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    Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification.
    Biophys J 2018 May 11;114(10):2363-2375. Epub 2018 May 11.
    Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg, Germany. Electronic address:
    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. Read More

    Random Motion of Chromatin Is Influenced by Lamin A Interconnections.
    Biophys J 2018 May 11;114(10):2465-2472. Epub 2018 May 11.
    Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany. Electronic address:
    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. Read More

    Assembly Kinetics of Vimentin Tetramers to Unit-Length Filaments: A Stopped-Flow Study.
    Biophys J 2018 May 10;114(10):2408-2418. Epub 2018 May 10.
    Institute of Neuropathology, University Hospital Erlangen, Erlangen, Germany; Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany. Electronic address:
    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. Read More

    Membrane Potential Distinctly Modulates Mobility and Signaling of IL-2 and IL-15 Receptors in T Cells.
    Biophys J 2018 May 10;114(10):2473-2482. Epub 2018 May 10.
    Department of Biophysics and Cell Biology, Faculty of Medicine. Electronic address:
    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. Read More

    Widefield High Frame Rate Single-Photon SPAD Imagers for SPIM-FCS.
    Biophys J 2018 May 10;114(10):2455-2464. Epub 2018 May 10.
    German Cancer Research Center, Heidelberg, Germany.
    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. They are increasingly being applied for time-resolved applications with the added advantage of enabling real-time options such as autocorrelation. Read More

    Nuclear Transport and Accumulation of Smad Proteins Studied by Single-Molecule Microscopy.
    Biophys J 2018 May;114(9):2243-2251
    Department of Biology, Temple University, Philadelphia, Pennsylvania. Electronic address:
    Nuclear translocation of stimulated Smad heterocomplexes is a critical step in the signal transduction of transforming growth factor β (TGF-β) from transmembrane receptors into the nucleus. Specifically, normal nuclear accumulation of Smad2/Smad4 heterocomplexes induced by TGF-β1 is involved in carcinogenesis. However, the relationship between nuclear accumulation and the nucleocytoplasmic transport kinetics of Smad proteins in the presence of TGF-β1 remains obscure. Read More

    Electromechanics and Volume Dynamics in Nonexcitable Tissue Cells.
    Biophys J 2018 May;114(9):2231-2242
    Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland; Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland; Johns Hopkins Physical Sciences-Oncology Center, Johns Hopkins University, Baltimore, Maryland. Electronic address:
    Cell volume regulation is fundamentally important in phenomena such as cell growth, proliferation, tissue homeostasis, and embryogenesis. How the cell size is set, maintained, and changed over a cell's lifetime is not well understood. In this work we focus on how the volume of nonexcitable tissue cells is coupled to the cell membrane electrical potential and the concentrations of membrane-permeable ions in the cell environment. Read More

    The Margination of Particles in Areas of Constricted Blood Flow.
    Biophys J 2018 May;114(9):2221-2230
    Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut; Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut. Electronic address:
    Stroke is a leading cause of death globally and is caused by stenoses, abnormal narrowings of blood vessels. Recently, there has been an increased interest in shear-activated particle clusters for the treatment of stenosis, but there is a lack of literature investigating the impact of different stenosis geometries on particle margination. Margination refers to the movement of particles toward the blood vessel wall and is desirable for drug delivery. Read More

    Simultaneous Detection of Local Polarizability and Viscosity by a Single Fluorescent Probe in Cells.
    Biophys J 2018 May;114(9):2212-2220
    NEST, Scuola Normale Superiore and NANO-CNR, Pisa, Italy. Electronic address:
    Many intracellular reactions are dependent on the dielectric ("polarity") and viscosity properties of their milieu. Fluorescence imaging offers a convenient strategy to report on such environmental properties. Yet, concomitant and independent monitoring of polarity and viscosity in cells at submicron scale is currently hampered by the lack of fluorescence probes characterized by unmixed responses to both parameters. Read More

