- by Aazmi, O., Aswale, A. R., Chugh, J.Proteins exist as dynamic ensembles, with their native states comprising interconverting conformational substates critical to their physiological functions and participation in disease states. Fused in Sarcoma (FUS), an RNA-binding protein implicated in neurodegenerative diseases such as Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD), contains an RNA recognition motif (RRM) known to form fibrillar aggregates. Here, we investigate the conformational plasticity of FUS-RRM in its native state using advanced NMR techniques, particularly 15N chemical exchange saturation transfer and heteronuclear adiabatic […]
- by Perros, T., Joly, S., Mbaye, A., Marcq, P., Cochet-Escartin, O.Hydra vulgaris is a powerful model organism in the study of axial patterning and regeneration. While recent models emphasize the importance of mechanical cues in establishing body axis symmetry in Hydra tissue spheres, the precise role of the Wnt pathway, known to be central to axial patterning, in regulating tissue mechanics and cytoskeletal organization remains unclear. In this paper, we pharmacologically modulated the canonical Wnt pathway using Alsterpaullone and iCRT14 and assessed their effects on regeneration, tissue rheology, and actin […]
- by Howell, M. R., Xu, R. J., Cohen, A. E.Voltage-gated ion channels are found in many membrane-enclosed structures, including synaptic vesicles, endosomes, mitochondria, chloroplasts, viruses and bacteria. In small compartments, assumptions underlying Hodgkin-Huxley-type models must be relaxed: [1] stochastic gating of individual ion channels can substantially change the membrane voltage, even during a single gating event; and [2] ionic currents, even through a single channel, can substantially alter internal ionic concentrations. We adapted conductance-based models to incorporate these effects, and we then simulated voltage dynamics of small vesicles as […]
- by Arroyo, E. Y. D., De Guzman, J. A., Aziz, M. M., Cardenas-Rios, H., Roman, R. J., Steele, R., Ahrar, S.Hydra, a simple freshwater cnidarian, occurs in both moving and still bodies of water. Flow and corresponding forces are ubiquitous factors in Hydra's environment. Even in still water, brief exposure to a burst of flow (e.g., due to wind) can influence the surface attachment and dispersal of polyps. Additionally, alignment with flow may play a crucial role in minimizing forces and regulating feeding behaviors in Hydra. However, the response to flow (particularly in the presence of gravity) has remained underexplored. […]
- by Elsner, C., Hanke, A., Vadas, O., Gervasio, F. L., Bordignon, E.Intrinsic apoptosis is a form of cell death which is activated, executed and inhibited by the Bcl-2 protein family. The structural basis of the inhibition mechanisms remains elusive. Here, we characterize the ensemble structure of the inhibitory Bcl-xL/tBid complex at the mitochondrial membrane by probing inter-residue distances and dynamic solvent accessibilities complemented by integrative modelling and molecular dynamics simulations. We show that Bcl-xL and tBid form a heterodimer anchored to the membrane by the C-terminal helix of Bcl-xL. The BH3 […]
- by McCarthy, L. A., Way, L. E., Dai, X., Ren, Z., Fuller, D. E. H., Dhiman, I., Larkin, L., Sieben, J. J. D., Westerlaken, I., Abbondanzieri, E. A., Hardy, G. G., Meyer, A. S., Wang, X., Biteen, J. S.Dps is the most abundant nucleoid-associated protein in starved Escherichia coli with ~180,000 copies per cell. Dps binds DNA and oxidises iron, facilitating survival in harsh environments. Dps-DNA complexes can form crystalline structures, leading to the proposed model that Dps reorganises the starved E. coli nucleoid into a compact liquid crystal, slowing chromosome dynamics and limiting access of other proteins to DNA. In this work, we directly tested this model using live-cell super-resolution microscopy and Hi-C analysis. We found that […]
- by Choi, J., Langlen Chanu, A., Awasthi, S.Intracellular calcium ion (Ca2+) exhibits diverse dynamical behaviors, including complex oscillations such as bursting and chaos. The distinction of diverse dynamical patterns in time series data holds significant biochemical and biophysical implications, as these patterns are intimately related to physiological cellular states associated with health and disease. In this work, we introduce a deep learning framework based on a large kernel convolutional neural network (LKCNN) for the classification of dynamical states of intracellular Ca2+ dynamics. We use a chemical Langevin […]
