Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit

Maxim Igaev,Helmut Grubmüller

doi:10.7554/elife.34353

Abstract

Microtubules (MTs) are key components of the cytoskeleton and play a central role in cell division and development. MT assembly is known to be associated with a structural change in [Formula: see text]-tubulin dimers from kinked to straight conformations. How GTP binding renders individual dimers polymerization-competent, however, is still unclear. Here, we have characterized the conformational dynamics and energetics of unassembled tubulin using atomistic molecular dynamics and free energy calculations. Contrary to existing allosteric and lattice models, we find that GTP-tubulin favors a broad range of almost isoenergetic curvatures, whereas GDP-tubulin has a much lower bending flexibility. Moreover, irrespective of the bound nucleotide and curvature, two conformational states exist differing in location of the anchor point connecting the monomers that affects tubulin bending, with one state being strongly favored in solution. Our findings suggest a new combined model in which MTs incorporate and stabilize flexible GTP-dimers with a specific anchor point state.

Highlights

Microtubules (MTs) are dynamic cytoskeletal filaments formed from ab-tubulin heterodimers that are abundant in eukaryotic cells and involved in many processes that are essential for cell physiology, for example, cell division and neural growth (Hyams and Lloyd, 1994)
To study how the nucleotide state affects the dynamics and intrinsic bending of tubulin, we performed multiple microsecond long molecular dynamics (MD) simulations starting from tubulin structures in two different nucleotide states: guanosine triphosphate (GTP) and guanosine diphosphate (GDP)
Our results suggest a new mechanism by which GTP binding by unassembled tubulin is linked to its conformational dynamics

Summary

Introduction

Microtubules (MTs) are dynamic cytoskeletal filaments formed from ab-tubulin heterodimers that are abundant in eukaryotic cells and involved in many processes that are essential for cell physiology, for example, cell division and neural growth (Hyams and Lloyd, 1994). Unlike other cytoskeletal components in the cell, for example, actin filaments which continuously grow as long as enough G-actin is present, MTs stochastically switch between growing and shrinking phases even under sufficient free tubulin concentrations This dynamic instability is observed both in vitro and in living cells and allows the MT cytoskeleton to be rapidly remodelled in response to internal and external signals (Mitchison and Kirschner, 1984; Gardner et al, 2011). Free tubulin requires guanosine triphosphate (GTP) to initiate the formation of new MTs (nucleation) and elongate already existing ones (growth) (Weisenberg et al, 1968; Weisenberg, 1972) In the latter case, GTP-tubulin stacks head-to-tail at the tips of growing MTs (primarily those capped by b-tubulin) and forms one-dimensional protofilaments that associate laterally to create a hollow cylinder typically comprising 13–14 protofilaments.

Methods

Results

Conclusion