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Biophysical Journal

Rueyhung Roc Weng, T Tony Yang, Chia-En Huang, Chih-Wei Chang, Won-Jing Wang, Jung-Chi Liao
The primary cilium is an essential organelle mediating key signaling activities, such as sonic hedgehog signaling. The molecular composition of the ciliary compartment is distinct from that of the cytosol, with the transition zone (TZ) gated the ciliary base. The TZ is a packed and organized protein complex containing multiple ciliopathy-associated protein species. Tectonic 2 (TCTN2) is one of the TZ proteins in the vicinity of the ciliary membrane, and its mutation is associated with Meckel syndrome. Despite its importance in ciliopathies, the role of TCTN2 in ciliary structure and molecules remains unclear...
June 1, 2018: Biophysical Journal
Shipeng Shao, Boxin Xue, Yujie Sun
Many critical processes occurring in mammalian cells are stochastic and can be directly observed at the single-molecule level within their physiological environment, which would otherwise be obscured in an ensemble measurement. There are various fundamental processes in the nucleus, such as transcription, replication, and DNA repair, the study of which can greatly benefit from intranuclear single-molecule imaging. However, the number of such studies is relatively small mainly because of lack of proper labeling and imaging methods...
June 1, 2018: Biophysical Journal
Xuefeng Wang, Seongjin Park, Lanying Zeng, Ankur Jain, Taekjip Ha
Single-molecule pull-down (SiMPull) can capture native protein complexes directly from cell lysates for analysis of complex composition and activities at the single-molecule level. Although SiMPull requires many fewer cells compared to conventional pull-down assays, all studies so far have been performed using lysates from many cells. In principle, extending SiMPull to the single-cell level will allow the investigation of cell-to-cell variations on the stoichiometry and activities of biomolecular complexes...
May 24, 2018: Biophysical Journal
Mehmet Ali Öztürk, Vlad Cojocaru, Rebecca C Wade
Linker histone (LH) proteins play a key role in higher-order structuring of chromatin for the packing of DNA in eukaryotic cells and in the regulation of genomic function. The common fruit fly (Drosophila melanogaster) has a single somatic isoform of the LH (H1). It is thus a useful model organism for investigating the effects of the LH on nucleosome compaction and the structure of the chromatosome, the complex formed by binding of an LH to a nucleosome. The structural and mechanistic details of how LH proteins bind to nucleosomes are debated...
May 11, 2018: Biophysical Journal
Fereydoon Taheri, Buse Isbilir, Gabriele Müller, Jan W Krieger, Giuseppe Chirico, Jörg Langowski, Katalin Tóth
Using fluorescence correlation spectroscopy in single-plane illumination microscopy, we investigated the dynamics of chromatin in interphase mouse adult fibroblast cell nuclei under the influence of the intermediate filament protein lamin A. We find that 1) lamin A-eGFP and histone H2A-mRFP show significant comobility, indicating that their motions are clearly interconnected in the nucleus, and 2) that the random motion of histones H2A within the chromatin network is subdiffusive, i.e., the effective diffusion coefficient decreases for slow timescales...
May 11, 2018: Biophysical Journal
Norbert Mücke, Lara Kämmerer, Stefan Winheim, Robert Kirmse, Jan Krieger, Maria Mildenberger, Jochen Baßler, Ed Hurt, Wolfgang H Goldmann, Ueli Aebi, Katalin Toth, Jörg Langowski, Harald Herrmann
Intermediate filaments (IFs) are principal components of the cytoskeleton, a dynamic integrated system of structural proteins that provides the functional architecture of metazoan cells. They are major contributors to the elasticity of cells and tissues due to their high mechanical stability and intrinsic flexibility. The basic building block for the assembly of IFs is a rod-like, 60-nm-long tetrameric complex made from two antiparallel, half-staggered coiled coils. In low ionic strength, tetramers form stable complexes that rapidly assemble into filaments upon raising the ionic strength...
