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Multiscale modelling of active hydrogel elasticity driven by living polymers: softening by bacterial motor protein FtsZ.
Soft Matter
January 2025
Department of Physical Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
We present a neo-Hookean elasticity theory for hybrid mechano-active hydrogels, integrating motor proteins into polymer meshes to create composite materials with active softening due to modulable chain overlaps. Focusing on polyacrylamide (PA) hydrogels embedded with FtsZ, a bacterial cytokinetic protein powered by GTP, we develop a multiscale model using microscopic Flory theory of rubbery meshes through mesoscopic De Gennes' scaling concepts for meshwork dynamics and phenomenological Landau's formalism for second-order phase transitions. Our theoretical multiscale model explains the active softening observed in hybrid FtsZ-PA hydrogels by incorporating modulable meshwork dynamics, such as overlapping functionality and reptation dynamics, into an active mean-field of unbinding interactions.
View Article and Find Full Text PDFBending elasticity of the reversible freely jointed chain.
J Chem Phys
December 2024
Department of Physics, Kyungpook National University, Daegu, South Korea.
The freely jointed chain model with reversible hinges (rFJC) is the simplest theoretical model, which captures reversible transitions of the local bending stiffness along the polymer chain backbone (e.g., helix-coil-type of local conformational changes or changes due to the binding/unbinding of ligands).
View Article and Find Full Text PDFWater Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.
J Chem Inf Model
December 2024
Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland.
The utilization of tunnels and water transport within enzymes is crucial for their catalytic function as water molecules can stabilize bound substrates and help with unbinding processes of products and inhibitors. Since the choice of water models for molecular dynamics simulations was shown to determine the accuracy of various calculated properties of the bulk solvent and solvated proteins, we have investigated if and to what extent water transport through the enzyme tunnels depends on the selection of the water model. Here, we focused on simulating enzymes with various well-defined tunnel geometries.
View Article and Find Full Text PDFAnalysis of the Dynamics of a Complex, Multipathway Reaction: Insulin Dimer Dissociation.
J Phys Chem B
December 2024
Department of Chemistry, the University of Chicago, Chicago, Illinois 60637, United States.
The protein hormone insulin forms a homodimer that must dissociate to bind to its receptor. Understanding the kinetics and mechanism of dissociation is essential for the rational design of therapeutic analogs. In addition to its physiological importance, this dissociation process serves as a paradigm for coupled (un)folding and (un)binding.
View Article and Find Full Text PDFA 'through-DNA' mechanism for co-regulation of metal uptake and efflux.
Nat Commun
December 2024
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
Transition metals like Zn are essential for all organisms including bacteria, but fluctuations of their concentrations in the cell can be lethal. Organisms have thus evolved complex mechanisms for cellular metal homeostasis. One mechanistic paradigm involves pairs of transcription regulators sensing intracellular metal concentrations to regulate metal uptake and efflux.
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