Search our Database of Scientific Publications and Authors

I’m looking for a

    22147 results match your criteria Biophysical journal[Journal]

    1 OF 443

    Force Spectroscopy with 9-μs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry.
    Biophys J 2017 Nov 10. Epub 2017 Nov 10.
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado. Electronic address:
    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. Read More

    Single-Cell Defects Cause a Long-Range Mechanical Response in a Confluent Epithelial Cell Layer.
    Biophys J 2017 Nov 9. Epub 2017 Nov 9.
    Institute for Physical Chemistry, University of Göttingen, Göttingen, Germany. Electronic address:
    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. Read More

    Building Predictive Models of Genetic Circuits Using the Principle of Maximum Caliber.
    Biophys J 2017 Nov;113(9):2121-2130
    Department of Physics and Astronomy, Molecular and Cellular Biophysics, University of Denver, Denver, Colorado. Electronic address:
    Learning the underlying details of a gene network is a major challenge in cellular and synthetic biology. We address this challenge by building a chemical kinetic model that utilizes information encoded in the stochastic protein expression trajectories typically measured in experiments. The applicability of the proposed method is demonstrated in an auto-activating genetic circuit, a common motif in natural and synthetic gene networks. Read More

    Late-Arriving Signals Contribute Less to Cell-Fate Decisions.
    Biophys J 2017 Nov;113(9):2110-2120
    The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York; Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York. Electronic address:
    Gene regulatory networks are largely responsible for cellular decision-making. These networks sense diverse external signals and respond by adjusting gene expression, enabling cells to reach environment-dependent decisions crucial for their survival or reproduction. However, information-carrying signals may arrive at variable times. Read More

    Structure, Mechanics, and Instability of Fibrin Clot Infected with Staphylococcus epidermidis.
    Biophys J 2017 Nov;113(9):2100-2109
    Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan; Department of Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan. Electronic address:
    Health care-associated infection, over half of which can be attributed to indwelling medical devices, is a strong risk factor for thromboembolism. Although most experimental models of medical device infection draw upon isolated bacterial biofilms, in fact there is no infection without host protein contribution. Here we study, to our knowledge, a new model for medical device infection-that of an infected fibrin clot-and show that the common blood-borne pathogen Staphylococcus epidermidis influences this in vitro model of a blood clot mechanically and structurally on both microscopic and macroscopic scales. Read More

    Charge Influences Substrate Recognition and Self-Assembly of Hydrophobic FG Sequences.
    Biophys J 2017 Nov;113(9):2088-2099
    Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. Electronic address:
    The nuclear pore complex controls the passage of molecules via hydrophobic phenylalanine-glycine (FG) domains on nucleoporins. Such FG domains consist of repeating units of FxFG, FG, or GLFG sequences, many of which are interspersed with highly charged amino acid sequences. Despite the high density of charge in certain FG domains, if and how charge influences FG-domain self-assembly and selective binding of nuclear transport receptors is largely unexplored. Read More

    Cytoplasmic Flow and Mixing Due to Deformation of Motile Cells.
    Biophys J 2017 Nov;113(9):2077-2087
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California.
    The cytoplasm of a living cell is a dynamic environment through which intracellular components must move and mix. In motile, rapidly deforming cells such as human neutrophils, bulk cytoplasmic flow couples cell deformation to the transport and dispersion of cytoplasmic particles. Using particle-tracking measurements in live neutrophil-like cells, we demonstrate that fluid flow associated with the cell deformation contributes to the motion of small acidic organelles, dominating over diffusion on timescales above a few seconds. Read More

