22,899 results match your criteria Biophysical journal[Journal]


A Crucial Role for Side-Chain Conformation in the Versatile Charge Selectivity of Cys-Loop Receptors.

Biophys J 2019 Apr 2. Epub 2019 Apr 2.

Center for Biophysics and Quantitative Biology, Urbana, Illinois; Department of Molecular and Integrative Physiology, Urbana, Illinois; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois. Electronic address:

Whether synaptic transmission is excitatory or inhibitory depends, to a large extent, on whether the ion channels that open upon binding the released neurotransmitter conduct cations or anions. The mechanistic basis of the opposite charge selectivities of Cys-loop receptors has only recently begun to emerge. It is now clear that ionized side chains-whether pore-facing or buried-in the first α-helical turn of the second transmembrane segments underlie this phenomenon and that the electrostatics of backbone atoms are not critically involved. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.022DOI Listing
April 2019
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The Oligomerization Landscape of Histones.

Biophys J 2019 Apr 17. Epub 2019 Apr 17.

Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Chemical Physics Program, Institute for Physical Science and Technology; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland. Electronic address:

In eukaryotes, DNA is packaged within nucleosomes. The DNA of each nucleosome is typically centered around an octameric histone protein core: one central tetramer plus two separate dimers. Studying the assembly mechanisms of histones is essential for understanding the dynamics of entire nucleosomes and higher-order DNA packaging. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.021DOI Listing

Allostery in Coagulation Factor VIIa Revealed by Ensemble Refinement of Crystallographic Structures.

Biophys J 2019 Apr 2. Epub 2019 Apr 2.

Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark. Electronic address:

A critical step in injury-induced initiation of blood coagulation is the formation of the complex between the trypsin-like protease coagulation factor VIIa (FVIIa) and its cofactor tissue factor (TF), which converts FVIIa from an intrinsically poor enzyme to an active protease capable of activating zymogens of downstream coagulation proteases. Unlike its constitutively active ancestor trypsin, FVIIa is allosterically activated (by TF). Here, ensemble refinement of crystallographic structures, which uses multiple copies of the entire structure as a means of representing structural flexibility, is applied to explore the impacts of inhibitor binding to trypsin and FVIIa, as well as cofactor binding to FVIIa. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.024DOI Listing

Dynamics Properties of Photosynthetic Microorganisms Probed by Incoherent Neutron Scattering.

Biophys J 2019 Apr 2. Epub 2019 Apr 2.

CNR Istituto di Cristallografia, Monterotondo Stazione, Rome, Italy.

Studies on the dynamical properties of photosynthetic membranes of land plants and purple bacteria have been previously performed by neutron spectroscopy, revealing a tight coupling between specific photochemical reactions and macromolecular dynamics. Here, we probed the intrinsic dynamics of biotechnologically useful mutants of the green alga Chlamydomonas reinhardtii by incoherent neutron scattering coupled with prompt chlorophyll fluorescence experiments. We brought to light that single amino acid replacements in the plastoquinone (PQ)-binding niche of the photosystem II D1 protein impair electron transport (ET) efficiency between quinones and confer increased flexibility to the host membranes, expanding to the entire cells. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.029DOI Listing

Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane.

Biophys J 2019 Mar 19. Epub 2019 Mar 19.

Department of Chemistry, The University of Texas at Austin, Austin, Texas. Electronic address:

Transmembrane peptides contain polar residues in the interior of the membrane, which may alter the electrostatic environment and favor hydration in the otherwise nonpolar environment of the membrane core. Here, we demonstrate a general, nonperturbative strategy to probe hydration of the peptide backbone at specific depths within the bilayer using a combination of site-specific isotope labels, ultrafast two-dimensional infrared spectroscopy, and spectral modeling based on molecular dynamics simulations. Our results show that the amphiphilic pH-low insertion peptide supports a highly heterogeneous environment, with significant backbone hydration of nonpolar residues neighboring charged residues. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.002DOI Listing
March 2019
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Adaptation of Cochlear Amplification to Low Endocochlear Potential.

Biophys J 2019 Mar 30. Epub 2019 Mar 30.

Biomedical Engineering, Columbia University, New York, New York; Otalaryngology/Head & Neck Surgery, Columbia University, New York, New York. Electronic address:

Endocochlear potential (EP) is essential for cochlear amplification by providing the voltage source needed to drive outer hair cell (OHC) transducer current, which leads to OHC electromechanical force. An early study using furosemide to reversibly reduce EP showed that distortion product otoacoustic emissions (DPOAEs) recovered before EP. This indicated that cochlear amplification may be able to adjust to a new, lower EP. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.020DOI Listing
March 2019
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Shear-Induced Migration of a Transmembrane Protein within a Vesicle.