    Single-Molecule Light-Sheet Imaging of Suspended T Cells.
    Biophys J 2018 May;114(9):2200-2211
    Department of Chemistry, University of Cambridge, Cambridge, United Kingdom. Electronic address:
    Adaptive immune responses are initiated by triggering of the T cell receptor. Single-molecule imaging based on total internal reflection fluorescence microscopy at coverslip/basal cell interfaces is commonly used to study this process. These experiments have suggested, unexpectedly, that the diffusional behavior and organization of signaling proteins and receptors may be constrained before activation. Read More

    Traction Force Screening Enabled by Compliant PDMS Elastomers.
    Biophys J 2018 May;114(9):2194-2199
    Department of Bioengineering, McGill University, Montreal, Quebec, Canada. Electronic address:
    Actomyosin contractility is an essential element of many aspects of cellular biology and manifests as traction forces that cells exert on their surroundings. The central role of these forces makes them a novel principal therapeutic target in diverse diseases. This requires accurate and higher-capacity measurements of traction forces; however, existing methods are largely low throughput, limiting their utility in broader applications. Read More

    Analysis of the Precision, Robustness, and Speed of Elastic Resonator Interference Stress Microscopy.
    Biophys J 2018 May;114(9):2180-2193
    Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom. Electronic address:
    Localization-microscopy-based methods are widely used to map the forces that cells apply to their substrates and to study important questions of cellular biomechanics. By contrast, elastic resonator interference stress microscopy (ERISM) uses an interference-based approach, which requires low light intensity and facilitates imaging of cellular forces with extreme precision (down to pN forces) and robustness (e.g. Read More

    Motor-like Properties of Nonmotor Enzymes.
    Biophys J 2018 May;114(9):2174-2179
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California. Electronic address:
    Molecular motors are thought to generate force and directional motion via nonequilibrium switching between energy surfaces. Because all enzymes can undergo such switching, we hypothesized that the ability to generate rotary motion and torque is not unique to highly adapted biological motor proteins but is instead a common feature of enzymes. We used molecular dynamics simulations to compute energy surfaces for hundreds of torsions in three enzymes-adenosine kinase, protein kinase A, and HIV-1 protease-and used these energy surfaces within a kinetic model that accounts for intersurface switching and intrasurface probability flows. Read More

    DPPC Bilayers in Solutions of High Sucrose Content.
    Biophys J 2018 May;114(9):2165-2173
    Université de Strasbourg, CNRS, Institut Charles Sadron, UPR022, Strasbourg Cedex, France. Electronic address:
    The properties of lipid bilayers in sucrose solutions have been intensely scrutinized over recent decades because of the importance of sugars in the field of biopreservation. However, a consensus has not yet been formed on the mechanisms of sugar-lipid interaction. Here, we present a study on the effect of sucrose on 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayers that combines calorimetry, spectral fluorimetry, and optical microscopy. Read More

    Membrane Bending Moduli of Coexisting Liquid Phases Containing Transmembrane Peptide.
    Biophys J 2018 May;114(9):2152-2164
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York. Electronic address:
    A number of highly curved membranes in vivo, such as epithelial cell microvilli, have the relatively high sphingolipid content associated with "raft-like" composition. Given the much lower bending energy measured for bilayers with "nonraft" low sphingomyelin and low cholesterol content, observing high curvature for presumably more rigid compositions seems counterintuitive. To understand this behavior, we measured membrane rigidity by fluctuation analysis of giant unilamellar vesicles. Read More

    Mechanism of Long-Chain Free Fatty Acid Protonation at the Membrane-Water Interface.
    Biophys J 2018 May;114(9):2142-2151
    Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria. Electronic address:
    Long-chain free fatty acids (FFAs) play an important role in several physiological and pathological processes such as lipid fusion, adjustments of membrane permeability and fluidity, and the regulation of enzyme and protein activities. FFA-facilitated membrane proton transport (flip-flop) and FFA-dependent proton transport by membrane proteins (e.g. Read More

