Biology subjects

Ngo, K. X.

Publications and source records attributed to Ngo, K. X..

9 recordsLinked to original sources

bioRxiv2026

CAMSAP2 condensates drive a γ-TuRC-independent pathway for non-centrosomal microtubule nucleation

Microtubule nucleation is commonly viewed as a {gamma}-tubulin ring complex ({gamma}-TuRC)-templated process 1-3, yet many differentiated cells build extensive non-centrosomal microtubule arrays of unclear origin 4-6. Although spontaneous tubulin nucleation has long been observed in vitro as a {gamma}-TuRC-independent nucleation process 7-10, its mechanism and cellular relevance have remained unclear. Here we show that CAMSAP2, a microtubule minus-end-binding protein, links spontaneous nucleation to non-centrosomal microtubule organization. Cryo-electron microscopy (cryo-EM), high-speed atomic force microscopy (hsAFM), and molecular dynamics simulations reveal that CAMSAP2 lowers the nucleation barrier by straightening tubulin oligomers and promoting lateral protofilament interactions that drive sheet formation and closure into microtubules. hsAFM captures stepwise nucleation and early growth, revealing that tubulin rings can serve as productive intermediates rather than dead-end depolymerization products. CAMSAP2 further self-organizes through liquid-liquid phase separation (LLPS) to concentrate tubulin and assembly intermediates, thereby promoting efficient microtubule formation at non-centrosomal microtubule-organizing centers. In HeLa cells, dispersed CAMSAP2 condensates act as {gamma}-TuRC-independent microtubule-organizing centers alongside centrosomal asters, supporting a model in which spontaneous nucleation contributes to non-centrosomal microtubule biogenesis.

cell biology↗

bioRxiv2025

Conformational dynamics of actin filaments crosslinked with alpha-actinin and their roles in suppressing cofilin-induced helical shortening and cluster formation

Actin is a conserved cytoskeletal protein essential for morphogenesis, motility, and division. Its versatility arises from filament assembly and regulation by actin binding proteins. Among these, alpha-actinin organizes filaments into bipolar or unipolar networks, whereas cofilin binds preferentially to ADP-actin regions and forms clusters to shorten the half helical pitch (HHP). Here, we investigated the molecular mechanism of how alpha-actinin alters filament and protomer conformations and influences cofilin binding. Using all-atom molecular dynamics simulations, principal component analysis, and high-speed atomic force microscopy, we show that alpha-actinin crosslinking stabilizes actin filaments in the canonical helical state, thereby preventing the cofilin-induced helical shortening required for cooperative filament decoration. Stabilization occurs without significant changes in protomer twist and rise and subdomain geometry and maintains a flattened protomer conformation that restricts twisting needed for cofilin cooperative binding. By contrast, the isolated alpha-actinin-1 actin binding domain mutant (ABD-E235K), comprising two calponin homology domains (CH1-CH2), transiently binds to actin filaments and induces local transitions from the canonical double-helical filament to the single- and parallel-helical protofilament states, weakly affecting cofilin binding and cluster formation through a distinct structural and binding mechanism. Together, these findings reveal a mechanistically distinct function of full-length alpha-actinin and its isolated ABD and support a stepwise mechanism in which cooperative cofilin binding to double-helical actin filaments requires initial binding to actin regions with shortened HHP, followed by protomer twisting and further helical shortening. By stabilizing the canonical filament architecture or perturbing filament organization, alpha-actinin suppresses these structural transitions and thereby perturbs cofilin cooperativity. TeaserAlpha-actinin stabilizes actin helices, suppressing cofilin cooperative binding through distinct structural mechanisms.

biophysics↗

bioRxiv2025

Atomic Conformational Dynamics and Actin-Crosslinking Function of Alpha-Actinin Revealed by SimHS-AFMfit

Many molecular systems, such as intrinsically disordered proteins and flexible multi-domain complexes, are highly dynamic and often inaccessible to conventional X-ray crystallography or cryo-EM due to their conformational heterogeneity and flexibility. As a result, resolving their atomic-level dynamics remains a significant challenge. In this study, we present SimHS-AFMfit-MD, an integrative framework that combines high-speed atomic force microscopy (HS-AFM), molecular dynamics (MD) simulations, and AFMfit-based structural modeling to reconstruct dynamic protein conformations at atomic resolution. Using alpha-actinin, an actin crosslinking protein, as a challenging test system, we show that AFMfit guided by nonlinear normal mode analysis (AFMfit-NMA) enables accurate structural fitting, while guiding AFMfit with MD trajectories (AFMfit-MD) further enhances the flexible fitting performance, achieving closer agreement with unbiased all-atom MD simulation results. This strategy allows us to convert thousands of three-dimensional HS-AFM images into atomic-scale conformational ensembles, revealing the twisting and bending transitions underlying Ca{superscript 2}-bound and Ca{superscript 2}-unbound alpha-actinin. Together, our results establish a hybrid computational-experimental approach that bridges the spatial and, to some extent, temporal resolution gaps between simulation and imaging, paving the way for real-time visualization of protein conformational dynamics at the atomic scale. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/647477v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@147c1aforg.highwire.dtl.DTLVardef@1fd0036org.highwire.dtl.DTLVardef@118da3forg.highwire.dtl.DTLVardef@a062c3_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Developing the Computational Image Processing Methodfor Quantitative Analysis of Nanopore Structure Obtained from HS-AFM (AFMnanoQ)