Biophys J 2019 Mar 28. Epub 2019 Mar 28.

Department of Finemechanics, Tohoku University, Sendai, Miyagi, Japan.

Biomembranes feature phospholipid bilayers and serve as the interface between cells or organelles and the extracellular and/or cellular environment. Lipids can move freely throughout the membrane; the lipid bilayer behaves like a fluid. Such fluidity is important in terms of the actions of membrane transport proteins, which often mediate biological functions; membrane protein motion has attracted a great deal of attention. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.017DOI Listing

A Matched-Filter-Based Algorithm for Subcellular Classification of T-System in Cardiac Tissues.

Biophys J 2019 Mar 22. Epub 2019 Mar 22.

Department of Chemistry, University of Kentucky, Lexington, Kentucky; Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky.

In mammalian ventricular cardiomyocytes, invaginations of the surface membrane form the transverse tubular system (T-system), which consists of transverse tubules (TTs) that align with sarcomeres and Z-lines as well as longitudinal tubules (LTs) that are present between Z-lines in some species. In many cardiac disease etiologies, the T-system is perturbed, which is believed to promote spatially heterogeneous, dyssynchronous Ca release and inefficient contraction. In general, T-system characterization approaches have been directed primarily at isolated cells and do not detect subcellular T-system heterogeneity. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.010DOI Listing
March 2019
3 Reads

Active Transport of Membrane Components by Self-Organization of the Min Proteins.

Biophys J 2019 Mar 23. Epub 2019 Mar 23.

Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan. Electronic address:

Heterogeneous distribution of components in the biological membrane is critical in the process of cell polarization. However, little is known about the mechanisms that can generate and maintain the heterogeneous distribution of the membrane components. Here, we report that the propagating wave patterns of the bacterial Min proteins can impose steric pressure on the membrane, resulting in transport and directional accumulation of the component in the membrane. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.011DOI Listing
March 2019
2 Reads

Cholesterol Depletion by MβCD Enhances Cell Membrane Tension and Its Variations-Reducing Integrity.

Biophys J 2019 Mar 28. Epub 2019 Mar 28.

Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India. Electronic address:

Cholesterol depletion by methyl-β-cyclodextrin (MβCD) remodels the plasma membrane's mechanics in cells and its interactions with the underlying cytoskeleton, whereas in red blood cells, it is also known to cause lysis. Currently it's unclear if MβCD alters membrane tension or only enhances membrane-cytoskeleton interactions-and how this relates to cell lysis. We map membrane height fluctuations in single cells and observe that MβCD reduces temporal fluctuations robustly but flattens spatial membrane undulations only slightly. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.016DOI Listing

Nanobody-CD16 Catch Bond Reveals NK Cell Mechanosensitivity.

Biophys J 2019 Mar 23. Epub 2019 Mar 23.

Aix Marseille Univ, CNRS, INSERM, LAI, Laboratoire Adhesion et Inflammation, Marseille, France. Electronic address:

Antibodies are key tools in biomedical research and medicine. Their binding properties are classically measured in solution and characterized by an affinity. However, in physiological conditions, antibodies can bridge an immune effector cell and an antigen-presenting cell, implying that mechanical forces may apply to the bonds. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.012DOI Listing

A Biomechanical Model of Tumor-induced Intracranial Pressure and Edema in Brain Tissue.

Biophys J 2019 Mar 23. Epub 2019 Mar 23.

Department of Mathematics, Florida State University, Tallahassee, Florida. Electronic address:

Brain tumor growth and tumor-induced edema result in increased intracranial pressure (ICP), which, in turn, is responsible for conditions as benign as headaches and vomiting or as severe as seizures, neurological damage, or even death. Therefore, it has been hypothesized that tracking ICP dynamics may offer improved prognostic potential in terms of early detection of brain cancer and better delimitation of the tumor boundary. However, translating such theory into clinical practice remains a challenge, in part because of an incomplete understanding of how ICP correlates with tumor grade. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00063495193020
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http://dx.doi.org/10.1016/j.bpj.2019.02.030DOI Listing
March 2019
2 Reads

Thermodynamic Stability of the Transcription Regulator PaaR2 from Escherichia coli O157:H7.

Biophys J 2019 Mar 28. Epub 2019 Mar 28.

Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium. Electronic address:

PaaR2 is a putative transcription regulator encoded by a three-component parDE-like toxin-antitoxin module from Escherichia coli O157:H7. Although this module's toxin, antitoxin, and toxin-antitoxin complex have been more thoroughly investigated, little remains known about its transcription regulator PaaR2. Using a wide range of biophysical techniques (circular dichroism spectroscopy, size-exclusion chromatography-multiangle laser light scattering, dynamic light scattering, small-angle x-ray scattering, and native mass spectrometry), we demonstrate that PaaR2 mainly consists of α-helices and displays a concentration-dependent octameric build-up in solution and that this octamer contains a global shape that is significantly nonspherical. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.015DOI Listing
March 2019
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Measuring the Permeability of Endothelial Cell Monolayers: Teaching New Tricks to an Old Dog.

Authors:
Joachim Wegener

Biophys J 2019 Mar 28. Epub 2019 Mar 28.

Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Regensburg, Germany; Fraunhofer Research Institution for Microsystems and Solid State Technologies EMFT, Munich, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2019.03.018DOI Listing

Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model.

Biophys J 2019 Mar 21. Epub 2019 Mar 21.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan. Electronic address:

The binding interactions of small nuclear RNAs (snRNA) and the associated protein factors are critical to the function of spliceosomes in alternatively splicing primary RNA transcripts. Although molecular dynamics simulations are a powerful tool to interpret the mechanism of biological processes, the atomic-level simulations are, however, too expensive and with limited accuracy for the large-size systems, such as snRNA-protein complexes. We extend the coarse-grained Gaussian network model, which models the RNA-protein complexes as a harmonic chain of Cα, P, and O4' atoms, to investigating the impact of the snRNA-binding interaction on the dynamic stability of the human U1A protein, which is a major component of the spliceosomal U1 small nuclear ribonucleoprotein particle. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.008DOI Listing
March 2019
2 Reads

Multiple CheY Homologs Control Swimming Reversals and Transient Pauses in Azospirillum brasilense.

Biophys J 2019 Mar 21. Epub 2019 Mar 21.

Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee. Electronic address:

Chemotaxis, together with motility, helps bacteria foraging in their habitat. Motile bacteria exhibit a variety of motility patterns, often controlled by chemotaxis, to promote dispersal. Motility in many bacteria is powered by a bidirectional flagellar motor. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.006DOI Listing

Molecular Dynamics Simulations of Molecules in Uniform Flow.

Biophys J 2019 Feb 8. Epub 2019 Feb 8.

Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, Heidelberg University, Mathematikon, Heidelberg, Germany. Electronic address:

Flow at the molecular level induces shear-induced unfolding of single proteins and can drive their assembly, the mechanisms of which are not completely understood. To be able to analyze the role of flow on molecules, we present uniform-flow molecular dynamics simulations at atomic level. The pull module of the GRoningen MAchine for Chemical Simulations package was extended to be able to force-group atoms within a defined layer of the simulation box. Read More

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http://dx.doi.org/10.1016/j.bpj.2018.12.025DOI Listing
February 2019

Rad54 Phosphorylation Promotes Homologous Recombination by Balancing Rad54 Mobility and DNA Binding.

Biophys J 2019 Mar 19. Epub 2019 Mar 19.

Institute for Condensed Matter Physics, Darmstadt University of Technology, Darmstadt, Germany.

The repair of DNA double-strand breaks by homologous recombination is of crucial importance for maintaining genomic stability. Two major players during this repair pathway are Rad51 and Rad54. Previously, it was shown that Rad54 exists as a monomer or oligomer when bound to DNA and drives the displacement of Rad51 by translocating along the DNA. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.001DOI Listing

Conformational Dynamics of the HIV-Vif Protein Complex.

Biophys J 2019 Mar 23. Epub 2019 Mar 23.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California. Electronic address:

Human immunodeficiency virus-1 viral infectivity factor (Vif) is an intrinsically disordered protein responsible for the ubiquitination of the APOBEC3 (A3) antiviral proteins. Vif folds when it binds Cullin-RING E3 ligase 5 and the transcription cofactor CBF-β. A five-protein complex containing the substrate receptor (Vif, CBF-β, Elongin-B, Elongin-C (VCBC)) and Cullin5 (CUL5) has a published crystal structure, but dynamics of this VCBC-CUL5 complex have not been characterized. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.014DOI Listing

Phosphatidylserine Asymmetry Promotes the Membrane Insertion of a Transmembrane Helix.

Biophys J 2019 Mar 19. Epub 2019 Mar 19.

Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee. Electronic address:

The plasma membrane (PM) contains an asymmetric distribution of lipids between the inner and outer bilayer leaflets. A lipid of special interest in eukaryotic membranes is the negatively charged phosphatidylserine (PS). In healthy cells, PS is actively sequestered to the inner leaflet of the PM, but PS redistributes to the outer leaflet when the cell is damaged or at the onset of apoptosis. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.003DOI Listing

Subdiffusive Dynamics Lead to Depleted Particle Densities near Cellular Borders.

