Tubulin Bond Energies and Microtubule Biomechanics Determined from Nanoindentation in Silico

Abstract

Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral noncovalent bonds between the tubulin subunits. However, the thermodynamics of these bonds and the microtubule physicochemical properties are poorly understood. Here, we explore the biomechanics of microtubule polymers using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close match between the simulated and experimental force–deformation spectra enabled us to correlate the microtubule biomechanics with dynamic structural transitions at the nanoscale. Our mechanical testing revealed that the compressed MT behaves as a system of rigid elements interconnected through a network of lateral and longitudinal elastic bonds. The initial regime of continuous elastic deformation of the microtubule is followed by the transition regime, during which the microtubule lattice undergoes discrete structural changes, which include first the reversible dissociation of lateral bonds followed by irreversible dissociation of the longitudinal bonds. We have determined the free energies of dissociation of the lateral (6.9 ± 0.4 kcal/mol) and longitudinal (14.9 ± 1.5 kcal/mol) tubulin–tubulin bonds. These values in conjunction with the large flexural rigidity of tubulin protofilaments obtained (18,000–26,000 pN·nm2) support the idea that the disassembling microtubule is capable of generating a large mechanical force to move chromosomes during cell division. Our computational modeling offers a comprehensive quantitative platform to link molecular tubulin characteristics with the physiological behavior of microtubules. The developed in silico nanoindentation method provides a powerful tool for the exploration of biomechanical properties of other cytoskeletal and multiprotein assemblies.

Mechanical splitting of microtubules into protofilament bundles by surface-bound kinesin-1

“…Here the work done by the two kinesin motors will be ~8 × 10 −20 J, which needs to be sufficient to break two lateral tubulin-tubulin bonds (the tails are C-shaped and connected on the top and bottom of the C’s in the MT), or ~4 × 10 −20 J of work to split apart a single lateral tubulin-tubulin bond. This value is in reasonable agreement with that determined from in silico modeling of 4.8 × 10 −20 J (6.9 ± 0.4 kcal/mol) for this bond32, suggesting that having one motor on each end might be sufficient to split the MT. At high motor surface densities, there are likely more than one motor on each end, which would produce ample force to split the MT.…”

Assembly and Mechanical Properties of the Cargo-Free and Cargo-Loaded Bacterial Nanocompartment Encapsulin

“…As we showed in our recent study 38 Table 2). As we demonstrated previously [35][36][37] , the entropy increase observed in the course of forced deformation is accompanied by the increase in the capsid stiffness, which occurs due to remodeling of the shell structure, whose protein subunits tend to re-arrange underneath the cantilever tip. Subsequent Crooks theorem based estimation of the reversible deformation work revealed that the large ~1 Mcal/mol free energy is required to induce structural collapse of the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 17 nanocompartment.…”

“…This approach uniquely combines the all-atom Molecular Dynamics simulations of atomic structural models of biological particles and the Langevin simulations of their native-topology based Self-Organized Polymer (SOP)33, 34 coarse-grained reconstructions (see Supplementary Methods). We employed this approach in earlier work to explore the biomechanical properties of virus particles and microtubule polymers[35][36][37] . The use of high-performance computing on Graphics Processing Units (GPUs)33,37,46 has enabled us to perform nanoindentations in silico on the millisecond time…”

Forced-rupture of Cell-Adhesion Complexes Reveals abrupt switch between two Brittle States

“…Here, we used the SOP model [13] with modifications for CACs and Brownian Dynamics to investigate the rupture dynamics in the mechanical unbinding of LFA-1 from ICAM-1 and ICAM-3. Several previous studies [14][15][16][17][18][19][20][21]. in a variety of systems (proteins, RNA, viruses, and complexes) have established that simulations based on the coarse-grained Self-Organized Polymer (SOP) model have provided a molecular bases for interpreting and predicting the outcomes of experiments.…”