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Biophysical Journal
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3.67
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62854
Papers 62180
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Abstract We describe a technique for simultaneous quantification of the contractile forces and cytosolic calcium dynamics of muscle fibers embedded in three-dimensional biopolymer gels under auxotonic loading conditions. We derive a scaling law for linear elastic matrices such as basement membrane extract hydrogels (Matrigel) that allows us to measure contractile force from the shape of the relaxed and contracted muscle cell and the Young's modulus of the matrix, without further knowledge of the...
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Abstract Fatty acid binding proteins (FABPs) play an important role in transportation of fatty acids. Despite intensive studies, how fatty acids enter the protein cavity for binding is still controversial. Here, a gap-closed variant of human intestinal FABP was generated by mutagenesis, in which the gap is locked by a disulfide bridge. According to its structure determined here by NMR, this variant has no obvious openings as the ligand entrance and the gap cannot be widened by internal dynamics....
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Abstract We modelled the relaxation dynamics of (lipid) vesicles upon osmotic upshift taking into account volume variation, chemical reaction kinetics and passive transport across the membrane. We focused on the relaxation-kinetics upon addition of impermeable osmolytes like KCl and membrane-permeable solutes like weak acids. We studied the effect of the most relevant physical parameters on the dynamic behavior of the system, as well as, on the relaxation rates. We observe that: (i) the dynamic ...
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Abstract Muscle contraction is governed by tropomyosin (Tpm) shifting azimuthally between three states on F-actin (Blocked, Closed and Open) in response to calcium-binding to troponin and acto-myosin cross-bridge formation. The Tpm coiled coil polymerizes head-to-tail along the long-pitch helix of F-actin to form continuous super-helical cables that wrap around the actin filaments. The end-to-end bonds formed between the N- and C- terminus of adjacent Tpm molecules define Tpm continuity and play...
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Abstract About 3/4 of the human DNA molecules are wrapped into nucleosomes, protein spools with DNA. Nucleosomes are highly dynamic, transiently exposing their DNA through spontaneous unspooling. Recent experiments allowed to observe the DNA of an ensemble of such breathing nucleosomes through x-ray diffraction with contrast matching between the solvent and the protein core. In the current study we calculate such an ensemble through a Monte Carlo simulation of a coarse-grained nucleosome model w...
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Abstract Bush-crickets have tympanal ears located in the forelegs. Their ears are elaborated as they have outer, middle and inner ear components. The outer ear comprises an air-filled tube derived from the respiratory trachea, the acoustic trachea (AT), which transfers sound from the prothoracic acoustic spiracle to the internal side of the ear drums in the legs. A key feature of the AT is its capacity to reduce the velocity of sound propagation and alter the acoustic driving forces of the tympa...
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Abstract Precise quantification of the energetics and interactions that stabilize membrane proteins in a lipid bilayer is a long-sought goal. Toward this end, atomic force microscopy (AFM) has been used to unfold individual membrane proteins embedded in their native lipid bilayer, typically by retracting the cantilever at a constant velocity. Recently, unfolding intermediates separated by as few as two amino acids were detected using focused-ion-beam modified ultrashort cantilevers. However, una...
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Abstract In eukaryotic cells, DNA is packaged into chromatin where nucleosomes are the basic packaging unit. Important cellular processes including gene expression, DNA replication, and DNA repair require nucleosomal DNA to be unwrapped so that functional proteins can access their target sites, which otherwise are sterically occluded. A key question in this process is what are the unwrapped conformations individual nucleosomes adopt within chromatin. Here, we develop a concurrent nucleosome unwr...
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