Publications

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Microtubules are stiff biopolymers that self-assemble via the addition of GTP-tubulin (αβ-dimer bound to GTP), but hydrolysis of GTP- to GDP-tubulin within the tubules destabilizes them toward catastrophically-fast depolymerization. The molecular mechanisms and features of the individual tubulin proteins that drive such behavior are still not well-understood. Using molecular dynamics simulations of whole microtubules built from a coarse-grained model of tubulin, we demonstrate how conformational shape changes (i.e., deformations) in subunits that frustrate tubulin-tubulin binding within microtubules drive depolymerization of stiff tubules via unpeeling "ram's horns" consistent with experiments. We calculate the sensitivity of these behaviors to the length scales and strengths of binding attractions and varying degrees of binding frustration driven by subunit shape change, and demonstrate that the dynamic instability and mechanical properties of microtubules can be produced based on either balanced or imbalanced strengths of lateral and vertical binding attractions. Finally, we show how catastrophic depolymerization can be interrupted by small regions of the microtubule containing undeformed dimers, corresponding to incomplete lattice hydrolysis. The results demonstrate a mechanism by which microtubule rescue can occur.

Microtubules exhibit a dynamic instability between growth and catastrophic depolymerization. GTP-tubulin (αβ-dimer bound to GTP) self-assembles, but dephosphorylation of GTP- to GDP-tubulin within the tubule results in destabilization. While the mechanical basis for destabilization is not fully understood, one hypothesis is that dephosphorylation causes tubulin to change shape, frustrating bonds and generating stress. To test this idea, we perform molecular dynamics simulations of microtubules built from coarse-grained models of tubulin, incorporating a small compression of α-subunits associated with dephosphorylation in experiments. We find that this shape change induces depolymerization of otherwise stable systems via unpeeling "ram's horns" characteristic of microtubules. Depolymerization can be averted by caps with uncompressed α-subunits, i.e., GTP-rich end regions. Thus, the shape change is sufficient to yield microtubule behavior.

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Nanoparticle (NP) clusters with diameters ranging from 20 to 100 nm are reversibly assembled from 5 nm gold (Au) primary particles coated with glutathione (GSH) in aqueous solution as a function of pH in the range of 5.4 to 3.8. As the pH is lowered, the GSH surface ligands become partially zwitterionic and form interparticle hydrogen bonds that drive the self-limited assembly of metastable clusters in <1 min. Whereas clusters up to 20 nm in size are stable against cluster-cluster aggregation for up to 1 day, clusters up to 80 nm in size can be stabilized over this period via the addition of citrate to the solution in equal molarity with GSH molecules. The cluster diameter may be cycled reversibly by tuning pH to manipulate the colloidal interactions; however, modest background cluster-cluster aggregation occurs during cycling. Cluster sizes can be stabilized for at least 1 month via the addition of PEG-thiol as a grafted steric stabilizer, where PEG-grafted clusters dissociate back to starting primary NPs at pH 7 in fewer than 3 days. Whereas the presence of excess citrate has little effect on the initial size of the metastable clusters, it is necessary for both the cycling and dissociation to mediate the GSH-GSH hydrogen bonds. In summary, these metastable clusters exhibit significant characteristics of equilibrium self-limited assembly between primary particles and clusters on time scales where cluster-cluster aggregation is not present.

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