Tamara Carla Bidone

The conformational activation of α _IIb β ₃ integrin is crucial for platelet aggregation, a central event in hemostasis and thrombosis. Although activation can be triggered by extracellular arginine-glycine-aspartic acid (RGD)-containing ligands as well as mechanical forces, how these biochemical and mechanical cues exactly govern the structural dynamics of α _IIb β ₃ remains unclear. Here, using all-atom molecular dynamics simulations, we show that mechanical force and RGD binding promote activation α _IIb β ₃ through distinct mechanisms. Mechanical force applied to the RGD-binding site induces long-range, correlated motions of distant parts of the receptor, facilitating head–leg separation. In contrast, RGD binding increases localized, non-correlated fluctuations that weaken leg coordination but do not generate long-range motions. Despite these differences, both cues stabilize the open, extended conformation of α _IIb β ₃ . Together, these findings suggest that mechanical and biochemical stimuli play complementary yet distinct roles in integrin conformational activation. A balance between global coordination and local fluctuations likely governs integrin activation in complex environments where the dominance of mechanical or biochemical cues could lead to distinct activation pathways and functional outcomes.

A cell’s ability to sense and respond to the mechanical properties of the extracellular matrix (ECM) is essential for maintaining tissue homeostasis, and its disruption contributes to diseases such as fibrosis, cardiovascular disorders, and cancer. Effective mechanical coupling between the plasma membrane, the underlying filamentous actin (F-actin) cytoskeleton, and integrin-based adhesion complexes (IACs) is required to link ECM mechanics to cell morphology, yet the underlying mechanisms remain incompletely understood. Here, we combine computational modeling and high-resolution imaging to show that integrin–ECM bonds determine F-actin cytoskeleton organization. On soft substrates, short-lived IACs bonds allow rapid actin retrograde flow and dense branching, restricting protrusion and limiting cell spreading. In contrast, stiff substrates or Mn²⁺-mediated integrin activation stabilize adhesions, promote filament alignment, and drive membrane protrusion for cell spreading. These cytoskeletal transitions arise from feedback between adhesion strength and the spatial positioning of the F-actin barbed ends relative to the leading-edge membrane. This positioning determines whether filaments polymerize into linear bundles or branch into dendritic networks, each generating distinct protrusive forces that regulate cell spreading. Collectively, our findings establish integrin–ECM bond stability as a key regulator of F-actin cytoskeleton organization and cell morphology.

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.

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, ram’s 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. SIGNIFICANCE: Understanding 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.

The adhesion protein integrin is a transmembrane heterodimer that plays a pivotal role in cellular processes such as cell signaling and cell migration. To execute its function, integrin undergoes extensive conformational changes from a bent-closed to an extended-open state. Resolving the structures across these changes remains a challenge with both experimental and computational methods, but is crucial for understanding the activation mechanism of integrin. We address this challenge for the platelet integrin α _IIb β ₃ by employing finite temperature string method with structures of the images along the initial guess path generated by a multiscale data-driven framework. The full-length all-atom structures along the resulting minimum free energy path between the inactive bent-closed and active extended-open states of α _IIb β ₃ integrin are consistent with a variety of experimentally resolved structures. Changes in these predicted structures along the path show that the extension and separation of the α and β subunits from the bent-closed to the extended-open state require correlated movements between the subdomain pairs in α _IIb β ₃ . These results provide new insights into integrin activation mechanism and the predicted structures have potential applications in guiding the design of integrin targeting therapeutics.

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 statement: Hemozoin crystal formation is a major antimalarial drug target as it is essential for survival of Plasmodium parasites that cause malaria, one of the world’s 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.