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Biophysical Journal

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https://www.readbyqxmd.com/read/29153319/thermodynamic-coupling-function-analysis-of-allosteric-mechanisms-in-the-human-dopamine-transporter
#1
Michael V LeVine, Michel A Cuendet, Asghar M Razavi, George Khelashvili, Harel Weinstein
Allostery plays a crucial role in the mechanism of neurotransmitter-sodium symporters, such as the human dopamine transporter. To investigate the molecular mechanism that couples the transport-associated inward release of the Na(+) ion from the Na2 site to intracellular gating, we applied a combination of the thermodynamic coupling function (TCF) formalism and Markov state model analysis to a 50-μs data set of molecular dynamics trajectories of the human dopamine transporter, in which multiple spontaneous Na(+) release events were observed...
November 15, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29132641/force-spectroscopy-with-9-%C3%AE-s-resolution-and-sub-pn-stability-by-tailoring-afm-cantilever-geometry
#2
Devin T Edwards, Jaevyn K Faulk, Marc-André LeBlanc, Thomas T Perkins
Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize the unfolding/refolding dynamics of individual molecules and resolve closely spaced, transiently occupied folding intermediates. On a modern commercial AFM, these applications and others are now limited by the mechanical properties of the cantilever. Specifically, AFM-based SMFS data quality is degraded by a commercial cantilever's limited combination of temporal resolution, force precision, and force stability...
November 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29129266/single-cell-defects-cause-a-long-range-mechanical-response-in-a-confluent-epithelial-cell-layer
#3
Susanne Karsch, Deqing Kong, Jörg Großhans, Andreas Janshoff
Epithelial cells are responsible for tissue homeostasis and form a barrier to maintain chemical gradients and mechanical integrity. Therefore, rapid wound closure is crucial for proper tissue function and restoring homeostasis. In this study, the mechanical properties of cells surrounding a single-cell wound are investigated during closure of the defect. The single-cell wound is induced in an intact layer using micropipette action and responses in neighboring cells are monitored with atomic force microscopy...
November 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29111155/drift-and-behavior-of-e-%C3%A2-coli-cells
#4
Gabriele Micali, Rémy Colin, Victor Sourjik, Robert G Endres
Chemotaxis of the bacterium Escherichia coli is well understood in shallow chemical gradients, but its swimming behavior remains difficult to interpret in steep gradients. By focusing on single-cell trajectories from simulations, we investigated the dependence of the chemotactic drift velocity on attractant concentration in an exponential gradient. Whereas maxima of the average drift velocity can be interpreted within analytical linear-response theory of chemotaxis in shallow gradients, limits in drift due to steep gradients and finite number of receptor-methylation sites for adaptation go beyond perturbation theory...
October 27, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29102037/single-molecule-imaging-of-proteoglycans-in-the-pericellular-matrix
#5
Jan Scrimgeour, Louis T McLane, Patrick S Chang, Jennifer E Curtis
The pericellular matrix is a robust, hyaluronan-rich polymer brush-like structure that controls access to the cell surface, and plays an important role in cell adhesion, migration, and proliferation. We report the observation of single bottlebrush proteoglycan dynamics in the pericellular matrix of living chondrocytes. Our investigations show that the pericellular matrix undergoes gross extension on the addition of exogenous aggrecan, and that this extension is significantly in excess of that observed in traditional particle exclusion assays...
October 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29056231/mitochondrial-adp-atp-carrier-in-dodecylphosphocholine-binds-cardiolipins-with-non-native-affinity
#6
François Dehez, Paul Schanda, Martin S King, Edmund R S Kunji, Christophe Chipot
Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins...
October 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212011/temperature-induced-transitions-in-the-structure-and-interfacial-rheology-of-human-meibum
#7
Danielle L Leiske, Christopher I Leiske, Daniel R Leiske, Michael F Toney, Michelle Senchyna, Howard A Ketelson, David L Meadows, Gerald G Fuller
No abstract text is available yet for this article.
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212010/moving-in-the-right-direction-protein-vibrations-steering-function
#8
Katherine A Niessen, Mengyang Xu, Alessandro Paciaroni, Andrea Orecchini, Edward H Snell, Andrea G Markelz
No abstract text is available yet for this article.