May 10, 2018: Biophysical Journal
Éva Nagy, Gábor Mocsár, Veronika Sebestyén, Julianna Volkó, Ferenc Papp, Katalin Tóth, Sándor Damjanovich, György Panyi, Thomas A Waldmann, Andrea Bodnár, György Vámosi
The high electric field across the plasma membrane might influence the conformation and behavior of transmembrane proteins that have uneven charge distributions in or near their transmembrane regions. Membrane depolarization of T cells occurs in the tumor microenvironment and in inflamed tissues because of K+ release from necrotic cells and hypoxia affecting the expression of K+ channels. However, little attention has been given to the effect of membrane potential (MP) changes on membrane receptor function...
May 10, 2018: Biophysical Journal
Jan Buchholz, Jan Krieger, Claudio Bruschini, Samuel Burri, Andrei Ardelean, Edoardo Charbon, Jörg Langowski
Photon-counting sensors based on standard complementary metal-oxide-semiconductor single-photon avalanche diodes (SPADs) represent an emerging class of imagers that enable the counting and/or timing of single photons at zero readout noise (better than high-speed electron-multiplying charge-coupling devices) and over large arrays. They have seen substantial progress over the last 15 years, increasing their spatial resolution, timing accuracy, and sensitivity while reducing spurious signals such as afterpulsing and dark counts...
May 9, 2018: Biophysical Journal
J Michael Schurr
No abstract text is available yet for this article.
May 7, 2018: Biophysical Journal
Anatoly Zinchenko, Nikolay V Berezhnoy, Qinming Chen, Lars Nordenskiöld
The megabase-sized length of chromatin is highly relevant to the state of chromatin in vivo, where it is subject to a highly crowded environment and is organized in topologically associating domains of similar dimension. We developed an in vitro experimental chromatin model system reconstituted from T4 DNA (approximately 166 kbp) and histone octamers and studied the monomolecular compaction of this megabase-sized chromatin fiber under the influence of macromolecular crowding. We used single-molecule fluorescence microscopy and observed compaction in aqueous solutions containing poly(ethylene glycol) in the presence of monovalent (Na+ and K+ ) and divalent (Mg2+ ) cations...
May 2, 2018: Biophysical Journal
Frederik Steiert, Eugene P Petrov, Peter Schultz, Petra Schwille, Thomas Weidemann
Fluorescent proteins (FPs) feature complex photophysical behavior that must be considered when studying the dynamics of fusion proteins in model systems and live cells. In this work, we characterize mNeonGreen (mNG), a recently introduced FP from the bilaterian Branchiostoma lanceolatum, in comparison to the well-known hydrozoan variants enhanced green fluorescent protein (EGFP) and Aequorea coerulescens GFP by steady-state spectroscopy and fluorescence correlation spectroscopy in solutions of different pH...
April 26, 2018: Biophysical Journal
Willy Carrasquel-Ursulaez, Osvaldo Alvarez, Francisco Bezanilla, Ramon Latorre
Two families of accessory proteins, β and γ, modulate BK channel gating and pharmacology. Notably, in the absence of internal Ca2+ , the γ1 subunit promotes a large shift of the BK conductance-voltage curve to more negative potentials. However, very little is known about how α- and γ1 subunits interact. In particular, the association stoichiometry between both subunits is unknown. Here, we propose a method to answer this question using lanthanide resonance energy transfer. The method assumes that the kinetics of lanthanide resonance energy transfer-sensitized emission of the donor double-labeled α/γ1 complex is the linear combination of the kinetics of the sensitized emission in single-labeled complexes...
April 25, 2018: Biophysical Journal
Achillefs N Kapanidis, Alessia Lepore, Meriem El Karoui
Bacteria are microorganisms central to health and disease, serving as important model systems for our understanding of molecular mechanisms and for developing new methodologies and vehicles for biotechnology. In the past few years, our understanding of bacterial cell functions has been enhanced substantially by powerful single-molecule imaging techniques. Using single fluorescent molecules as a means of breaking the optical microscopy limit, we can now reach resolutions of ∼20 nm inside single living cells, a spatial domain previously accessible only by electron microscopy...