High-Speed Atomic Force Microscopy (HS-AFM) enables imaging of biological structures and dynamics with nanometer spatial and millisecond temporal resolution. AFM images contain three-dimensional (3D) surface information, comprising two-dimensional (2D) lateral (x-y) and one-dimensional (1D) height (z) encoded in pixel intensity. This dynamic structure poses significant challenges for instance boundary detection and morphological analysis. To address this, we develop AFMnanoSALQ, a feature-driven computational framework for semi-automatic labeling and quantitative (SALQ) detection and morphological measurement of HS-AFM data. Unlike conventional methods that rely solely on either visual or geometric features for 2D boundary detection, AFM- nanoSALQ integrates both to extract 3D morphology. It requires neither annotated data nor intensive training, enabling fast deployment at minimal cost. With performance comparable to typical deep-learning models, AFMnanoSALQ facilitates semi-automatic labeling, making it a practical tool for preliminary data inspection and accelerating the creation of training datasets. As a case study, we focus on -hemolysin (HL), a {beta}-barrel pore-forming toxin secreted by Staphylococcus aureus, using both synthetic and experimental AFM data. AFMnanoSALQ provides a foundation for future deep learning studies, enabling both dataset generation and cross-validation between feature-driven and data-driven approaches.

bioinformatics↗

bioRxiv2023

Deciphering the actin structure-dependent preferential cooperative binding of cofilin

The mechanism underlying the preferential and cooperative binding of cofilin and the expansion of clusters toward the pointed-end side of actin filaments remains poorly understood. To address this, we conducted a principal component analysis based on available filamentous actin (F-actin) and C-actin (cofilins were excluded from cofilactin) structures and compared to monomeric G-actin. The results strongly suggest that C-actin, rather than F-ADP-actin, represented the favourable structure for binding preference of cofilin. High-speed atomic force microscopy explored that the shortened bare half helix adjacent to the cofilin clusters on the pointed end side included fewer actin protomers than normal helices. The mean axial distance (MAD) between two adjacent actin protomers along the same long-pitch strand within shortened bare half helices was longer (5.0-6.3 nm) than the MAD within typical helices (4.3-5.6 nm). The inhibition of torsional motion during helical twisting, achieved through stronger attachment to the lipid membrane, led to more pronounced inhibition of cofilin binding and cluster formation than the presence of inorganic phosphate (Pi) in solution. F-ADP-actin exhibited more naturally supertwisted half helices than F-ADP.Pi-actin, explaining how Pi inhibits cofilin binding to F-actin with variable helical twists. We propose that protomers within the shorter bare helical twists, either influenced by thermal fluctuation or induced allosterically by cofilin clusters, exhibit characteristics of C-actin-like structures with an elongated MAD, leading to preferential and cooperative binding of cofilin.

molecular biology↗

bioRxiv2023

S100A11 promotes focal adhesion disassembly via myosin II-driven contractility and Piezo1-mediated Ca2+ entry

S100A11 is a small Ca2+-activatable protein with an established role in different cellular processes involving actin cytoskeleton remodeling, such as cell migration, membrane protrusion formation, and plasma membrane repair. It also displays Ca2+-dependent F-actin binding activity and localizes to actin stress fibers (SFs), but its precise role in regulating these structures remains unclear. Analyzing endogenous S100A11 localization in HeLa and U2OS osteosarcoma cells confirmed SF association but in addition revealed steady localization to stable focal adhesions (FAs), typically at the end of dorsal stress fibers. In contrast, S100A11 levels at FAs increased sharply, but transiently, at the onset of peripheral FA disassembly. Elevating intracellular Ca2+ levels using the Ca2+ ionophore ionomycin reliably stimulated both S100A11 recruitment and subsequent FA disassembly. However, pre-incubation with the non-muscle myosin II (NM II) inhibitor blebbistatin, or with an inhibitor to the stretch-activatable Ca2+ channel Piezo1 effectively suppressed S100A11 recruitment, implicating S100A11 in an actomyosin contractility-driven FA disassembly mechanism involving Piezo1-dependent Ca2+ influx. Applying external mechanical forces on peripheral FAs via a micropipette likewise recruited S100A11 to FAs, even when NM II was inhibited by blebbistatin or in NM IIA knockout cells, corroborating the mechanosensitive recruitment mechanism of S100A11. However, extracellular Ca2+ and Piezo1 function was still indispensable, indicating that NM II-dependent contraction forces act upstream of Piezo1-mediated Ca2+ influx, in turn leading to S100A11 activation and FA recruitment. Moreover, S100A11 knockout cells feature enlarged FAs and display delayed FA disassembly during cell membrane retraction, consistent with impaired FA turnover in these cells. Our results thus demonstrate a novel mechano-sensitive function for S100A11 in promoting actomyosin contractility-driven FA disassembly.