    Membrane Curvature Sensing by Amphipathic Helices: Insights from Implicit Membrane Modeling.
    Biophys J 2018 May;114(9):2128-2141
    Department of Chemistry, City College of New York, New York, New York; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York. Electronic address:
    Sensing and generation of lipid membrane curvature, mediated by the binding of specific proteins onto the membrane surface, play crucial roles in cell biology. A number of mechanisms have been proposed, but the molecular understanding of these processes is incomplete. All-atom molecular dynamics simulations have offered valuable insights but are extremely demanding computationally. Read More

    Molecular Dynamics Analysis of Cardiolipin and Monolysocardiolipin on Bilayer Properties.
    Biophys J 2018 May;114(9):2116-2127
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut. Electronic address:
    The mitochondrial lipid cardiolipin (CL) contributes to the spatial protein organization and morphological character of the inner mitochondrial membrane. Monolysocardiolipin (MLCL), an intermediate species in the CL remodeling pathway, is enriched in the multisystem disease Barth syndrome. Despite the medical relevance of MLCL, a detailed molecular description that elucidates the structural and dynamic differences between CL and MLCL has not been conducted. Read More

    Bilayer Thickness and Curvature Influence Binding and Insertion of a pHLIP Peptide.
    Biophys J 2018 May;114(9):2107-2115
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut. Electronic address:
    The physical properties of lipid bilayers, such as curvature and fluidity, can affect the interactions of polypeptides with membranes, influencing biological events. Additionally, given the growing interest in peptide-based therapeutics, understanding the influence of membrane properties on membrane-associated peptides has potential utility. pH low insertion peptides (pHLIPs) are a family of water-soluble peptides that can insert across cell membranes in a pH-dependent manner, enabling the use of pH to follow peptide-lipid interactions. Read More

    Alternative Splicing at N Terminus and Domain I Modulates Ca1.2 Inactivation and Surface Expression.
    Biophys J 2018 May;114(9):2095-2106
    Department of Physiology, National University of Singapore, Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore; Neurobiology/Ageing Programme, National University of Singapore, Singapore, Singapore; National Neuroscience Institute, Singapore, Singapore. Electronic address:
    The Ca1.2 L-type calcium channel is a key conduit for Ca influx to initiate excitation-contraction coupling for contraction of the heart and vasoconstriction of the arteries and for altering membrane excitability in neurons. Its α pore-forming subunit is known to undergo extensive alternative splicing to produce many Ca1. Read More

    All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding.
    Biophys J 2018 May;114(9):2083-2094
    Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland. Electronic address:
    Protein misfolding is implicated in many diseases, including serpinopathies. For the canonical inhibitory serpin α-antitrypsin, mutations can result in protein deficiencies leading to lung disease, and misfolded mutants can accumulate in hepatocytes, leading to liver disease. Using all-atom simulations based on the recently developed bias functional algorithm, we elucidate how wild-type α-antitrypsin folds and how the disease-associated S (Glu264Val) and Z (Glu342Lys) mutations lead to misfolding. Read More

    Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells.
    Biophys J 2018 May;114(9):2072-2082
    Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts; Department of Ecology and Evolutionary Biology, Microbial Sciences Institute, Yale University, New Haven, Connecticut. Electronic address:
    Transcription is the dominant point of control of gene expression. Biochemical studies have revealed key molecular components of transcription and their interactions, but the dynamics of transcription initiation in cells is still poorly understood. This state of affairs is being remedied with experiments that observe transcriptional dynamics in single cells using fluorescent reporters. Read More

    Topological Constraints and Their Conformational Entropic Penalties on RNA Folds.
    Biophys J 2018 May;114(9):2059-2071
    Department of Chemistry, University of Southern California, Los Angeles, California.
    Functional RNAs can fold into intricate structures using a number of different secondary and tertiary structural motifs. Many factors contribute to the overall free energy of the target fold. This study aims at quantifying the entropic costs coming from the loss of conformational freedom when the sugar-phosphate backbone is subjected to constraints imposed by secondary and tertiary contacts. Read More

