  • Tubulin
  • Guanosine Diphosphate
  • Colchicine