    Arabidopsis Leaf Trichomes as Acoustic Antennae.
    Biophys J 2017 Nov;113(9):2068-2076
    Biomedical Engineering and Biomechanics Center (BEBC), School of Life Sciences, Xi'an Jiaotong University, Xi'an, China; Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri; Gladys Levis Allen Laboratory of Plant Sensory Physiology, Biology Department, Washington University in St. Louis, St. Louis, Missouri; NSF Center for Engineering MechanoBiology, Washington University in St. Louis, St. Louis, Missouri. Electronic address:
    The much studied plant Arabidopsis thaliana has been reported recently to react to the sounds of caterpillars of Pieris rapae chewing on its leaves by promoting synthesis of toxins that can deter herbivory. Identifying participating receptor cells-potential "ears"-of Arabidopsis is critical to understanding and harnessing this response. Motivated in part by other recent observations that Arabidopsis trichomes (hair cells) respond to mechanical stimuli such as pressing or brushing by initiating potential signaling factors in themselves and in the neighboring skirt of cells, we analyzed the vibrational responses of Arabidopsis trichomes to test the hypothesis that trichomes can respond acoustically to vibrations associated with feeding caterpillars. Read More

    Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.
    Biophys J 2017 Nov;113(9):2055-2067
    The Francis Crick Institute, Imperial College London, London, United Kingdom. Electronic address:
    Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. Read More

    The Role of Probe Photophysics in Localization-Based Superresolution Microscopy.
    Biophys J 2017 Nov;113(9):2037-2054
    Department of Physics and Astronomy, University of Maine, Orono, Maine. Electronic address:
    Fluorescent proteins are used extensively for biological imaging applications; photoactivatable and photoconvertible fluorescent proteins (PAFPs) are used widely in superresolution localization microscopy methods such as fluorescence photoactivation localization microscopy and photoactivated localization microscopy. However, their optimal use depends on knowledge of not only their bulk fluorescence properties, but also their photophysical properties at the single molecule level. We have used fluorescence correlation spectroscopy and cross-correlation spectroscopy to quantify the diffusion, photobleaching, fluorescence intermittency, and photoconversion dynamics of Dendra2, a well-known PAFP used in localization microscopy. Read More

    Lysenin Toxin Membrane Insertion Is pH-Dependent but Independent of Neighboring Lysenins.
    Biophys J 2017 Nov;113(9):2029-2036
    U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France; Departments of Anesthesiology and Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Electronic address:
    Pore-forming toxins form a family of proteins that act as virulence factors of pathogenic bacteria, but similar proteins are found in all kingdoms of life, including the vertebrate immune system. They are secreted as soluble monomers that oligomerize on target membranes in the so-called prepore state; after activation, they insert into the membrane and adopt the pore state. Lysenin is a pore-forming toxin from the earthworm Eisenida foetida, of which both the soluble and membrane-inserted structures are solved. Read More

    Membrane Cholesterol Reduces Polymyxin B Nephrotoxicity in Renal Membrane Analogs.
    Biophys J 2017 Nov;113(9):2016-2028
    Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada. Electronic address:
    Polymyxin B (PmB) is a "last-line" antibiotic scarcely used due to its nephrotoxicity. However, the molecular basis for antibiotic nephrotoxicity is not clearly understood. We prepared kidney membrane analogs of detergent-susceptible membranes, depleted of cholesterol, and cholesterol enriched, resistant membranes. Read More

    Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties.
    Biophys J 2017 Nov;113(9):2004-2015
    Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York. Electronic address:
    Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). Read More

    FRET Analysis of the Promiscuous yet Specific Interactions of the HIV-1 Vpu Transmembrane Domain.
    Biophys J 2017 Nov;113(9):1992-2003
    Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. Electronic address:
    The Vpu protein of HIV-1 functions to downregulate cell surface localization of host proteins involved in the innate immune response to viral infection. For several target proteins, including the NTB-A and PVR receptors and the host restriction factor tetherin, this antagonism is carried out via direct interactions between the transmembrane domains (TMDs) of Vpu and the target. The Vpu TMD also modulates homooligomerization of this protein, and the tetherin TMD forms homodimers. Read More