Authors:
William R Holmes

Biophys J 2019 Feb 28. Epub 2019 Feb 28.

Department of Pysics and Astronomy, Vanderbilt University, Nashville, Tennessee; Department of Mathematics, Vanderbilt University, Nashville, Tennessee; Quantitative Systems Biology Center, Vanderbilt University, Nashville, Tennessee. Electronic address:

It has long been known that the complex cellular environment leads to anomalous motion of intracellular particles. At a gross level, this is characterized by mean-squared displacements that deviate from the standard linear profile. Statistical analysis of particle trajectories has helped further elucidate how different characteristics of the cellular environment can introduce different types of anomalousness. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.021DOI Listing
February 2019
11 Reads

Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA.

Biophys J 2019 Mar 19. Epub 2019 Mar 19.

Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany. Electronic address:

DNA intercalators bind nucleic acids by stacking between adjacent basepairs. This causes a considerable elongation of the DNA backbone as well as untwisting of the double helix. In the past few years, single-molecule mechanical experiments have become a common tool to characterize these deformations and to quantify important parameters of the intercalation process. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.005DOI Listing
March 2019
1 Read

Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes.

Biophys J 2019 Mar 22. Epub 2019 Mar 22.

Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Material, University of Groningen, Groningen, The Netherlands. Electronic address:

Plant light-harvesting complex II (LHCII) is the key antenna complex for plant photosynthesis. We present coarse-grained molecular dynamics simulations of monomeric and trimeric LHCII in a realistic thylakoid membrane environment based on the Martini force field. The coarse-grained protein model has been optimized with respect to atomistic reference simulations. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.009DOI Listing
March 2019
3 Reads

AAA+ Protein-Based Technologies to Counter Neurodegenerative Disease.

Biophys J 2019 Mar 22. Epub 2019 Mar 22.

Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Electronic address:

Protein misfolding and overloaded proteostasis networks underlie a range of neurodegenerative diseases. No cures exist for these diseases, but developing effective therapeutic agents targeting the toxic, misfolded protein species in disease is one promising strategy. AAA+ (ATPases associated with diverse cellular activities) protein translocases, which naturally unfold and translocate substrate proteins, could be potent therapeutic agents to disassemble toxic protein conformers in neurodegenerative disease. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00063495193019
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http://dx.doi.org/10.1016/j.bpj.2019.03.007DOI Listing
March 2019
3 Reads

Nonlamellar-Phase-Promoting Colipids Enhance Segregation of Palmitoyl Ceramide in Fluid Bilayers.

Biophys J 2019 Mar 19. Epub 2019 Mar 19.

Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland. Electronic address:

Ceramide is an important intermediate in sphingolipid homeostasis. We examined how colipids, with negative intrinsic curvature and which may induce curvature stress in the bilayers, affected the segregation of palmitoyl ceramide (PCer). Such colipids include 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), and tetra-linoleoyl cardiolipin (CL). Read More

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http://dx.doi.org/10.1016/j.bpj.2019.03.004DOI Listing

Sliding Mechanism at a Coiled-Coil Interface.

Biophys J 2019 Apr 7;116(7):1228-1238. Epub 2019 Mar 7.

Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel. Electronic address:

The α-helical coiled coil (CC) is a common protein motif that because of the simplicity of its sequence/structure relationship, it has been studied extensively to address fundamental questions in protein science as well as to develop strategies for designing protein with novel architectures. Nevertheless, a complete understanding of CC structures and their dynamics is still far from achieved. Particularly, spontaneous sliding at interfaces of CC proteins was observed for some systems, but its mechanism and usage as an intrinsic conformational change at CCs in protein-protein interfaces is unclear. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451045PMC

Membrane Morphologies Induced by Arc-Shaped Scaffolds Are Determined by Arc Angle and Coverage.

Biophys J 2019 Apr 26;116(7):1239-1247. Epub 2019 Feb 26.

Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany. Electronic address:

The intricate shapes of biological membranes such as tubules and membrane stacks are induced by proteins. In this article, we systematically investigate the membrane shapes induced by arc-shaped scaffolds such as proteins and protein complexes with coarse-grained modeling and simulations. We find that arc-shaped scaffolds induce membrane tubules at membrane coverages larger than a threshold of ∼40%, irrespective of their arc angle. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451037PMC

The Role of Cohesiveness in the Permeability of the Spatial Assemblies of FG Nucleoporins.

