bioRxiv Science⌕ Search

Biology subjects

Sumikama, T.

Publications and source records attributed to Sumikama, T..

10 recordsLinked to original sources

Conformational dynamics of an intrinsically disordered receptor enable signal transduction

Signal transduction is initiated when activated cell-surface receptors physically engage intracellular signaling proteins. Although structural and biochemical studies have established the molecular architecture of receptor tyrosine kinase (RTK) signaling, the earliest dynamic events that couple receptor activation to intracellular signal propagation have remained inaccessible because existing approaches provide static structural snapshots or ensemble-averaged measurements rather than direct observation of molecular motion. Here, using high-speed atomic force microscopy (HS-AFM), we directly visualize these initial molecular events at the single-molecule level in real time. Using fibroblast growth factor receptor 1 (FGFR1) as a model, we show that receptor autophosphorylation releases its intrinsically disordered juxtamembrane region, enabling extensive conformational dynamics of the kinase domain that permit productive engagement of the signaling adaptor FRS2, a key initiator of downstream RTK signaling. In contrast, a kinase-inactive mutation or the clinically approved FGFR inhibitor futibatinib restricts receptor motion, stabilizes a compact receptor configuration, and markedly reduces adaptor engagement. Molecular dynamics simulations suggest that the disruption of inhibitory interactions between the juxtamembrane region and the kinase domain provides a structural explanation for the observed receptor dynamics. Together, our findings uncover a previously inaccessible physical mechanism underlying the initiation of RTK signaling and establish HS-AFM as a powerful platform for visualizing receptor dynamics, providing a framework for mechanistic studies of signal transduction and for the development and mechanistic evaluation of compounds that modulate receptor signaling.

biophysics↗

Opto-MDMi: a dual-lock optogenetic system for robust activation of endogenous p53

Optogenetics has emerged as a powerful technology for manipulating biological functions with high spatiotemporal resolution, yet the precise control of endogenous molecules remains a significant challenge. In this study, we developed Opto-MDMi, a dual-lock optogenetic platform designed to control the activity of endogenous p53, a master regulator of cell cycle and apoptosis. The p53 pathway is strictly governed by its negative regulators, MDM2 and MDMX, which inhibit p53 through direct binding and ubiquitination. Our system integrates two distinct light-responsive modules: Opto-MDMi (LOVTRAP), which regulates the nuclear translocation of p53-activating peptides, and Opto-MDMi (LOV2-PMI), which controls the binding activity of these peptides by photocaging them within the AsLOV2 domain. Through extensive in vitro screening and live-cell assays, we discovered that truncating the J helix of LOV2 effectively restricts the movement of fused inhibitory peptides, thereby masking their interaction with MDM2/MDMX under dark conditions. By combining these two regulatory layers into a dual-lock system, we achieved robust light-dependent activation of endogenous p53 while significantly suppressing basal activity in the dark. Our findings not only provide a potent tool for p53 research but also establish a general design principle for optogenetically regulating functional peptides with the LOV2 domain, offering a versatile framework for the future development of optogenetic actuators.

systems biology↗

CaMKIIα holoenzymes self-organize into worm-like mesoscale clusters

Ca2+/calmodulin-dependent protein kinase II (CaMKII) is highly enriched in dendritic spines at concentrations comparable to those of cytoskeletal proteins and plays a central role in synaptic plasticity. During long-term potentiation (LTP), CaMKII further accumulates in spines. However, the mechanisms governing its higher-order organization remain poorly understood. Here, we use high-speed atomic force microscopy to visualize inter-holoenzyme interaction of CaMKII at mesoscopic scales (5-500 nm). Under freely diffusible conditions, CaMKII holoenzymes do not form stable clusters. In contrast, when spatially confined, they assemble into worm-like chain clusters mediated by kinase-domain interactions. These clusters expand upon activation, concomitant with the dissociation of the regulatory segment. Notably, the CaMKII P212L mutant associated with neurodevelopmental disorders, forms extensive clusters even in the basal state. Together, our findings demonstrate that CaMKII-CaMKII interactions drive mesoscale cluster formation and that precise regulation of cluster size and activation-dependent growth might be critical for synaptic signaling.

neuroscience↗

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↗

Structural dynamics of mixed-subunit CaMKIIα/β heterododecamers filmed by high-speed AFM

CaMKII predominantly assembles into a 12-meric ring assembly, primarily consisting of CaMKII and CaMKII{beta} variants in the brain. Previous biochemical studies have reported varying ratios of these CaMKII variants across different brain regions and developmental stages. However, direct evidence for the formation of CaMKII/{beta} heterooligomers within a 12-meric ring assembly has been lacking at the single-molecule level. Here, we employed high-speed atomic force microscopy to visualize the conformational dynamics of forebrain-mimicked CaMKII/{beta} at a 3:1 ratio. Our findings revealed that the CaMKII and CaMKII{beta} subunits are intermixed within the 12-meric ring assembly, with more than 83% probability that CaMKII{beta} subunits adjacent to one another. Furthermore, in the activated state, CaMKII/{beta} heterooligomers form a stable kinase domain complex via interactions between adjacent CaMKII{beta} subunits, resulting in a long-lasting structure with an exposed target binding site. Collectively, our observations provide insights into the structural role of CaMKII{beta} subunits within the CaMKII/{beta} heterododecamer.