    The Fast Component of hERG Gating Charge: An Interaction between D411 in the S1 and S4 Residues.
    Biophys J 2017 Nov;113(9):1979-1991
    Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address:
    Kv11.1 (hERG) is a voltage-gated potassium channel that shows very slow ionic current activation kinetics, and an unusual underlying biphasic gating charge movement with fast and slow components that differ greatly in time course. The structural basis and role of the fast component of gating charge (Qfast) is unclear, and its relationship to the slow activation of hERG channels is not understood. Read More

    Sparse Labeling PELDOR Spectroscopy on Multimeric Mechanosensitive Membrane Channels.
    Biophys J 2017 Nov;113(9):1968-1978
    Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom. Electronic address:
    Pulse electron paramagnetic resonance (EPR) is being applied to ever more complex biological systems comprising multiple subunits. Membrane channel proteins are of great interest as pulse EPR reports on functionally significant but distinct conformational states in a native environment without the need for crystallization. Pulse EPR, in the form of pulsed electron-electron double resonance (PELDOR), using site-directed spin labeling, is most commonly employed to accurately determine distances (in the nanometer range) between different regions of the structure. Read More

    Phosphorylated Calmodulin Promotes PI3K Activation by Binding to the SH2 Domains.
    Biophys J 2017 Nov;113(9):1956-1967
    Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel. Electronic address:
    How calmodulin (CaM) acts in KRAS-driven cancers is a vastly important question. CaM binds to and stimulates PI3Kα/Akt signaling, promoting cell growth and proliferation. Phosphorylation of CaM at Tyr(99) (pY99) enhances PI3Kα activation. Read More

    High Tensile Strength of Engineered β-Solenoid Fibrils via Sonication and Pulling.
    Biophys J 2017 Nov;113(9):1945-1955
    Department of Chemistry, University of California, Davis, Davis, California.
    We present estimates of ultimate tensile strength (UTS) for two engineered β-solenoid protein mutant fibril structures (spruce budworm and Rhagium inquisitor antifreeze proteins) derived from sonication-based measurements and from force pulling molecular dynamics simulations, both in water. Sonication experiments generate limiting scissioned fibrils with a well-defined length-to-width correlation for the mutant spruce budworm protein and the resultant UTS estimate is 0.66 ± 0. Read More

    Protein Sequence and Membrane Lipid Roles in the Activation Kinetics of Bovine and Human Rhodopsins.
    Biophys J 2017 Nov;113(9):1934-1944
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California. Electronic address:
    Rhodopsin is a G protein-coupled receptor found in the rod outer segments in the retina, which triggers a visual response under dim light conditions. Recently, a study of the late, microsecond-to-millisecond kinetics of photointermediates of the human and bovine rhodopsins in their native membranes revealed a complex, double-square mechanism of rhodopsin activation. In this kinetic scheme, the human rhodopsin exhibited more Schiff base deprotonation than bovine rhodopsin, which could arise from the ∼7% sequence difference between the two proteins, or from the difference between their membrane lipid environments. Read More

    Role of Disulfide Bonds on DNA Packaging Forces in Bull Sperm Chromatin.
    Biophys J 2017 Nov;113(9):1925-1933
    Department of Chemistry, University of Kentucky, Lexington, Kentucky. Electronic address:
    Short arginine-rich proteins called protamines mediate the near crystalline DNA packaging in most vertebrate sperm cells. Protamines are synthesized during spermiogenesis and condense the paternal genome into a transcriptionally inactive state in late-stage spermatids. Protamines from eutherian mammals, including bulls and humans, also contain multiple cysteine residues that form intra- and interprotamine sulfur-sulfur bonds during the final stages of sperm maturation. Read More

    Computational Lipidomics of the Neuronal Plasma Membrane.
    Biophys J 2017 Nov 4. Epub 2017 Nov 4.
    Biosciences and Biotechnology Division, Physical and Life Sciences Directorate. Electronic address:
    Membrane lipid composition varies greatly within submembrane compartments, different organelle membranes, and also between cells of different cell stage, cell and tissue types, and organisms. Environmental factors (such as diet) also influence membrane composition. The membrane lipid composition is tightly regulated by the cell, maintaining a homeostasis that, if disrupted, can impair cell function and lead to disease. Read More

