Biology subjects

Igaev, M.

Publications and source records attributed to Igaev, M..

7 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↗

bioRxiv2021

Bending-torsional elasticity and energetics of the plus-end microtubule tip

Microtubules (MTs), mesoscopic cellular filaments, grow primarily by the addition of GTP-bound tubulin dimers at their dynamic flaring plus-end tips. They operate as chemomechanical energy transducers with stochastic transitions to an astounding shortening motion upon hydrolyzing GTP to GDP. Time-resolved dynamics of the MT tip - a key determinant of this behavior - as a function of nucleotide state, internal lattice strain, and stabilizing lateral interactions have not been fully understood. Here, we use atomistic simulations to study the spontaneous relaxation of complete GTP-MT and GDP-MT tip models from unfavorable straight to relaxed splayed conformations and to comprehensively characterize the elasticity of MT tips. Our simulations reveal the dominance of viscoelastic dynamics of MT protofilaments during the relaxation process, driven by the stored bending-torsional strain and counterbalanced by the inter-protofilament interactions. We show that the post-hydrolysis MT tip is exposed to higher activation energy barriers for straight lattice formation, which translates into its inability to elongate. Our study provides an information ratchet mechanism for the elastic energy conversion and release by MT tips and offers new insights into the mechanoenzymatics of MTs.

biophysics↗

bioRxiv2020

Choice of fluorophore affects dynamic DNA nanostructures

The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular fluorophores, which are often exchanged without considering the potential impact on the system. Here, we show that the choice of fluorophore can strongly affect the reconfiguration of DNA nanostructures. To this end, we encapsulate a triple-stranded DNA (tsDNA) into water-in-oil compartments and functionalize their periphery with a single-stranded DNA handle (ssDNA). Thus, the tsDNA can bind and unbind from the periphery by reversible opening of the triplex and subsequent strand displacement. Using a combination of experiments, molecular dynamics (MD) simulations, and reaction-diffusion modeling, we demonstrate for twelve different fluorophore combinations that it is possible to alter or even inhibit the DNA nanostructure formation - without changing the DNA sequence. Besides its immediate importance for the design of pH-responsive switches and fluorophore labelling, our work presents a strategy to precisely tune the energy landscape of dynamic DNA nanodevices.

biophysics↗

bioRxiv2020

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

This paper describes outcomes of the 2019 Cryo-EM Map-based Model Metrics Challenge sponsored by EMDataResource (www.emdataresource.org). The goals of this challenge were (1) to assess the quality of models that can be produced using current modeling software, (2) to check the reproducibility of modeling results from different software developers and users, and (3) compare the performance of current metrics used for evaluation of models. The focus was on near-atomic resolution maps with an innovative twist: three of four target maps formed a resolution series (1.8 to 3.1 [A]) from the same specimen and imaging experiment. Tools developed in previous challenges were expanded for managing, visualizing and analyzing the 63 submitted coordinate models, and several novel metrics were introduced. The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual laboratory experiments and holdings of structure data archives such as the Protein Data Bank. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived from these benchmark maps by 13 participating teams, representing both widely used and novel modeling approaches. We also evaluate the pros and cons of the commonly used metrics to assess model quality and recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed density in the cryo-EM map.

biochemistry↗

bioRxiv2020

Microtubule instability driven by longitudinal and lateral strain propagation

Tubulin dimers associate longitudinally and laterally to form metastable microtubules (MTs). MT disassembly is preceded by subtle structural changes in tubulin fueled by GTP hydrolysis. These changes render the MT lattice unstable, but it is unclear exactly how they affect lattice energetics and strain. We performed long-time atomistic simulations to interrogate the impacts of GTP hydrolysis on tubulin lattice conformation, lateral inter-dimer interactions, and (non-)local lateral coordination of dimer motions. The simulations suggest that most of the hydrolysis energy is stored in the lattice in the form of longitudinal strain. While not significantly affecting lateral bond stability, the stored elastic energy results in more strongly confined and correlated dynamics of GDP-tubulins, thereby entropically destabilizing the MT lattice.

biophysics↗