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Protein dynamics in the synaptic bouton are still not well understood, despite many quantitative studies of synaptic structure and function. The complexity of the synaptic environment makes investigations of presynaptic protein mobility challenging. Here, we present an in vitro approach to create a minimalist model of the synaptic environment by patterning synaptic vesicles (SVs) on glass coverslips. We employed fluorescence correlation spectroscopy (FCS) to measure the mobility of monomeric enhanced green fluorescent protein (mEGFP)-tagged proteins in the presence of the vesicle patterns. We observed that the mobility of all eleven measured proteins is strongly reduced in the presence of the SVs, suggesting that they all bind to the SVs. The mobility observed in these conditions is within the range of corresponding measurements in synapses of living cells. Overall, our simple, but robust, approach should enable numerous future studies of organelle-protein interactions in general.
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http://dx.doi.org/10.1038/s41598-020-77887-1 | DOI Listing |
J Am Chem Soc
September 2025
College of Medical Engineering, Beijing Institute of Technology, 6 Jinfeng Road, Zhuhai, 519088, China.
Multiple biological barriers severely restrict the delivery efficiency of nanoparticles (NPs) to tumors. To overcome biological barriers, traditional NPs usually require a complex design, which increases the difficulty of clinical translation. Therefore, there appears to be a dilemma between the complex biological barriers and clinical requirement for a simple molecular structure of NPs.
View Article and Find Full Text PDFA variety of biomolecular systems rely on exploratory dynamics to reach target locations or states within a cell. Without a mechanism to remotely sense and move directly towards a target, the system must sample over many paths, often including resetting transitions back to the origin. We investigate how exploratory dynamics can confer an important functional benefit: the ability to respond to small changes in parameters with large shifts in the steady-state behavior.
View Article and Find Full Text PDFBiosystems
August 2025
Department of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia. Electronic address:
The role of energy dissipation in the evolution of living systems remains a subject of ongoing debate. Here, we quantify the dissipation associated with enzyme catalysis using minimalistic models of enzyme kinetics and a complete set of microscopic rate constants. We identify a power-law proportionality between total dissipated energy and key kinetic parameters- specifically, the catalytic constant and the specificity constant.
View Article and Find Full Text PDFNPJ Biofilms Microbiomes
August 2025
State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
Colonization resistance is a fundamental mechanism by which microbiomes suppress pathogen invasion; however, the ecological and mechanistic determinants of its efficacy remain incompletely understood. Here, we constructed a defined microbial consortium and employed in vivo shrimp infection models to investigate the synergistic interaction between commensal microbes and a pathogen-specific phage in suppressing the pathogen Vibrio parahaemolyticus. Our in vitro experiment revealed that combining key taxa, particularly with phage integration, markedly enhanced pathogen exclusion.
View Article and Find Full Text PDFAberrations in minimalist optical imaging systems present significant challenges for achieving high-quality imaging. Traditional methods often rely on precise aberration models, while deep learning approaches typically do not incorporate prior knowledge and lack interpretability. To address these limitations, we introduce the deep attention Wiener network (DAWNet), a differentiable framework that combines deep learning with Wiener deconvolution.
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