- by Bohec, P., Khoromskaia, D., Kelkar, M., Ferber, E., Duprez, G., Lavoie, G., Valon, L., Roux, P. P., Salbreux, G., Charras, G.Shape changes are ubiquitous in biology, from cytokinesis at the single cell scale to tissue-scale morphogenesis involving coordinated changes in hundreds of cells. In all cases, morphogenesis is powered by gradients in mechanical tension that arise downstream of signalling. Many pathways converge on RhoGTPases that modulate the cytoskeleton and cell contractility to control cell mechanics and, subsequently, shape changes. Despite their physiological importance, our understanding of how changes in signalling alter cortical mechanics to drive cell shape changes remains poor. […]
- by Krebs, M. S., Risselada, H. J.Membrane-targeting peptide motifs recognize characteristic features of biological membrane targets through specific interactions with their lipid composition. To elucidate the complex relationship between binding sequences and lipid composition, we propose an alternative computational framework to leverage limited sequence activity data by combining genetic algorithms with coarse-grained molecular dynamics simulations. We demonstrate through evolutionary optimization of plasma membrane lipid compositions how four true positive and four false positive antimicrobial peptide sequences encode sufficient information to resolve model membranes with a discriminative […]
- by Sun, P., Wang, X., Huang, Y., Zhang, J. k., Shen, X., Dong, A., Wang, S., Guo, X., Shi, G., Ding, J., Chi, Y., Yang, H.Maintaining pH homeostasis is essential for neuronal excitability and for regulating cerebrospinal fluid (CSF). The Na+-dependent Cl-/HCO3- exchanger, NCBE (SLC4A10), abundant in the choroid plexus, contributes to CSF pH control by mediating bicarbonate flux, yet its molecular mechanism has remained unclear. Here we report cryo-EM structures of human NCBE in multiple functional states, revealing conserved binding sites for Na+, Cl-, and HCO3-, as well as an unexpected K+ site indicating relaxed cation selectivity. The inhibitor DIDS binds above the substrate […]
- by Vasarhelyi, R. G., Cojocaru, V.The Dead End protein, a key regulator of germline cell fate, utilizes two RNA Recognition Motifs (RRM) in tandem to bind AU-rich RNA in a non-canonical manner. Only one RRM uses the known RNA binding interface, whereas the second motif has only minimal contacts with the RNA. To characterize the structural features and dynamics that contribute to RNA binding, we performed a series of atomistic molecular dynamics simulations and show that the complex is highly flexible, undergoing large conformational transitions […]
- by Ivanovskaya, E. V., Bykov, G. A., Osidak, E. O., Sveshnikova, A. N.Metastatic dissemination remains the leading cause of mortality in malignant tumors, yet the processes of intravasation and extravasation of circulating tumor cells (CTC) are still not fully understood. Existing microfluidic experimental systems possess a number of limitations that prevent them from reproducing physiological conditions. Here we propose a perfused biotechnological system designed to model key stages of the metastatic cascade under controlled flow. The construction includes a parallel-plate flow chamber formed between polyethylene terephthalate plates and surrounded by a collagen […]
- by Felker, A., Schaefer, J.-H., Tanzusch, K., Wortmann, M., Moeller, A., Piehler, J.TIRAP (MAL) is an essential adaptor protein in Toll-like receptor (TLR) signaling, bridging activated receptors to downstream effectors such as MyD88 to initiate pro-inflammatory responses. Assembly of TLR signaling complexes is driven by homotypic interactions between Toll/interleukin-1 receptor (TIR) domains. Although previous studies demonstrated that isolated TIR domains of TIRAP can form filaments in vitro, the structural organization and membrane-dependent regulation of full-length TIRAP remained poorly understood. Here, we report a 3.3 [A] cryo-electron microscopy (cryo-EM) structure of full-length human […]
- by Rooke, S., Choi, S., Balasubramanian, V.Ocular Dominance Columns (ODCs), structures in the early visual cortex that demarcate inputs from each eye, have been observed in a wide range of mammals. The extent and arrangement of these columnar structures can vary drastically from species to species, and even along the visual cortex of a single individual. While previous studies show that these structures can form by competitive Hebbian learning, the relationship between system parameters and the resulting organizational patterns remains unclear. Here, we use a mesoscopic […]