    Drift and Behavior of E. coli Cells.
    Biophys J 2017 Oct 27. Epub 2017 Oct 27.
    Department of Life Sciences, Imperial College, London, United Kingdom; Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom. Electronic address:
    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. Read More

    Biophysical Characterization of Genetically Encoded Voltage Sensor ASAP1: Dynamic Range Improvement.
    Biophys J 2017 Nov 3. Epub 2017 Nov 3.
    Committee on Neurobiology, University of Chicago, Chicago, Illinois; Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois. Electronic address:
    Recent work has introduced a new fluorescent voltage sensor, ASAP1, which can monitor rapid trains of action potentials in cultured neurons. This indicator is based on the Gallus gallus voltage-sensitive phosphatase with the phosphatase domain removed and a circularly permuted GFP placed in the S3-S4 linker. However, many of the biophysical details of this indicator remain unknown. Read More

    Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure.
    Biophys J 2017 Nov 3. Epub 2017 Nov 3.
    LCRB, UMR 8015 CNRS Université Paris Descartes, Paris, France.
    Internal cavities are crucial for conformational flexibility of proteins and can be mapped through noble gas diffusion and docking. Here we investigate the hydrophobic cavities and tunnel network in neuroglobin (Ngb), a hexacoordinated heme protein likely to be involved in neuroprotection, using crystallography under noble gas pressure, mostly at room temperature. In murine Ngb, a large internal cavity is involved in the heme sliding mechanism to achieve binding of gaseous ligands through coordination to the heme iron. Read More

    Voltage and Calcium Imaging of Brain Activity.
    Biophys J 2017 Nov 1. Epub 2017 Nov 1.
    Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea; NeuroImaging Cluster, Marine Biological Laboratory, Woods Hole, Massachusetts.
    Sensors for imaging brain activity have been under development for almost 50 years. The development of some of these tools is relatively mature, whereas qualitative improvements of others are needed and are actively pursued. In particular, genetically encoded voltage indicators are just now starting to be used to answer neurobiological questions and, at the same time, more than 10 laboratories are working to improve them. Read More

    Single Molecule Imaging of Proteoglycans in the Pericellular Matrix.
    Biophys J 2017 Oct 25. Epub 2017 Oct 25.
    School of Physics, Georgia Institute of Technology, Atlanta, Georgia; Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia.
    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. Read More

    Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-native Affinity.
    Biophys J 2017 Oct 20. Epub 2017 Oct 20.
    Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no. 7565, Université de Lorraine, Vandœuvre-lès-Nancy, France; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois. Electronic address:
    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. Read More

    Untangling the Hairball: Fitness-Based Asymptotic Reduction of Biological Networks.
    Biophys J 2017 Oct;113(8):1893-1906
    Ernest Rutherford Physics Building, McGill University, Montreal, Québec, Canada. Electronic address:
    Complex mathematical models of interaction networks are routinely used for prediction in systems biology. However, it is difficult to reconcile network complexities with a formal understanding of their behavior. Here, we propose a simple procedure (called ϕ¯) to reduce biological models to functional submodules, using statistical mechanics of complex systems combined with a fitness-based approach inspired by in silico evolution. Read More

    Confocal Rheology Probes the Structure and Mechanics of Collagen through the Sol-Gel Transition.
    Biophys J 2017 Oct;113(8):1882-1892
    Department of Chemistry, Columbia University, New York, New York. Electronic address:
    Fibrillar type I collagen-based hydrogels are commonly used in tissue engineering and as matrices for biophysical studies. Mechanical and structural properties of these gels are known to be governed by the conditions under which fibrillogenesis occurs, exhibiting variation as a function of protein concentration, temperature, pH, and ionic strength. Deeper understanding of how macroscopic structure affects viscoelastic properties of collagen gels over the course of fibrillogenesis provides fundamental insight into biopolymer gel properties and promises enhanced control over the properties of such gels. Read More