    PolNet: A Tool to Quantify Network-Level Cell Polarity and Blood Flow in Vascular Remodeling.
    Biophys J 2018 May;114(9):2052-2058
    Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal. Electronic address:
    In this article, we present PolNet, an open-source software tool for the study of blood flow and cell-level biological activity during vessel morphogenesis. We provide an image acquisition, segmentation, and analysis protocol to quantify endothelial cell polarity in entire in vivo vascular networks. In combination, we use computational fluid dynamics to characterize the hemodynamics of the vascular networks under study. Read More

    PLANT: A Method for Detecting Changes of Slope in Noisy Trajectories.
    Biophys J 2018 May;114(9):2044-2051
    ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain; Universitat de Vic - Universitat Central de Catalunya, Vic, Spain. Electronic address:
    Time traces obtained from a variety of biophysical experiments contain valuable information on underlying processes occurring at the molecular level. Accurate quantification of these data can help explain the details of the complex dynamics of biological systems. Here, we describe PLANT (Piecewise Linear Approximation of Noisy Trajectories), a segmentation algorithm that allows the reconstruction of time-trace data with constant noise as consecutive straight lines, from which changes of slopes and their respective durations can be extracted. Read More

    ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.
    Biophys J 2018 May;114(9):2040-2043
    Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania. Electronic address:
    Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. Read More

    How Do We Know when Single-Molecule Force Spectroscopy Really Tests Single Bonds?
    Biophys J 2018 May;114(9):2032-2039
    Department of Bioengineering, University of Washington, Seattle, Washington. Electronic address:
    Single-molecule force spectroscopy makes it possible to measure the mechanical strength of single noncovalent receptor-ligand-type bonds. A major challenge in this technique is to ensure that measurements reflect bonds between single biomolecules because the molecules cannot be directly observed. This perspective evaluates different methodologies for identifying and reducing the contribution of multiple molecule interactions to single-molecule measurements to help the reader design experiments or assess publications in the single-molecule force spectroscopy field. Read More

    Atomic-Scale Insights into Physical Mechanisms Driving Enzymes' "Working Cycles".
    Biophys J 2018 May;114(9):2027-2029
    Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia; Dmitry Rogachev National Research Center for Hematology, Oncology, and Immunology, Moscow, Russia; Moscow State University, Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia. Electronic address:

    Compaction of Single-Molecule Megabase-Long Chromatin under the Influence of Macromolecular Crowding.
    Biophys J 2018 May 3;114(10):2326-2335. Epub 2018 May 3.
    School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. Electronic address:
    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 (Mg) cations. Read More

    Photophysical Behavior of mNeonGreen, an Evolutionarily Distant Green Fluorescent Protein.
    Biophys J 2018 May 27;114(10):2419-2431. Epub 2018 Apr 27.
    Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany. Electronic address:
    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. Blind spectral unmixing of sets of absorption spectra reveals three interconverting electronic states of mNG: a nonfluorescent protonated state, a bright state showing bell-shaped pH dependence, and a similarly bright state dominating at high pH. Read More

    Determination of the Stoichiometry between α- and γ1 Subunits of the BK Channel Using LRET.
    Biophys J 2018 Apr 25. Epub 2018 Apr 25.
    Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile. Electronic address:
    Two families of accessory proteins, β and γ, modulate BK channel gating and pharmacology. Notably, in the absence of internal Ca, 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. Read More

    Cytoskeleton Remodeling Induces Membrane Stiffness and Stability Changes of Maturing Reticulocytes.
    Biophys J 2018 Apr;114(8):2014-2023
    Division of Applied Mathematics, Brown University, Providence, Rhode Island. Electronic address:
    Reticulocytes, the precursors of erythrocytes, undergo drastic alterations in cell size, shape, and deformability during maturation. Experimental evidence suggests that young reticulocytes are stiffer and less stable than their mature counterparts; however, the underlying mechanism is yet to be fully understood. Here, we develop a coarse-grained molecular-dynamics reticulocyte membrane model to elucidate how the membrane structure of reticulocytes contributes to their particular biomechanical properties and pathogenesis in blood diseases. Read More