cell biology↗

bioRxiv2021

Unraveling the host-selective toxic interaction of cassiicolin with lipid membranes and its cytotoxicity

Cassiicolin (Cas), a toxin produced by Corynespora cassiicola, is responsible for corynespora leaf fall disease in rubber trees. Currently, the molecular mechanism of the cytotoxicity of Cas and its host selectivity have not been fully elucidated. Here, we analyzed the binding of Cas1 and Cas2 to membranes consisting of different plant lipids and their membrane-disruption activities. Using high-speed atomic force microscopy and confocal microscopy, we reveal that the binding and disruption activities of Cas1 and Cas2 on lipid membranes are strongly dependent on the specific plant lipids. The negative phospholipids, glycerolipids, and sterols are more susceptible to membrane damage caused by Cas1 and Cas2 than neutral phospholipids and betaine lipids. Cytotoxicity tests on rubber leaves of RRIV 1, RRIV 4, and PB 255 clones suggest that the toxins cause necrosis of rubber leaves, except for the strong resistance of PB 255 against Cas2. Cryo- SEM analyses of necrotic leaf tissues exposed to Cas1 confirm that cytoplasmic membranes are vulnerable to the toxin. Thus, the host selectivity of Cas toxin is attained by the lipid-dependent binding activity of Cas to the membrane, and the cytotoxicity of Cas arises from its ability to form biofilm-like structures and disrupt specific membranes. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/438527v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@17ef3f4org.highwire.dtl.DTLVardef@1c24d41org.highwire.dtl.DTLVardef@15e071aorg.highwire.dtl.DTLVardef@24740e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICas1 and Cas2 directly damage and cause necrosis in the leaves of specific rubber clones. C_LIO_LICas1 and Cas2 can form biofilm-like structures on specific lipid membranes (negative phospholipids, glycerolipids, and sterols). The biofilm-like formation of Cas toxin plays an important role in selective disruption on lipid membranes. C_LIO_LIVulnerability of the specific cytoplasmic membranes to the selective Cas toxin that is the most remarkable feature of cytotoxicity of Cas toxin on plant cells. C_LI

biochemistry↗

bioRxiv2020

Actin binding domain of Rng2 strongly inhibits actin movement on myosin II HMM through structural changes of actin filaments

Substoichiometric binding of certain actin-binding proteins induces conformational changes in a disproportionally large number of actin protomers in actin filaments. Here, we report a case in which such conformational changes in actin filaments have profound functional consequences. Rng2 is an IQGAP protein implicated in the assembly and contraction of contractile rings in Schizosaccharomyces pombe. We found that the calponin-homology actin-binding domain of Rng2 (Rng2CHD) strongly inhibits the motility of actin filaments on myosin II in vitro. On skeletal muscle myosin II-coated surfaces, Rng2CHD halved the sliding speed of actin filaments at a binding ratio of 1.3% (=1/77), and virtually stopped movement at a binding ratio of 11% (=1/9). Rng2CHD also inhibited actin movements on Dictyostelium myosin II, but in this case by inducing the detachment of actin filaments from myosin II-coated surfaces. Rng2CHD induced cooperative structural changes of actin filaments accompanied by shortening of the filament helical pitch, and reduced the affinity between actin filaments and subfragment 1 (S1) of muscle myosin II in the presence of ADP. Intriguingly, actin-activated ATPase of S1 was hardly inhibited by Rng2CHD. We suggest that sparsely bound Rng2CHD induces global structural changes of actin filaments and interferes with the force generation by actin-myosin II.

biophysics↗

bioRxiv2020

GTP-dependent formation of straight oligomers leads to nucleation of microtubules

Microtubule (MT) nucleation is essential for cellular activities, but its mechanism is not known because of the difficulty involved in capturing rare stochastic events in the early stage of polymerization. In cells, MTs are nucleated at tubulin concentrations significantly lower than those required for spontaneous nucleation in vitro. The high efficiency of nucleation is due to the synergistic effects of various cellular factors, but the underlying mechanism has not been clarified yet. Here, combining negative stain electron microscopy and kinetic analysis, we demonstrate that the formation of single-stranded straight oligomers with critical size is essential for nucleation in vitro. While the single-stranded oligomers of GTP-tubulin that form prior to MT nucleation show variable curvatures including a few straight oligomers, only curved oligomers are observed among the GDP-bound counterparts. The Y222F mutation in {beta}-tubulin increases the proportion of straight oligomers and drastically accelerates MT nucleation. Our results support a model in which GTP binding causes a small shift in the distribution of oligomer curvature, generating a minor population of straight oligomers compatible with lateral association and further growth to MTs. Our study suggests that cellular factors involved in nucleation promote it via stabilization of straight oligomers.

biophysics↗