neuroscience↗

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↗

High-speed AFM reveals fluctuations and dimer splitting of the N-terminal domain of GluA2-γ2

AMPA glutamate receptors (AMPARs) enable rapid excitatory synaptic transmission by localizing to the postsynaptic density of glutamatergic spines. AMPARs possess large extracellular N-terminal domains (NTDs), which participate in AMPAR clustering at synapses. Nevertheless, the dynamics of NTDs and the molecular mechanism governing their synaptic clustering remain elusive. Here, we employed high-speed atomic force microscopy (HS-AFM) to directly visualize the conformational dynamics of NTDs in the GluA2 subunit with TARP {gamma}2 in lipid environments. HS-AFM videos of GluA2-{gamma}2 in the resting and open states revealed fluctuations in NTD dimers. Conversely, in the desensitized state, the two NTD dimers adopted a separated conformation with less fluctuation. Notably, we visualized individual NTD dimers transitioning into monomers. Furthermore, this NTD-dimer splitting resulted in intersubunit exchange between NTD dimers and an increased number of binding sites with the synaptic protein neuronal pentraxin 1. Therefore, our findings illuminate the significance of NTD dynamics in the synaptic clustering of AMPARs.

neuroscience↗

Antithetic effects of agonists and antagonists on the structural fluctuations of TRPV1 channel

Transient receptor potential vanilloid member 1 (TRPV1) is a heat and capsaicin receptor that allows cations to permeate and cause pain. As the molecular basis for temperature sensing, the heat capacity ({Delta}Cp) model (D. E. Clapham, C. Miller, Proc. Natl. Acad. Sci. U. S. A. 108, 19492-19497 (2011).) has been proposed and experimentally supported. Theoretically, heat capacity is proportional to a variance in enthalpy, presumably related to structural fluctuation; however, the fluctuation of TRPV1 has not been directly visualized. In this study, we directly visualized single-molecule structural fluctuations of the TRPV1 channels in a lipid bilayer with the ligands resiniferatoxin (RTX: agonist, 1000 times hotter than capsaicin) and capsazepine (CPZ: antagonist) by high-speed atomic force microscopy (HS-AFM). We observed the structural fluctuations of TRPV1 in an apo state and found that RTX binding enhances structural fluctuations, while CPZ binding suppresses fluctuations. These ligand-dependent differences in structural fluctuation would play a key role in the gating of TRPV1.

physiology↗

Evolutionarily acquired activity-dependent transformation of the CaMKII holoenzyme

Ca2+/calmodulin-dependent protein kinase II (CaMKII) has long been central in synaptic plasticity research. CaMKII is a dodecameric serine/threonine kinase that has been essentially conserved across metazoans for over a million years. While the mechanisms of CaMKII activation are well studied, its "behavior" at the molecular level has remained unobserved. Here, high-speed atomic force microscopy was used to visualize the activity-dependent structural dynamics of rat/hydra/C. elegans CaMKII in various states at nanometer resolution. Among the species, rat CaMKII underwent internal kinase domain aggregation in an activity-dependent manner and showed a higher tolerance to dephosphorylation by phosphatase. Our findings suggest that mammalian CaMKII has evolutionarily acquired a new structural form and a tolerance to phosphatase to maintain robust CaMKII activity for proper neuronal function. One-Sentence SummaryHigh-speed atomic force microscopy reveals the activity-dependent structural dynamics of rat/hydra/C. elegans CaMKII

neuroscience↗

Rapid intuitive interpretation of heterochromatin and euchromatin through Hi-C analysis

Hi-C is a technique that provides contact frequencies between pairs of loci on chromosomes. The conventional classification of heterochromatin and euchromatin based on Hi-C data is performed by principal component analysis; however, it requires long computational times and does not provide insight into the difference in contact frequencies between heterochromatin and euchromatin. Here, we propose a simple, intuitive and rapid method named the scaled contact number (SCN), which allows the contact frequencies to be visually interpreted and heterochromatin and euchromatin to be classified based on Hi-C results in a few minutes for long chromosomes at 1-kb resolution. The robustness of SCN was validated by confirming that SCN with reduced reads gives almost the same results as the original SCN. Overall, the approach described herein thus considerably decreases the time and computing power required to analyze Hi-C and further provides mechanistic insight indicating that euchromatin has more contacts than heterochromatin.

genomics↗