    A Model for Link Pruning to Establish Correctly Polarized and Oriented Tip Links in Hair Bundles.
    Biophys J 2017 Oct;113(8):1868-1881
    Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, Oregon. Electronic address:
    Tip links are thought to gate the mechanically sensitive transduction channels of hair cells, but how they form during development and regeneration remains mysterious. In particular, it is unclear how tip links are strung between stereocilia so that they are oriented parallel to a single axis; why their polarity is uniform despite their constituent molecules' intrinsic asymmetry; and why only a single tip link is present at each tip-link position. We present here a series of simple rules that reasonably explain why these phenomena occur. Read More

    Probing Cell Adhesion Profiles with a Microscale Adhesive Choice Assay.
    Biophys J 2017 Oct;113(8):1858-1867
    University of California Los Angeles, Los Angeles, California; California NanoSystems Institute, Los Angeles, California; Jonsson Comprehensive Cancer Center, Los Angeles, California. Electronic address:
    In this work, we introduce, to our knowledge, a new set of adhesion-based biomarkers for characterizing mammalian cells. Mammalian cell adhesion to the extracellular matrix influences numerous physiological processes. Current in vitro methods to probe adhesion focus on adhesive force to a single surface, which can investigate only a subcomponent of the adhesive, motility, and polarization cues responsible for adhesion in the 3D tissue environment. Read More

    Homodimeric Kinesin-2 KIF3CC Promotes Microtubule Dynamics.
    Biophys J 2017 Oct;113(8):1845-1857
    Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York. Electronic address:
    KIF3C is one subunit of the functional microtubule-based kinesin-2 KIF3AC motor, an anterograde cargo transporter in neurons. However, KIF3C has also been implicated as an injury-specific kinesin that is a key regulator of axonal growth and regeneration by promoting microtubule dynamics for reorganization at the neuronal growth cone. To test its potential role as a modulator of microtubule dynamics in vitro, an engineered homodimeric KIF3CC was incorporated into a dynamic microtubule assay and examined by total internal reflection fluorescence microscopy. Read More

    Self-Organization of FtsZ Polymers in Solution Reveals Spacer Role of the Disordered C-Terminal Tail.
    Biophys J 2017 Oct;113(8):1831-1844
    Centro de Investigaciones Biológicas, CSIC, Madrid, Spain. Electronic address:
    FtsZ is a self-assembling GTPase that forms, below the inner membrane, the mid-cell Z-ring guiding bacterial division. FtsZ monomers polymerize head to tail forming tubulin-like dynamic protofilaments, whose organization in the Z-ring is an unresolved problem. Rather than forming a well-defined structure, FtsZ protofilaments laterally associate in vitro into polymorphic condensates typically imaged on surfaces. Read More

    Elastic Properties of Pore-Spanning Apical Cell Membranes Derived from MDCK II Cells.
    Biophys J 2017 Oct;113(8):1822-1830
    Georg-August-Universität Göttingen, Institute of Physical Chemistry, Göttingen, Germany. Electronic address:
    The mechanical response of adherent, polarized cells to indentation is frequently attributed to the presence of an endogenous actin cortex attached to the inner leaflet of the plasma membrane. Here, we scrutinized the elastic properties of apical membranes separated from living cells and attached to a porous mesh in the absence of intracellular factors originating from the cytosol, organelles, the substrate, neighbors, and the nucleus. We found that a tension-based model describes the data very well providing essentially the prestress of the shell generated by adhesion of the apical membrane patches to the pore rim and the apparent area compressibility modulus, an intrinsic elastic modulus modulated by the surface excess stored in membrane reservoirs. Read More