- by Xu, M., Wang, L., Wang, W., Yang, H., Jiang, H.Postmenopausal osteoporosis (PMOP), affecting about half of postmenopausal women, is a major global health burden characterized by fragile bones and frequent comorbidity with obesity. Bone marrow mesenchymal stem cells (BMSCs) differentiation imbalance underpins PMOP pathogenesis and represents an attractive therapeutic target. Here, we demonstrate mechanically confining BMSCs to soft substrates mimicking physiological bone marrow stiffness completely suppresses adipogenic differentiation while inducing osteogenic differentiation. Mechanistically, confinement-induced elevation of nuclear envelope tension upregulates Lamin A/C expression, which in turn modulates Runx2 nuclear […]
- by Rech, J., Valera, O., Hu, L., Mathieu-Demaziere, C., Nesterova, t., Bouet, J.-Y., Liu, J.ParABS system is a conserved machinery that drives the partitions of genome and other large intracellular cargos in bacteria. It works as a ParA concentration based Brownian ratchet, which ensures the partition fidelity by operating at the critical point in its parameter space and localizing the ParA nearby to buffer against the large fluctuations in the ParA intracellular concentration. Despite these progresses, our understanding of the ParABS driven partition mechanism remains incomplete. It is not understood what causes the large […]
- by Dayan, N. A., Long, M., Miralavy, I., Scalzitti, N., Holmes, D., Kocherovsky, M., Banzhaf, W., Gilad, A. A.Gadolinium-based contrast agents (GBCAs) are indispensable tools in magnetic resonance imaging (MRI), yet their clinical use is limited by non-specific tissue accumulation, low molecular specificity, and safety concerns. Protein and peptide scaffolds provide a promising alternative because they can bind metal ions with high selectivity and enable precise molecular targeting. However, identifying short peptide motifs with optimal gadolinium (Gd3+) coordination and high relaxivity remains a major challenge. Here, we used a machine-learning-driven peptide evolution platform, the Protein Optimization Engineering Tool […]
- by Balogun, T., Kearns, F., Calvo-Tusell, C., Tse, A. L., Acreman, C. M., Casalino, L., Lasso, G., Miller, E. H., Chandran, K., McLellan, J. S., Amaro, R. E.SARS-like bat coronaviruses (CoVs) pose ongoing public health risks due to their zoonotic potential, making it important to understand the molecular pathways driving their evolution. We recently showed that SHC014-CoV can infect human cell lines in an ACE2-dependent manner after acquiring two spike ectodomain mutations (F294L and A835D). However, how the wild-type (WT) SHC014 spike differs dynamically from these mutants remains unclear. Here, we built fully glycosylated ectodomain models of WT and three mutants (F294L, A835D, and the double mutant, […]
- by Fernando, L. D., Yang, X., Archer-Hartmann, S., Heiss, C., Azadi, P.O-Acetylation, a common modification in rhamnogalacturonan I (RG-I), is critical for various biological processes, including plant growth, stress responses, and pathogen defense. Precise determination of the degree and specific positions of acetylation is therefore essential. To date, nuclear magnetic resonance (NMR) and tandem mass spectrometry have been employed to identify acetyl positions in pectin oligosaccharides. Although NMR is effective, it requires pure, high-concentration samples. Tandem mass spectrometry (MS), which uses lower sample amounts, faces challenges due to acetyl migration between […]
- by Fu, R., Ramamoorthy, A.In this study, we report a two-dimensional NMR technique that correlates the chemical shifts of homonuclear spin systems in solids under MAS. The pulse sequence employs double spin-lock RF pulses to facilitate magnetization exchange among low-{gamma} nuclei (such as 13C or 15N) through cross-relaxation driven by a combination of spin diffusion and RF field. We systematically investigate how the efficiency of the magnetization exchange depends on the Hartmann-Hahn mismatch and the MAS frequency. Experimental results obtained from 13C-labeled Fmoc-Leucine powder […]
- by Morton, W. S., Vacha, R.Biomolecular condensates underpin the spatial and temporal organization of cellular biochemistry in the cell. Their architectures often arises from complex, multicomponent mixtures whose behavior is governed by weak, multivalent interactions, frequently mediated by intrinsically disordered regions (IDRs) of proteins. However, current approaches lack generalizable metrics to determine whether IDRs will mix or segregate within condensates. Here, we show that our domain decomposition method can both accurately determine concentrations in the dense/dilute phases, and provide a continuous metric for characterizing IDR […]