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212009/snare-mediated-single-vesicle-fusion-events-with-supported-and-freestanding-lipid-membranes
#9
Jan W Kuhlmann, Meike Junius, Ulf Diederichsen, Claudia Steinem
No abstract text is available yet for this article.
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212008/stochastic-pacing-inhibits-spatially-discordant-cardiac-alternans
#10
Dan Wilson, Bard Ermentrout
Depressed heart rate variability is a well-established risk factor for sudden cardiac death in survivors of acute myocardial infarction and for those with congestive heart failure. Although measurements of heart rate variability provide a valuable prognostic tool, it is unclear whether reduced heart rate variability itself is proarrhythmic or if it simply correlates with the severity of autonomic nervous system dysfunction. In this work, we investigate a possible mechanism by which heart rate variability could protect against cardiac arrhythmia...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212007/ultrahigh-resolution-optical-coherence-elastography-images-cellular-scale-stiffness-of-mouse-aorta
#11
Philip Wijesinghe, Niloufer J Johansen, Andrea Curatolo, David D Sampson, Ruth Ganss, Brendan F Kennedy
Cellular-scale imaging of the mechanical properties of tissue has helped to reveal the origins of disease; however, cellular-scale resolution is not readily achievable in intact tissue volumes. Here, we demonstrate volumetric imaging of Young's modulus using ultrahigh-resolution optical coherence elastography, and apply it to characterizing the stiffness of mouse aortas. We achieve isotropic resolution of better than 15 μm over a 1-mm lateral field of view through the entire depth of an intact aortic wall...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212006/reconstruction-of-cell-focal-adhesions-using-physical-constraints-and-compressive-regularization
#12
Joshua C Chang, Yanli Liu, Tom Chou
We develop a method to reconstruct, from measured displacements of an underlying elastic substrate, the spatially dependent forces that cells or tissues impart on it. Given newly available high-resolution images of substrate displacements, it is desirable to be able to reconstruct small-scale, compactly supported focal adhesions that are often localized and exist only within the footprint of a cell. In addition to the standard quadratic data mismatch terms that define least-squares fitting, we motivate a regularization term in the objective function that penalizes vectorial invariants of the reconstructed surface stress while preserving boundaries...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212005/desmoglein-3-order-and-dynamics-in-desmosomes-determined-by-fluorescence-polarization-microscopy
#13
Emily I Bartle, Tara M Urner, Siddharth S Raju, Alexa L Mattheyses
Desmosomes are macromolecular cell-cell junctions that provide adhesive strength in epithelial tissue. Desmosome function is inseparably linked to structure, and it is hypothesized that the arrangement, or order, of desmosomal cadherins in the intercellular space is critical for adhesive strength. However, due to desmosome size, molecular complexity, and dynamics, the role that order plays in adhesion is challenging to study. Herein, we present an excitation resolved fluorescence polarization microscopy approach to measure the spatiotemporal dynamics of order and disorder of the desmosomal cadherin desmoglein 3 (Dsg3) in living cells...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212004/investigating-focal-adhesion-substructures-by-localization-microscopy
#14
Hendrik Deschout, Ilia Platzman, Daniel Sage, Lely Feletti, Joachim P Spatz, Aleksandra Radenovic
Cells rely on focal adhesions (FAs) to carry out a variety of important tasks, including motion, environmental sensing, and adhesion to the extracellular matrix. Although attaining a fundamental characterization of FAs is a compelling goal, their extensive complexity and small size, which can be below the diffraction limit, have hindered a full understanding. In this study we have used single-molecule localization microscopy (SMLM) to investigate integrin β3 and paxillin in rat embryonic fibroblasts growing on two different extracellular matrix-representing substrates (i...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212003/soce-is-important-for-maintaining-sarcoplasmic-calcium-content-and-release-in-skeletal-muscle-fibers
#15
Mónika Sztretye, Nikolett Geyer, János Vincze, Dána Al-Gaadi, Tamás Oláh, Péter Szentesi, Gréta Kis, Miklós Antal, Ildikó Balatoni, László Csernoch, Beatrix Dienes