    Magnetic Field Changes Macrophage Phenotype.
    Biophys J 2018 Apr;114(8):2001-2013
    The Houston Methodist Research Institute, Houston, Texas; Department of Surgery, The Houston Methodist Hospital, Houston, Texas; Department of Genetics, The University of Texas, M.D. Anderson Cancer Center, Houston, Texas. Electronic address:
    Macrophages play a crucial role in homeostasis, regeneration, and innate and adaptive immune responses. Functionally different macrophages have different shapes and molecular phenotypes that depend on the actin cytoskeleton, which is regulated by the small GTPase RhoA. The naive M0 macrophages are slightly elongated, proinflammatory M1 are round, and M2 antiinflammatory macrophages are elongated. Read More

    Influence of Micropatterning on Human Periodontal Ligament Cells' Behavior.
    Biophys J 2018 Apr;114(8):1988-2000
    Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, China; Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, China; National Research Center for Rehabilitation Technical Aids, Beijing, China. Electronic address:
    The periodontal ligament (PDL) is highly ordered connective tissue located between the alveolar bone and cementum. An aligned and organized architecture is required for its physiological function. We applied micropatterning technology to arrange PDL cells in 10- or 20-μm-wide extracellular protein patterns. Read More

    Extended-Depth 3D Super-Resolution Imaging Using Probe-Refresh STORM.
    Biophys J 2018 Apr;114(8):1980-1987
    Department of Chemistry, University of Washington, Seattle, Washington; Department of Physiology and Biophysics, University of Washington, Seattle, Washington. Electronic address:
    Single-molecule localization microscopy methods for super-resolution fluorescence microscopy such as STORM (stochastic optical reconstruction microscopy) are generally limited to thin three-dimensional (3D) sections (≤600 nm) because of photobleaching of molecules outside the focal plane. Although multiple focal planes may be imaged before photobleaching by focusing progressively deeper within the sample, image quality is compromised in this approach because the total number of measurable localizations is divided between detection planes. Here, we solve this problem on fixed samples by developing an imaging method that we call probe-refresh STORM (prSTORM), which allows bleached fluorophores to be straightforwardly replaced with nonbleached fluorophores. Read More

    Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance.
    Biophys J 2018 Apr;114(8):1970-1979
    Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands. Electronic address:
    Single-molecule manipulation techniques have provided unprecedented insights into the structure, function, interactions, and mechanical properties of biological macromolecules. Recently, the single-molecule toolbox has been expanded by techniques that enable measurements of rotation and torque, such as the optical torque wrench (OTW) and several different implementations of magnetic (torque) tweezers. Although systematic analyses of the position and force precision of single-molecule techniques have attracted considerable attention, their angle and torque precision have been treated in much less detail. Read More

    Dynamics of a Protein Chain Motor Driving Helical Bacteria under Stress.
    Biophys J 2018 Apr;114(8):1955-1969
    Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany. Electronic address:
    The wall-less, helical bacterial genus Spiroplasma has a unique propulsion system; it is not driven by propeller-like flagella but by a membrane-bound, cytoplasmic, linear motor that consists of a contractile chain of identical proteins spanning the entire cell length. By a coordinated spread of conformational changes of the proteins, kinks propagate in pairs along the cell body. However, the mechanisms for the initiation or delay of kinks and their coordinated spread remain unclear. Read More

    Synergism of Antimicrobial Frog Peptides Couples to Membrane Intrinsic Curvature Strain.
    Biophys J 2018 Apr;114(8):1945-1954
    Institute of Molecular Biosciences, Biophysics Division, University of Graz, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria. Electronic address:
    Mixtures of the frog peptides magainin 2 and PGLa are well-known for their pronounced synergistic killing of Gram-negative bacteria. We aimed to gain insight into the underlying biophysical mechanism by interrogating the permeabilizing efficacies of the peptides as a function of stored membrane curvature strain. For Gram-negative bacterial-inner-membrane mimics, synergism was only observed when the anionic bilayers exhibited significant negative intrinsic curvatures imposed by monounsaturated phosphatidylethanolamine. Read More

