Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability

Thirteen tubulin protofilaments, made of αβ-tubulin heterodimers, interact laterally to produce cytoskeletal microtubules. Microtubules exhibit the striking property of dynamic instability, manifested in their intermittent growth and shrinkage at both ends. This behavior is key to many cellular processes, such as cell division, migration, maintenance of cell shape, etc. Although assembly and disassembly of microtubules is known to be linked to hydrolysis of a guanosine triphosphate molecule in the pocket of β-tubulin, detailed mechanistic understanding of corresponding conformational changes is still lacking. Here we take advantage of the recent generation of in-microtubule structures of tubulin to examine the properties of protofilaments, which serve as important microtubule assembly and disassembly intermediates. We find that initially straight tubulin protofilaments, relax to similar non-radially curved and slightly twisted conformations. Our analysis further suggests that guanosine triphosphate hydrolysis primarily affects the flexibility and conformation of the inter-dimer interface, without a strong impact on the shape or flexibility of αβ-heterodimer. Inter-dimer interfaces are significantly more flexible compared to intra-dimer interfaces. We argue that such a difference in flexibility could be key for distinct stability of the plus and minus microtubule ends. The higher flexibility of the inter-dimer interface may have implications for development of pulling force by curving tubulin protofilaments during microtubule disassembly, a process of major importance for chromosome motions in mitosis.Author summary: The ability to self-assemble from tubulin dimers in presence of guanosine triphosphate (GTP) and spontaneously disassemble, when GTP molecules in tubulin pockets are hydrolyzed, is a dramatic and essential feature of microtubules. This behavior has many important roles, including chromosome segregation in mitosis, rapid remodeling of the microtubule networks, establishing cell polarity and other. Nevertheless, the mechanism, linking the associated nucleotide with the conformational changes in tubulins, remains elusive. Most studies suggested that the nucleotide should affect either the equilibrium shape of tubulin dimers or the strengths of the lateral bonds between them. But existing experimental methods have lacked spatio-temporal resolution to test that. Theoretical studies, until recently, have suffered from the absence of high-resolution microtubule structures with different nucleotides to build on and the lack of computational efficiency to examine large tubulin assemblies. Here we use recent cryo electron microscopy structures of GDP and GTP-like microtubules, and employ all-atom molecular dynamics simulations to examine tubulin protofilaments. We find that the nucleotide primarily affects the interface between two tubulin dimers, making it more flexible in the GTP state. This makes the GTP-bound tubulin protofilament easier to incorporate into microtubule lattice, providing a simple mechanism for microtubule dynamic instability.