Biology subjects

Skora, T.

Publications and source records attributed to Skora, T..

3 recordsLinked to original sources

bioRxiv2025

On the Curvature and Relaxation of Microtubule Plus-endTips

Microtubules are essential cytoskeletal components with a broad range of functions in which the structure and dynamics of their plus-end tips play critical roles. Existing mechanistic models explain the tips curving dynamics in different ways: the allosteric model suggests that GTP hydrolysis induces conformational changes in tubulin subunits that destabilize the lattice, leading to protofilament curving and depolymerization, while the lattice model posits that GTP hydrolysis directly destabilizes the microtubule lattice. However, the effect of GTP hydrolysis on the curving dynamics of microtubule tips remains incompletely understood. In this study, we employed a multiscale modeling approach, combining all-atom molecular dynamics simulations with Brownian dynamics simulations, to investigate the relaxation of microtubule plus-end tips into curved configurations. Our results show that both GDP- and GTP-bound tips exhibit an outward bending of protofilaments into curved, rams horn-like structures, characterized by a linear relationship between curvature and distance from the plus-end tip. These observations align with experimental cryo-ET images of microtubule plus-end tips in different nucleotide states. Collectively, our findings suggest that the outward bending of protofilaments at the plus-end tip is an intrinsic feature of microtubules, independent of the nucleotide state. SIGNIFICANCEUnderstanding how microtubules change shape is crucial for elucidating key cellular processes such as cell division and shape maintenance, which are fundamental to both physiological function and disease progression. This study supports the concept that the microtubule plus-end tip relaxation does not align with models that couple shape changes to GTP hydrolysis, at least for the topmost tubulin heterodimers. By interfacing bottom-up multiscale modeling -- using the longest reported atomistic molecular dynamics simulations of microtubule tips-- with existing cryo-ET data, it is shown that protofilament bending operates independently of nucleotide hydrolysis and likely depolymerization. These findings highlight the need for a new conceptual framework that separates GTP hydrolysis from microtubule tip flaring.

biophysics↗

bioRxiv2025

Chemical propulsion of hemozoin crystal motion in malaria parasites

Malaria parasites infect red blood cells where they digest host hemoglobin and release free heme inside a lysosome-like organelle called the food vacuole. To detoxify excess heme, parasites form hemozoin crystals that rapidly tumble inside this compartment. Hemozoin formation is critical for parasite survival and central to antimalarial drug activity. Although the static structural properties of hemozoin have been extensively investigated, crystal motion and its underlying mechanism have remained puzzling. We used quantitative image analysis to determine the timescale of motion, which requires the intact vacuole but does not require the parasite itself. Using single particle tracking and Brownian dynamics simulations with experimentally derived interaction potentials, we found that hemozoin motion exhibits unexpectedly tight confinement but is much faster than thermal diffusion. Hydrogen peroxide, which is generated at high levels in the food vacuole, has been shown to stimulate the motion of synthetic metallic nanoparticles via surface-catalyzed peroxide decomposition that generates propulsive kinetic energy. We observed that peroxide stimulated the motion of isolated crystals in solution and that conditions that suppress peroxide formation slowed hemozoin motion inside parasites. These data suggest that surface-exposed metals on hemozoin catalyze peroxide decomposition to drive crystal motion. This work reveals hemozoin motion in malaria parasites as a biological example of an endogenous self-propelled nanoparticle. This mechanism of propulsion likely serves a physiological role to reduce oxidative stress to parasites from hydrogen peroxide produced by large-scale hemoglobin digestion during blood-stage infection. Significance statementHemozoin crystal formation is a major antimalarial drug target as it is essential for survival of Plasmodium parasites that cause malaria, one of the worlds most devastating infectious diseases. Hemozoin crystals rapidly tumble inside the parasite food vacuole, and the mechanism and significance of this motion have been mysterious. Using quantitative live-cell imaging and computational modeling, we discovered that hemozoin motion is driven by catalytic decomposition of hydrogen peroxide on the crystal surface, a mechanism analogous to synthetic nanomotors. Hemozoin crystals have been viewed as inert detoxification products. Our work reframes the physiological role of these crystals as catalytically active nanoparticles whose mechanism of propulsion helps to neutralize toxic hydrogen peroxide generated by parasite digestion of hemoglobin during blood-stage infection.

biophysics↗

bioRxiv2024

Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation

Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5-triphosphate) to GDP (guanosine-5-diphosphate) within the {beta}-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the "equation-free" multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments x 8 heterodimers) comprising [~]21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 s unbiased all-atom simulation, we interleave coarse projective "equation-free" jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 s. Our 5.875 s of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whether {beta}-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. The approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution. SIGNIFICANCEThe dynamic instability of microtubules (MTs) is essential for a plethora of biological functions, from cell division to intracellular transport. Despite their importance, current computational models often struggle to handle the large-scale, long-term dynamics of all-atom simulations. This computational study employs the "equation-free" method to accelerate relaxation of the all-atom structures of MT tips in both GDP and GTP states which nearly halves the computational demands of simulating very large biomolecular systems. Our findings expose subtle but crucial structural differences between GDP-bound and GTP-bound MTs, particularly in the number of protofilament clusters, and is consistent with a relatively stronger lateral interactions in GTP-bound MT tips.

biophysics↗