    Protein Partitioning into Ordered Membrane Domains: Insights from Simulations.
    Biophys J 2018 Apr;114(8):1936-1944
    Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas. Electronic address:
    Cellular membranes are laterally organized into domains of distinct structures and compositions by the differential interaction affinities between various membrane lipids and proteins. A prominent example of such structures are lipid rafts, which are ordered, tightly packed domains that have been widely implicated in cellular processes. The functionality of raft domains is driven by their selective recruitment of specific membrane proteins to regulate their interactions and functions; however, there have been few general insights into the factors that determine the partitioning of membrane proteins between coexisting liquid domains. Read More

    FRET Detects the Size of Nanodomains for Coexisting Liquid-Disordered and Liquid-Ordered Phases.
    Biophys J 2018 Apr;114(8):1921-1935
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York. Electronic address:
    Biomembranes with as few as three lipid components can form coexisting liquid-disordered (Ld) and liquid-ordered (Lo) phases. In the coexistence region of Ld and Lo phases, the lipid mixtures 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/chol or brain sphingomyelin (bSM)/DOPC/chol form micron-scale domains that are easily visualized with light microscopy. Although large domains are not observed in the mixtures DSPC/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/chol and bSM/POPC/chol, lateral heterogeneity is nevertheless detected using techniques with nanometer-scale spatial resolution. Read More

    Vesicle Adhesion and Fusion Studied by Small-Angle X-Ray Scattering.
    Biophys J 2018 Apr;114(8):1908-1920
    Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany. Electronic address:
    We have studied the adhesion state (also denoted by docking state) of lipid vesicles as induced by the divalent ions Ca or Mg at well-controlled ion concentration, lipid composition, and charge density. The bilayer structure and the interbilayer distance in the docking state were analyzed by small-angle x-ray scattering. A strong adhesion state was observed for DOPC:DOPS vesicles, indicating like-charge attraction resulting from ion correlations. Read More

    Lipid Configurations from Molecular Dynamics Simulations.
    Biophys J 2018 Apr;114(8):1895-1907
    MEMPHYS-Centre for Biomembrane Physics, University of Southern Denmark, Odense M, Denmark; Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany. Electronic address:
    The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. Read More

    How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein?
    Biophys J 2018 Apr;114(8):1889-1894
    Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy. Electronic address:
    The mechanism of interaction of an intrinsically disordered protein (IDP) with its physiological partner is characterized by a disorder-to-order transition in which a recognition and a binding step take place. Even if the mechanism is quite complex, IDPs tend to bind their partner in a cooperative manner such that it is generally possible to detect experimentally only the disordered unbound state and the structured complex. The interaction between the disordered C-terminal domain of the measles virus nucleoprotein (N) and the X domain (XD) of the viral phosphoprotein allows us to detect and quantify the two distinct steps of the overall reaction. Read More

    Rotation-Activated and Cooperative Zipping Characterize Class I Viral Fusion Protein Dynamics.
    Biophys J 2018 Apr;114(8):1878-1888
    Department of Physics and Astronomy; Center for Theoretical Biological Physics, Rice University, Houston, Texas. Electronic address:
    Class I viral fusion proteins are α-helical proteins that facilitate membrane fusion between viral and host membranes through large conformational transitions. Although prefusion and postfusion crystal structures have been solved for many of these proteins, details about how they transition between these states have remained elusive. This work presents the first, to our knowledge, computational survey of transitions between pre- and postfusion configurations for several class I viral fusion proteins using structure-based models to analyze their dynamics. Read More

    Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2.
    Biophys J 2018 Apr;114(8):1858-1868
    Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China. Electronic address:
    Phosphatidylinositol 4,5-bisphosphate (PIP2) acts as a signaling lipid, mediating membrane trafficking and recruitment of proteins to membranes. A key example is the PIP2-dependent regulation of the adhesion of L-selectin to the cytoskeleton adaptors of the N-terminal subdomain of ezrin-radixin-moesin (FERM). The molecular details of the mediating behavior of multivalent anionic PIP2 lipids in this process, however, remain unclear. Read More

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