Biology subjects

Kalutskii, M.

Publications and source records attributed to Kalutskii, M..

3 recordsLinked to original sources

bioRxiv2026

Dynamic microtubule-end structure governs multivalent kinetochore coupling by the Dam1c ring

Accurate chromosome segregation relies on kinetochores maintaining load-bearing attachments to dynamic microtubule ends, a coupling in which the Dam1 complex ring is central. How the microtubule-end structure and ring-microtubule interactions collectively determine attachment stability and drive force transduction remains unresolved. Here, we use multiscale modeling to show that the ring forms a "fuzzy" complex mediated by a dynamic network of intrinsically disordered regions, enabling both high-affinity binding and free diffusion along the microtubule lattice. Crucially, we find that this prototypic disordered-disordered protein complex provides most of the kinetochore-microtubule stabilization. By contrast, protofilament bending, commonly thought to drive force transduction, is sensitive to the arrangement of protofilaments along the ring and insufficient on its own to establish a robust coupling. The architecture of the dynamic microtubule end unifies these mechanisms by controlling both the progressive loss of fuzzy contacts and the resistance generated by protofilament bending. By accounting for the full conformational ensemble of microtubule structures, our model produces rupture forces similar to those previously measured and explains the distinct, tension-dependent behavior of kinetochore attachments to growing versus shortening microtubule ends. We propose that the Dam1 complex ring acts as a biased-diffusion coupler that probes and gradually remodels the evolving conformational landscape of the microtubule end under tension.

biophysics↗

bioRxiv2025

Improving conformational ensembles of folded proteins in GoMartini

The Martini coarse-grained (CG) force field enables efficient simulations of biomolecular systems but cannot reliably maintain folded protein structures. To stabilize proteins during simulation, Martini is typically combined with structure-based force fields such as elastic network models (ENMs) or G[o] models. While these approaches preserve global folds and capture protein flexibility, their ability to reproduce conformational dynamics remains unclear. Here, we benchmark Martini combined with ENMs or G[o] models on three folded proteins and show that both approaches struggle to sample the conformational space observed in atomistic simulations, even when uniform interaction strengths or equilibrium bond distances are adjusted. This limitation arises from the assumption of a uniform interaction network, in which all bond energies are equal. To overcome this, we present a fully automated, perturbation-based optimization approach for G[o] networks, PoG[o], that iteratively refines a non-uniform G[o] network against a pre-computed atomistic free energy landscape in essential conformational space. Our approach converges rapidly, yielding CG ensembles in close agreement with reference atomistic simulations. As a cross-validation, the optimization also improves the root-mean-square fluctuation profile.

biophysics↗

bioRxiv2024

Microtubule dynamics are defined by conformations and stability of clustered protofilaments

Microtubules are dynamic cytoskeletal polymers that add and lose tubulin dimers at their ends. Microtubule growth, shortening and transitions between them are linked to GTP hydrolysis. Recent evidence suggests that flexible tubulin protofilaments at microtubule ends adopt a variety of shapes, complicating structural analysis using conventional techniques. Therefore, the link between GTP hydrolysis, protofilament structure and microtubule polymerization state is poorly understood. Here, we investigate the conformational dynamics of microtubule ends using coarse-grained modeling supported by atomistic simulations and cryo-electron tomography. We show that individual bent protofilaments organize in clusters, transient precursors to a straight microtubule lattice, with GTP-bound ends showing elevated and more persistent cluster formation. Differences in the mechanical properties of GTP- and GDP-protofilaments result in differences in intra-cluster tension, determining both clustering propensity and protofilament length. We propose that conformational selection at microtubule ends favors long-lived clusters of short GTP-protofilaments that are more prone to form a straight microtubule lattice and accommodate new tubulin dimers. Conversely, microtubule ends trapped in states with unevenly long and stiff GDP-protofilaments are more prone to shortening. We conclude that protofilament clustering is the key phenomenon that links the hydrolysis state of single tubulins to the polymerization state of the entire microtubule.

biophysics↗