April 18, 2018: Biophysical Journal
Dilara Batan, Esther Braselmann, Michael Minson, Dieu My Thanh Nguyen, Pascale Cossart, Amy E Palmer
Listeria monocytogenes is an intracellular food-borne pathogen that has evolved to enter mammalian host cells, survive within them, spread from cell to cell, and disseminate throughout the body. A series of secreted virulence proteins from Listeria are responsible for manipulation of host-cell defense mechanisms and adaptation to the intracellular lifestyle. Identifying when and where these virulence proteins are located in live cells over the course of Listeria infection can provide valuable information on the roles these proteins play in defining the host-pathogen interface...
April 10, 2018: Biophysical Journal
Dhanya T Jayaram, Samantha M Pustulka, Robert G Mannino, Wilbur A Lam, Christine K Payne
Nanoparticles used in cellular applications encounter free serum proteins that adsorb onto the surface of the nanoparticle, forming a protein corona. This protein layer controls the interaction of nanoparticles with cells. For nanomedicine applications, it is important to consider how intravenous injection and the subsequent shear flow will affect the protein corona. Our goal was to determine if shear flow changed the composition of the protein corona and if these changes affected cellular binding. Colorimetric assays of protein concentration and gel electrophoresis demonstrate that polystyrene nanoparticles subjected to flow have a greater concentration of serum proteins adsorbed on the surface, especially plasminogen...
April 9, 2018: Biophysical Journal
Weria Pezeshkian, Himanshu Khandelia, Derek Marsh
No abstract text is available yet for this article.
June 5, 2018: Biophysical Journal
J Boutet de Monvel, W E Brownell, M Ulfendahl
No abstract text is available yet for this article.
June 5, 2018: Biophysical Journal
Camelia G Tusan, Yu-Hin Man, Hoda Zarkoob, David A Johnston, Orestis G Andriotis, Philipp J Thurner, Shoufeng Yang, Edward A Sander, Eileen Gentleman, Bram G Sengers, Nicholas D Evans
Extracellular matrix stiffness has a profound effect on the behavior of many cell types. Adherent cells apply contractile forces to the material on which they adhere and sense the resistance of the material to deformation-its stiffness. This is dependent on both the elastic modulus and the thickness of the material, with the corollary that single cells are able to sense underlying stiff materials through soft hydrogel materials at low (<10 μm) thicknesses. Here, we hypothesized that cohesive colonies of cells exert more force and create more hydrogel deformation than single cells, therefore enabling them to mechanosense more deeply into underlying materials than single cells...
June 5, 2018: Biophysical Journal
Franci Bajd, Igor Serša
Mucus scaffolds represent one of the most common barriers in targeted drug delivery and can remarkably reduce the outcome of pharmacological therapies. An efficient transport of drug particles through a mucus barrier is a precondition for an efficient drug delivery. Understanding the transport mechanism is particularly important for treatment of disorders such as cystic fibrosis. These are characterized by an onset of high-density mucus scaffolds imposing an increased steric filtering. In this study, we employed the bond-fluctuation model to analyze the effect of steric interactions on slowing the translational dynamics of compound chain-like particles traversing through scaffolds of different configurations (regular isotropic and anisotropic versus irregular random)...
June 5, 2018: Biophysical Journal
Jia-Jye Lee, Satish Rao, Gaurav Kaushik, Evren U Azeloglu, Kevin D Costa
Atomic force microscopy (AFM) is used to study mechanical properties of biological materials at submicron length scales. However, such samples are often structurally heterogeneous even at the local level, with different regions having distinct mechanical properties. Physical or chemical disruption can isolate individual structural elements but may alter the properties being measured. Therefore, to determine the micromechanical properties of intact heterogeneous multilayered samples indented by AFM, we propose the Hybrid Eshelby Decomposition (HED) analysis, which combines a modified homogenization theory and finite element modeling to extract layer-specific elastic moduli of composite structures from single indentations, utilizing knowledge of the component distribution to achieve solution uniqueness...
June 5, 2018: Biophysical Journal
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