Subnanoscale mechanics of microtubule dynamic instability
Structural Biology
Final Report Abstract
Eukaryotic microtubules (MTs), empowering cell division and trafficking, are the archetypal model of mechanochemical transduction in living cells achieved by ordering and disordering of αβ-tubulin heterodimers into micrometer-sized tubular filaments and driven by a fundamental chemical reaction cycle that hydrolyzes GTP1,2. Their stochastic switching between phases of growth and shrinkage – also known as dynamic instability – is crucial for MT function but still poorly understood. More specifically, the system complexity and the inability of modern structural methods to directly visualize structural intermediates during MT assembly/disassembly at high resolutions do not allow to establish a robust relationship between the dynamics and energetics of individual dimers and the global MT behavior. If successful, disclosing the mechanism of MT dynamic instability would resolve one of the classical biophysical problems and contribute substantially to our understanding of many physiological processes that are the foundation of cell physiology. Accordingly, we addressed two lines of questions: (1) Why does GTP-tubulin polymerize and GDP-tubulin does not? Does tubulin exist in different nucleotide-dependent states that modulate its polymerization kinetics? (2) What is the trigger of MT depolymerization? Exactly how do hydrolysis-driven shape changes in tubulin dimers destabilize the MT lattice? To address these questions, we had set the long-term goal of characterizing – by fully atomistic, molecular dynamics (MD) simulations – the conformational dynamics and energetics of unassembled tubulin as well as hydrolysis-driven structural rearrangements in the MT lattice preceding the disassembly event. In line with the submitted proposal, all simulations have been accomplished in time, and the results have been documented in 3 peer-reviewed, open-access publications, as anticipated originally. To our surprise, a number of results have led to unexpected biological conclusions, some of which have been/are being verified experimentally. Furthermore, a technical step needed to address question (2) has triggered the development and implementation of an accurate and automated method for refining atomistic models into cryo-EM densities of arbitrary resolution – a substantial and unplanned deviation from the original proposal.
Publications
- Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit. eLife 7, e34353 (2018)
Igaev, M. and H. Grubmüller
(See online at https://doi.org/10.7554/elife.34353) - Automated cryo-EM structure refinement using correlation-driven molecular dynamics. eLife 8, e43542 (2019)
Igaev, M., C. Kutzner, L. Bock, A. C. Vaiana, H. Grubmüller
(See online at https://doi.org/10.7554/elife.43542) - Microtubule instability driven by longitudinal and lateral strain propagation. PLoS Comput. Biol. 16(9): e1008132 (2020)
Igaev, M. and H. Grubmüller
(See online at https://doi.org/10.1371/journal.pcbi.1008132)