    The Effect of Solutes on the Temperature of Miscibility Transitions in Multicomponent Membranes.
    Biophys J 2017 Oct;113(8):1814-1821
    Department of Physics, University of Washington, Seattle, Washington. Electronic address:
    We address questions posed by experiments that show small-chain alcohols reduce the miscibility transition temperature when added to giant plasma membrane vesicles (GPMVs), but increase that temperature when added to giant unilamellar vesicles. In giant unilamellar vesicles the change in temperature displays a definite minimum, between decanol and tetradecanol, as a function of alcohol chain length; in GPMVs there is no such minimum. To emphasize the competition between internal entropies of the components and the interactions between them, we model the system as consisting of three different linear polymers. Read More

    Dynamic Scaling Analysis of Molecular Motion within the LAT:Grb2:SOS Protein Network on Membranes.
    Biophys J 2017 Oct;113(8):1807-1813
    Department of Chemistry, University of California, Berkeley, Berkeley, California. Electronic address:
    Biochemical signaling pathways often involve proteins with multiple, modular interaction domains. Signaling activates binding sites, such as by tyrosine phosphorylation, which enables protein recruitment and growth of networked protein assemblies. Although widely observed, the physical properties of the assemblies, as well as the mechanisms by which they function, remain largely unknown. Read More

    Nanoscale Membrane Budding Induced by CTxB and Detected via Polarized Localization Microscopy.
    Biophys J 2017 Oct;113(8):1795-1806
    Department of Physics and Astronomy, Wayne State University, Detroit, Michigan. Electronic address:
    For endocytosis and exocytosis, membranes transition among planar, budding, and vesicular topographies through nanoscale reorganization of lipids, proteins, and carbohydrates. However, prior attempts to understand the initial stages of nanoscale bending have been limited by experimental resolution. Through the implementation of polarized localization microscopy, this article reports the inherent membrane bending capability of cholera toxin subunit B (CTxB) in quasi-one-component-supported lipid bilayers. Read More

    The Detection of Nanoscale Membrane Bending with Polarized Localization Microscopy.
    Biophys J 2017 Oct;113(8):1782-1794
    Department of Physics and Astronomy, Wayne State University, Detroit, Michigan. Electronic address:
    The curvature of biological membranes at the nanometer scale is critically important for vesicle trafficking, organelle morphology, and disease propagation. The initiation of membrane bending occurs at a length scale that is irresolvable by most superresolution optical microscopy methods. Here, we report the development of polarized localization microscopy (PLM), a pointillist optical imaging technique for the detection of nanoscale membrane curvature in correlation with single-molecule dynamics and molecular sorting. Read More

    Mapping Cell Membrane Fluctuations Reveals Their Active Regulation and Transient Heterogeneities.
    Biophys J 2017 Oct;113(8):1768-1781
    Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, India. Electronic address:
    Shape fluctuations of the plasma membrane occur in all cells, are incessant, and are proposed to affect membrane functioning. Although studies show how membrane fluctuations are affected by cellular activity in adherent cells, their spatial regulation and the corresponding change in membrane mechanics remain unclear. In this article, we study how ATP-driven activities and actomyosin cytoskeleton impact basal membrane fluctuations in adherent cells. Read More

    Exchange of Gramicidin between Lipid Bilayers: Implications for the Mechanism of Channel Formation.
    Biophys J 2017 Oct;113(8):1757-1767
    Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Electronic address:
    The canonical mechanism of gramicidin (gA) channel formation is transmembrane dimerization of nonconducting subunits that reside in opposite bilayer leaflets. The channels do not open and close; they appear and disappear due to subunit association and dissociation. Many different types of experiments support this monomer ↔ dimer mechanism. Read More