Store-operated Ca2+ entry (SOCE) is a Ca2+-entry process activated by the depletion of intracellular stores and has an important role in many cell types. In skeletal muscle, however, its role during physiological muscle activation has been controversial. To address this question, sarcoplasmic reticulum (SR) calcium release in a mouse strain with a naturally occurring mutation in the myostatin gene (Compact (Cmpt)) leading to a hypermuscular yet reduced muscle-force phenotype was compared to that in wild-type mice...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212002/going-with-the-flow-water-flux-and-cell-shape-during-cytokinesis
#16
Yizeng Li, Lijuan He, Nicolas A P Gonzalez, Jenna Graham, Charles Wolgemuth, Denis Wirtz, Sean X Sun
Cell shape changes during cytokinesis in eukaryotic cells have been attributed to contractile forces from the actomyosin ring and the actomyosin cortex. Here we propose an additional mechanism where active pumping of ions and water at the cell poles and the division furrow can also achieve the same type of shape change during cytokinesis without myosin contraction. We develop a general mathematical model to examine shape changes in a permeable object subject to boundary fluxes. We find that hydrodynamic flows in the cytoplasm and the relative drag between the cytoskeleton network phase and the water phase also play a role in determining the cell shape during cytokinesis...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212001/mechanism-of-kin-discriminatory-demarcation-line-formation-between-colonies-of-swarming-bacteria
#17
Pintu Patra, Christopher N Vassallo, Daniel Wall, Oleg A Igoshin
Swarming bacteria use kin discrimination to preferentially associate with their clonemates for certain cooperative behaviors. Kin discrimination can manifest as an apparent demarcation line (a region lacking cells or with much lower cell density) between antagonist strains swarming toward each other. In contrast, two identical strains merge with no demarcation. Experimental studies suggest contact-dependent killing between different strains as a mechanism of kin discrimination, but it is not clear whether this killing is sufficient to explain the observed patterns...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29212000/is-aggregate-dependent-yeast-aging-fortuitous-a-model-of-damage-segregation-and-aggregate-dynamics
#18
Martín Andrade-Restrepo
During cytokinesis in Saccharomyces cerevisiae, damaged proteins are distributed unequally between the daughter and mother cells. The retention of these proteins is correlated with yeast aging. Even though evidence suggests that aggregates are retained due to an underlying molecular mechanism, the debate on whether an active mechanism is necessary for this asymmetry remains unsolved. In particular, passive diffusion and a bud-specific dilution remain as possible explanations. Here, a computational and mathematical model is provided to test whether passive mechanisms alone are sufficient to account for the aggregate distribution patterns and the aggregate kinetics observed in living cells...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29211999/a-simple-and-powerful-analysis-of-lateral-subdiffusion-using-single-particle-tracking
#19
Marianne Renner, Lili Wang, Sabine Levi, Laetitia Hennekinne, Antoine Triller
In biological membranes, many factors such as cytoskeleton, lipid composition, crowding, and molecular interactions deviate lateral diffusion from the expected random walks. These factors have different effects on diffusion but act simultaneously, so the observed diffusion is a complex mixture of diffusive behaviors (directed, Brownian, anomalous, or confined). Therefore, commonly used approaches to quantify diffusion based on averaging of the displacements such as the mean square displacement, are not adapted to the analysis of this heterogeneity...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29211998/tropomyosin-must-interact-weakly-with-actin-to-effectively-regulate-thin-filament-function
#20
Michael J Rynkiewicz, Thavanareth Prum, Stephen Hollenberg, Farooq A Kiani, Patricia M Fagnant, Steven B Marston, Kathleen M Trybus, Stefan Fischer, Jeffrey R Moore, William Lehman
Elongated tropomyosin, associated with actin-subunits along the surface of thin filaments, makes electrostatic interactions with clusters of conserved residues, K326, K328, and R147, on actin. The association is weak, permitting low-energy cost regulatory movement of tropomyosin across the filament during muscle activation. Interestingly, acidic D292 on actin, also evolutionarily conserved, lies adjacent to the three-residue cluster of basic amino acids and thus may moderate the combined local positive charge, diminishing tropomyosin-actin interaction and facilitating regulatory-switching...
December 5, 2017: Biophysical Journal
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