- by Vieya, F. H., Pindi, C., Lisi, G. P., Morzan, U., Palermo, G.Expanding the range of Protospacer Adjacent Motifs (PAMs) recognized by CRISPR-Cas9 is essential for broadening genome-editing applications. Here, we combine molecular dynamics simulations with graph-theory and centrality analyses to dissect the principles of PAM recognition in three Cas9 variants – VQR, VRER, and EQR – that target non-canonical PAMs. We show that efficient recognition is not dictated solely by direct contacts between PAM-interacting residues and DNA, but also by a distal network that stabilizes the PAM-binding domain and preserves long-range […]
- by Hedger, G., Jiang, V., Ekman, F., Wang, Q., Shaw, D. E.CRISPR-Cas9 systems, adaptive defense mechanisms in bacteria and archaea, have been widely adopted as powerful gene editing tools, revolutionizing biological and medical research. In the first steps of CRISPR-Cas9 gene editing, the Cas9 protein, in complex with RNA, facilitates DNA melting and subsequent RNA-DNA hybrid formation, but the atomic-level mechanism of this fundamental process is not fully understood. Here, we present the results of long-timescale molecular dynamics simulations in which Cas9-RNA complexes bound to double-helical DNA and promoted the formation […]
- by Yan, L., Zhou, X., Li, M., Wang, C., Xiao, B., Xi, P., Zou, P., Gao, N.Stomatin, originally discovered in red blood cells, is a member of the SPFH (Stomatin, Prohibitin, Flotillin, and HflK/C) protein family, which has long been proposed to scaffold functional membrane microdomains (FMMs) enriched in saturated lipids such as cholesterol and sphingomyelin. Stomatin has been reported to associate with a variety of proteins involved in diverse physiological processes, including ion channel regulation, membrane fusion, mechanosensory regulation and vesicle trafficking; however, the mechanisms by which it modulates these interactions remain poorly understood. Here, […]
- by Tobita, C. A., Banerjee, S., Roth, J., Larson, E. K., Nikzad, A., Naiyer, A., Hoop, C. L., Baum, J.Collagen is the most abundant structural protein in the human body, and its supramolecular organization is central to tissue mechanics and cell matrix interactions. Integrins, key mediators of these interactions, are essential for key biological processes including adhesion, migration, differentiation, and platelet aggregation. While mutations in collagen are known to cause connective tissue disorders such as Osteogenesis Imperfecta (OI) with phenotypes ranging from mild to perinatal lethal, how these mutations alter fibril level architecture, dynamics and integrin-mediated interactions remains poorly […]
- by Zhou, Y., Gonzalez-Perez, V., Xia, X., Kallure, G. S., Chowdhury, S., Lingle, C. J.Ca2+- and voltage-activated BK-type K+ channels are influenced profoundly by associated regulatory subunits, including Ca2+- and voltage-activated BK-type K+ channels are influenced profoundly by associated regulatory subunits, including {beta} subunits (Kcnmb1-4; {beta}1-{beta}4). Although overlap in expression of different BK {beta} subunits occurs in native tissues, whether they can coassemble in the same channel complex is not known. We coexpress {beta}2- and {beta}3a subunits together with BK and, through a combination of macroscopic and single channel recordings, along with quantitative pull-down […]
- by Sanami, S., Rezaei, A., Tremblay, S. A., Potvin-Jutras, Z., Sabra, D., Intzandt, B., Gagnon, C., Mainville-Berthiaume, A., Wright, L., Gayda, M., Iglesies-Grau, J., Nigam, A., Bherer, L., Gauthier, C.Aerobic exercise training promotes cardiovascular, brain and cognitive health. Regular exercise is associated with higher cardiorespiratory fitness, commonly assessed by peak oxygen uptake (VO2peak) during maximal effort testing. Higher cardiorespiratory fitness has been linked to preserved brain health, particularly higher grey matter volume and perfusion. The brain relies heavily on oxidative metabolism, yet the relationship between cardiorespiratory fitness and brain oxidative metabolism remains underexplored. This study investigated the association between VO2peak and two key cerebral metabolic parameters: the cerebral metabolic […]
- by Kao, K. Y., Childers, M. C., Pathak, D., Goluguri, R. R., McMillen, T. S., Ruppel, K. M., Spudich, J. A., Regnier, M.Mutations in myosin alter its motor functions in diverse ways by affecting different structural and chemo-mechanical events. Multidisciplinary strategies can be used to understand how varying alterations in motor function converge to common phenotypes like hypercontractility and hypertrophic cardiomyopathy (HCM). Here, we combined molecular dynamics (MD) simulations with protein biochemical and myofibril mechanical analyses to study the HCM-causing myosin variant G256E. MD simulations demonstrated that G256E induces structural changes that increase the work required to displace ADP.Mg2+ from actomyosin complex. […]