- by Guo, W., Feletti, L., Radenovic, A.Fluorescence super-resolution microscopy has advanced optical imaging into the nanoscale regime, transforming biological and interdisciplinary research. However, conventional wide-field super-resolution techniques often compromise temporal resolution, thereby limiting the ability to capture rapid and transient biological events in living systems. Here, we introduce spatial polarization-induced fluorescence fluctuation imaging (SPIFFI), a multi-channel polarimetric method that enables single-shot super-resolution imaging and six-dimensional information extraction. By leveraging the inherently smaller point spread function (PSF) under polarized detection and capturing polarization-dependent spatial fluctuations across multiplexed […]
- by Pesen, T., Eren, B. C., Akgun, B.High-frequency imaging in acoustic microscopy requires the use of petri dishes with thin and acoustically transparent bottoms to minimize signal attenuation and distortion. Commercially available options suitable for this purpose are often expensive or limited in compatibility with custom setups. Here, we present a cost-effective and easily customizable alternative developed in our laboratory, consisting of a 3D-printed frame combined with commercially available stretch film. The stretch film serves as an ultrathin (8{micro}m thickness) base that supports efficient high-frequency acoustic transmission, […]
- by Tian, G., Zhang, X., Li, H., Sun, G., Xue, L., Yang, Y., Mao, Q., Gao, Y., Sun, L., Xu, G., Wang, Z., Xu, W.The serine/threonine protein phosphatase 2A (B55) holoenzyme (PP2A(B55)), a key cell cycle regulator, is tightly regulated by ENSA, whose phosphorylation at Ser67 inhibits PP2A(B55). The structural basis for how pENSA orchestrates this inhibition to govern mitotic progression remains unclear. In this study, we disapproved the previous hypothesis of direct ENSA-PP2A A subunit interaction, and showed that the ENSA-PP2A(B55) interaction requires the PP2A holoenzyme. We then determined cryo-EM structure of the PP2A(B55)-ENSAS67D complex at 3.03 [A] resolution, which reveals four distinct […]
- by Glaser, A., Padua, R., Ojoawo, A., Sullivan, C., Kern, D.SH2 domains are critical mediators of cellular signaling, although the molecular mechanisms by which they bind their phosphopeptide ligands remain incompletely understood. We investigate the atomic mechanisms underlying both healthy regulation and dysregulation of the human protein tyrosine phosphatase SHP2, a key regulator of cellular signaling. While most pathogenic mutations cluster near the PTP/N-SH2 interface, the E139D and T42A mutations are located within the regulatory SH2 domains, and their mechanisms of dysregulation remain controversial. The T42A mutation in the N-SH2 […]
- by Offerhaus, H. S., Jaskovikaite, I., Jones, S. K., Depken, M.Accurate prediction of CRISPR-based gene editing remains challenging since existing models often fail to generalize across experimental and cellular contexts. We introduce CRISPRzip, a mechanistic kinetic model that quantitatively links nucleotide sequence and environmental conditions to target interrogation. The model describes R-loop formation as movement through a sequence-dependent free-energy landscape, combining nearest-neighbor nucleic-acid energetics with protein-mediated contributions inferred from high-throughput binding and cleavage kinetics. Applying CRISPRzip to SpCas9, we predict the activity across diverse DNA targets and guide RNAs, and […]
- by Thornton, T., Lin, X.Computational modeling of large RNA structures and their dynamics is essential for uncovering the molecular mechanisms underlying various genomic processes and RNA-regulated cellular functions. Residue-resolution modeling is an effective approach for simulating large biomolecular structures while preserving essential sequence and struc-tural features presented in atomic structures. Here, we implemented a structure-based single-site-per-nucleotide (SSPN) RNA model using the GPU-accelerated OpenMM 1 software and evaluated its computational efficiency and accuracy by simulating RNA hairpins unfolding under force. Our simulations compare favorably with […]
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