    Metastability Gap in the Phase Diagram of Monoclonal IgG Antibody.
    Biophys J 2017 Oct;113(8):1750-1756
    Department of Chemistry and Biochemistry, University of North Carolina at Wilmington, Wilmington, North Carolina. Electronic address:
    Crystallization of IgG antibodies has important applications in the fields of structural biology, biotechnology, and biopharmaceutics. However, a rational approach to crystallize antibodies is still lacking. In this work, we report a method to estimate the solubility of antibodies at various temperatures. Read More

    Identification and Characterization of an Inside-Out Folding Intermediate of T4 Phage Sliding Clamp.
    Biophys J 2017 Oct;113(8):1738-1749
    Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India. Electronic address:
    Protein folding process involves formation of transiently occurring intermediates that are difficult to isolate and characterize. It is both necessary and interesting to characterize the structural conformations adopted by these intermediates, also called molten globules (MG), to understand protein folding. Here, we investigated the equilibrium (un)folding intermediate state of T4 phage gene product 45 (gp45, also known as DNA polymerase processivity factor or sliding clamp) obtained during chemical denaturation. Read More

    Enzyme-Triggered Dissociation of a FRET-Based Protein Biosensor Monitored by Synchrotron SAXS.
    Biophys J 2017 Oct;113(8):1731-1737
    Laboratory for Biointerfaces, Department "Materials Meet Life", Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland. Electronic address:
    Protein biosensors are widely used for the monitoring of metabolite concentration and enzymatic activities inside living cells and in in vitro applications. Neutrophil elastase (NE) is a serine protease of relevance in inflammatory diseases whose activity can lead to pathological conditions if unregulated. This study focuses on the structural characterization of a biosensor for NE activity based on Förster resonance energy transfer (FRET). Read More

    How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis.
    Biophys J 2017 Oct;113(8):1719-1730
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland. Electronic address:
    Quantifying the relationship between protein sequence and structure is key to understanding the protein universe. A fundamental measure of this relationship is the total number of amino acid sequences that can fold to a target protein structure, known as the "sequence capacity," which has been suggested as a proxy for how designable a given protein fold is. Although sequence capacity has been extensively studied using lattice models and theory, numerical estimates for real protein structures are currently lacking. Read More

    Cooperative Nucleotide Binding in Hsp90 and Its Regulation by Aha1.
    Biophys J 2017 Oct;113(8):1711-1718
    Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany. Electronic address:
    The function of the molecular chaperone Hsp90 depends on large conformational changes, the rearrangement of local motifs, and the binding and hydrolysis of ATP. The size and complexity of the Hsp90 system impedes the detailed investigation of their interplay using standard methods. To overcome this limitation, we developed a three-color single-molecule FRET assay to study the interaction of Hsp90 with a fluorescently labeled reporter nucleotide in detail. Read More

    Molecular Simulations Suggest a Force-Dependent Mechanism of Vinculin Activation.
    Biophys J 2017 Oct;113(8):1697-1710
    Center for Theoretical Biological Physics, Rice University, Houston, Texas. Electronic address:
    Focal adhesions are dynamic constructs at the leading edge of migrating cells, linking them to the extracellular matrix and enabling force sensing and transmission. The lifecycle of a focal adhesion is a highly coordinated process involving spatial and temporal variations of protein composition, interaction, and cellular tension. The assembly of focal adhesions requires the recruitment and activation of vinculin. Read More

    High-Pressure-Driven Reversible Dissociation of α-Synuclein Fibrils Reveals Structural Hierarchy.
    Biophys J 2017 Oct;113(8):1685-1696
    Department of Biology, University of Padova, Padova, Italy. Electronic address:
    The analysis of the α-synuclein (aS) aggregation process, which is involved in Parkinson's disease etiopathogenesis, and of the structural feature of the resulting amyloid fibrils may shed light on the relationship between the structure of aS aggregates and their toxicity. This may be considered a paradigm of the ground work needed to tackle the molecular basis of all the protein-aggregation-related diseases. With this aim, we used chemical and physical dissociation methods to explore the structural organization of wild-type aS fibrils. Read More

    1 OF 443