2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
June 3rd, 2025
Version: 1
Helmholtz Munich
biophysics
biorxiv

A histidine switch regulates pH-dependent filament formation by the caspase-9 CARD

Rawal, S.Open in Google Scholar•Kolaric, ĐesikaOpen in Google Scholar•Bohn, S.Open in Google Scholar•Kolb, D.Open in Google Scholar•Pavkov-Keller, T.Open in Google Scholar•Pritisanac, I.Open in Google Scholar•Madl, T.Open in Google Scholar•Desfosses, A.Open in Google Scholar•Alderson, T. R.Open in Google Scholar

The caspase activation and recruitment domain (CARD) mediates protein-protein interactions in apoptotic and inflammatory signaling pathways. In humans, more than 30 proteins contain a CARD, several of which have been reported to polymerize into helical filaments. Here we found that the CARD from the apoptotic protease caspase-9 (C9CARD) self assembles into filaments in vitro at physiological pH and salt concentrations. The C9CARD more readily polymerizes under low-salt or mildly acidic conditions, suggesting a significant role for electrostatic interactions in mediating filament formation. Using NMR spectroscopy, we determined the pKa of the lone histidine residue, H38, which supports a role for histidine protonation in enhancing filament formation. Indeed, mutation of H38 to introduce a positive (H38R) or negative (H38D) charge, or to remove the pH-dependence of the side chain at this site altogether (H38N), dramatically alters the filament propensity of the domain. Using cryo-election microscopy, we determined 3.2- and 3.4-[A] structures of the wild-type and H38R C9CARD filaments, respectively, which provide new insights into the molecular basis of C9CARD polymerization and its pH dependence via H38.

Similar Papers

biorxiv
Thu Jun 05 2025
Mechanism of Lipid-Dependent Thermosensation in an Ion Channel
Temperature sensing is a fundamental biological process that allows organisms to detect and respond to environmental. Ion channels that gate in response to temperature changes, known as thermoreceptors, play key roles in this process. Although the phenomena affected by temperature in many thermoreceptors have been widely studied, the molecular mechanisms by which these proteins sense temperature r...
Li, C.-C.
•
Nimigean, C. M.
biorxiv
Thu Jun 05 2025
Inference of VEGFR2 dimerization kinetics on the cell surface by integrating single-molecule imaging and mathematical modeling
Inter-receptor interactions play a key role in receptor signaling, which is the first step in cell signaling in response to external stimuli. In the case of Vascular Endothelial Growth Factor Receptor 2 (VEGFR2), dimerization is necessary for activation. VEGFR2 undergoes reversible interactions also in the absence of ligand. For a quantitative understanding of transmembrane signal transduction, it...
Guerrero, J.
•
Malik, Z.
•
Bilal, F.
•
Jana, S.
...•
Jaqaman, K.
biorxiv
Thu Jun 05 2025
Macrophage-derived reactive oxygen species promote Salmonella aggresome formation contributing to bacterial antibiotic persistence
In this study, we reveal that macrophage-derived reactive oxygen species (ROS) can trigger the rapid formation of Salmonella aggresomes, which substantially contribute to the increased frequency of persisters induced by phagocytosis. Salmonella containing aggresomes exhibited a dormant phenotype characterized by reduced adenosine triphosphate (ATP) levels and decreased metabolic activity. Furtherm...
Chen, X.
•
Fang, K.
•
Li, B.
•
Li, Y.
...•
Bai, F. C.
biorxiv
Thu Jun 05 2025
Non-Invasive Mechanical-Functional Analysis of Individual Liver Mitochondria by Atomic Force Microscopy
Mitochondria play a pivotal role in energy production, signaling, and apoptosis. Yet, probing their functional state at the single-organelle level without invasive labels remains a major challenge. Here, we introduce a novel, label-free approach that leverages Atomic Force Microscopy (AFM) beyond its traditional imaging role, transforming it into a powerful tool for functional analysis of individu...
Zorikova, E. O.
•
Chourasia, S.
•
Rosenhek-Goldian, I.
•
Cohen, S. R.
...•
Gross, A.
biorxiv
Wed Jun 04 2025
Finding signatures of low-dimensional geometric landscapes in high-dimensional cell fate transitions
Multicellular organisms develop a wide variety of highly-specialized cell types. The consistency and robustness of developmental cell fate trajectories suggests that complex gene regulatory networks effectively act as low-dimensional cell fate landscapes. A complementary set of works draws on the theory of dynamical systems to argue that cell fate transitions can be categorized into universal deci...
Yampolskaya, M.
•
Mehta, P.
•
Ikonomou, L.
biorxiv
Tue Jun 03 2025
Adhesive implant interfaces prevent fibrosis by disrupting mechanobiological feedback
Fibrotic encapsulation around medical implants affects millions of patients annually. Current approaches targeting inflammation or implant material properties have failed clinically, but the mechanical origins of implant-induced fibrosis remain unexplored. Here, we demonstrate that directional imbalance of mechanical forces (tension anisotropy) is the primary driver of fibroblast activation at imp...
Jafari, M.
•
Aymon, B.
•
Hong, Y.
•
Shakiba, D.
...•
Alisafaei, F.
biorxiv
Tue Jun 03 2025
Structures of protein folding intermediates on the ribosome
The ribosome biases the conformations sampled by nascent polypeptide chains along folding pathways towards biologically active states. A hallmark of the co-translational folding (coTF) of many proteins are highly stable folding intermediates that are absent or only transiently populated off the ribosome, yet persist during translation well-beyond complete emergence of the domain from the ribosome ...
Chan, S. H. S.
•
Streit, J. O.
•
Wlodarski, T.
•
Mitropoulou, A. N.
...•
Christodoulou, J.
biorxiv
Tue Jun 03 2025
Excitability and travelling waves in renewable active matter
Activity and renewability are distinctive features of living matter, and constitute a new class of materials that we term renewable active matter. A striking example is the cell cytoskeleton, where myosin filaments bind to the actin meshwork, apply contractile stresses and undergo continual stress/strain dependent turnover, thus acting as both force generators and sensors. As a consequence of nonr...
M, A.
•
Dhanuka, A.
•
Banerjee, D. S.
•
Rao, M.
biorxiv
Tue Jun 03 2025
A simple method for introducing a cutoff to hydrodynamic interactions in Brownian dynamics simulations
Brownian dynamics (BD) simulations that include hydrodynamic interactions (HIs) modeled at the Rotne-Prager-Yamakawa (RPY) level of theory are a valuable tool for accurately modeling the translational and rotational diffusion of macromolecules such as proteins and nucleic acids. A major drawback to the inclusion of HIs in BD simulations is their computational expense, and an obvious way to conside...
Elcock, A. H.
biorxiv
Tue Jun 03 2025
Physics-Inspired Single-Particle Tracking Accelerated with Parallelism
Data modeling tools face trade-offs between accuracy, computational efficiency, data efficiency, and model flexibility. Physics-inspired, rigorous likelihood-based approaches, while offering high accuracy and data efficiency, remain limited in practice due to high computational cost, particularly when applied to larger-scale problems. This general limitation is further compounded by reliance on tr...
Xu, L. W. Q.
•
Presse, S.