- by Pailing, M., van Beek, L., Maia de Oliveira, T., Flocco, M., Hoogenboom, B.AbstractCancers caused by mutations to the DNA repair machinery may be treated by inhibitors that target Poly(ADP-ribose) Polymerase 1 (PARP1). PARP inhibitors are thought to cause toxicity by trapping PARP1 at single strand breaks, preventing single strand break repair, thus leading to accumulation of DNA damage and cancer cell death. Intriguingly though, different PARP inhibitors display similar cellular toxicities and catalytic inhibition despite having widely varying trapping potencies. To better understand this apparent contradiction and identify complementary mechanisms of action, […]
- by Reuther, C., Santos-Otte, P., Grover, R., Korten, T., Diez, S.The length regulation of microtubules and their organization into complex arrays inside cells occurs through the activity of polymerases, depolymerases as well as severing enzymes such as katanin and spastin. The latter hexamerize on the microtubule lattice, pull out single tubulin dimers in an ATP-dependent manner and eventually generate internal breaks in the microtubule. While both, katanin and spastin, were shown to be regulated by posttranslational tubulin modifications, only katanin was reported to have microtubule lattice-defect- or crossover-sensing activity. Here, […]
- by Montenegro-Rojas, I., Andaur-Lobos, M., Soler, K., Castelli-Lacunza, D., Bertocchi, C., Matzavinos, A., Ravasio, A.The persistence of cell migration is a fundamental property of motile behavior, enabling cells to maintain directionality while adapting to fluctuations and external cues. This feature underlies essential processes such as development, immune responses, and cancer invasion. Classical mathematical models have offered key insights into directed migration, yet they often neglect temporal correlations arising from cellular mechanisms that stabilize polarity and protrusion dynamics, processes not well captured by simple white noise. Here, we introduce an agent-based model based on stochastic […]
- by Brakti, I., Lenton, S., Ausserwoger, H., Scrutton, R., Lorenzen, N., Nors Pedersen, M., Soendergaard Marino, J., Herranz-Trillo, F., Terry, A. E., Knowles, T. P. J., Groenning Jensen, M., Fodera, V.Liquid-liquid phase separation (LLPS) and high opalescence resulting from attractive interactions in the absence of large-scale self-association are commonly encountered in liquid monoclonal antibody (mAb) formulations and often associated with aggregation. Here, we evaluated the formulation dependent self-assembly behavior of a therapeutic mAb (termed mAb1) and provide a link to physical stability after applied stress. Using a combinatorial microdroplet platform to delineate the phase space of mAb1, we highlight its unusual solution properties. Specifically, mAb1 undergoes LLPS in a narrow […]
- by Mueller, S. H., Grimson, D. M., Paz, H., Fitch, A. C., Yu, H., Ribezzi-Crivellari, M., Griffiths, A. D., van Oijen, A. M., Spenkelink, L. M.Single-molecule techniques provide exceptional resolution of biomolecular dynamics but are limited by low-throughput. We present a barcoding strategy that enables simultaneous kinetic profiling of multiple protein variants at the single-molecule level. Each protein is covalently linked to a unique DNA barcode, decoded via transient hybridisation of fluorescent probes distinguished by colour and binding duration. We applied this method to a library of 16 ClpS variants to systematically explore evolutionary trajectories towards a variant adapted to recognise N-terminal amino acids with […]
- by Ekal, L., Wendscheck, D., David, Y., Chojnowski, G., Jeffries, C. M., Mullapudi, E., Schuldiner, M., Warscheid, B., Zalckvar, E., Wilmanns, M.Peroxisomes are essential cellular organelles that enable the sequestered execution of a broad range of metabolic processes. Due to the lack of an internal protein synthesis machinery, they entirely depend on the import of target proteins to carry out their functions within peroxisomes. While the process of cargo/receptor recognition is well understood, knowledge about the molecular mechanisms of the subsequent translocation steps, including cargo release and receptor recycling, is lacking behind. Here, we provide structural and functional evidence on the […]
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