Biophys J 2019 Apr 7;116(7):1204-1215. Epub 2019 Mar 7.

Department of Physics, University of Toronto, Toronto, Ontario, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada. Electronic address:

Nuclear pore complexes (NPCs) conduct selective, bidirectional transport across the nuclear envelope. The NPC passageway is lined by intrinsically disordered proteins that contain hydrophobic phenylalanine-glycine (FG) motifs, known as FG nucleoporins (FG nups), that play the key role in the NPC transport mechanism. Cohesive interactions among the FG nups, which arise from the combination of hydrophobic, electrostatic, and other forces, have been hypothesized to control the morphology of the assemblies of FG nups in the NPC, as well as their permeability with respect to the transport proteins. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451056PMC

Breast Cancer Cells Adapt Contractile Forces to Overcome Steric Hindrance.

Biophys J 2019 Apr 7;116(7):1305-1312. Epub 2019 Mar 7.

Department of Physics, University of Erlangen, Erlangen, Germany.

Cell migration through the extracellular matrix is governed by the interplay between cell-generated propulsion forces, adhesion forces, and resisting forces arising from the steric hindrance of the matrix. Steric hindrance in turn depends on matrix porosity, matrix deformability, cell size, and cell deformability. In this study, we investigate how cells respond to changes in steric hindrance that arise from altered cell mechanical properties. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451061PMC

Quantifying Molecular Forces with Serially Connected Force Sensors.

Biophys J 2019 Apr 7;116(7):1282-1291. Epub 2019 Mar 7.

Department of Chemistry, Biochemistry and Molecular Biology, The University of British Columbia, Kelowna, British Columbia, Canada. Electronic address:

To understand the mechanical forces involved in cell adhesion, molecular force sensors have been developed to study tension through adhesion proteins. Recently, a class of molecular force sensors called tension gauge tethers (TGTs) have been developed that rely on irreversible force-dependent dissociation of a DNA duplex to study cell adhesion forces. Although the TGT offers a high signal-to-noise ratio and is ideal for studying fast/single-molecular adhesion processes, quantitative interpretation of experimental results has been challenging. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451047PMC

The Two-Photon Reversible Reaction of the Bistable Jumping Spider Rhodopsin-1.

Biophys J 2019 Apr 5;116(7):1248-1258. Epub 2019 Mar 5.

Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland; Department of Biology, ETH Zürich, Zürich, Switzerland. Electronic address:

Bistable opsins are photopigments expressed in both invertebrates and vertebrates. These light-sensitive G-protein-coupled receptors undergo a reversible reaction upon illumination. A first photon initiates the cis to trans isomerization of the retinal chromophore-attached to the protein through a protonated Schiff base-and a series of transition states that eventually results in the formation of the thermally stable and active Meta state. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451042PMC
April 2019
1 Read

The Orphan Kinesin PAKRP2 Achieves Processive Motility via a Noncanonical Stepping Mechanism.

Biophys J 2019 Apr 28;116(7):1270-1281. Epub 2019 Feb 28.

Department of Physics, Oregon State University, Corvallis, Oregon; Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon. Electronic address:

Phragmoplast-associated kinesin-related protein 2 (PAKRP2) is an orphan kinesin in Arabidopsis thaliana that is thought to transport vesicles along phragmoplast microtubules for cell plate formation. Here, using single-molecule fluorescence microscopy, we show that PAKRP2 is the first orphan kinesin to exhibit processive plus-end-directed motility on single microtubules as individual homodimers. Our results show that PAKRP2 processivity is achieved despite having an exceptionally long (32 residues) neck linker. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451062PMC

Estimating Constraints for Protection Factors from HDX-MS Data.

Biophys J 2019 Apr 5;116(7):1194-1203. Epub 2019 Mar 5.

Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; School of Cellular and Molecular Biology, University of Leeds, Leeds, United Kingdom. Electronic address:

Hydrogen/deuterium exchange monitored by mass spectrometry is a promising technique for rapidly fingerprinting structural and dynamical properties of proteins. The time-dependent change in the mass of any fragment of the polypeptide chain depends uniquely on the rate of exchange of its amide hydrogens, but determining the latter from the former is generally not possible. Here, we show that, if time-resolved measurements are available for a number of overlapping peptides that cover the whole sequence, rate constants for each amide hydrogen exchange (or equivalently, their protection factors) may be extracted and the uniqueness of the solutions obtained depending on the degree of peptide overlap. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451051PMC
April 2019
3.972 Impact Factor

Ab Initio Derivation of the FRET Equations Resolves Old Puzzles and Suggests Measurement Strategies.

Authors:
Valerica Raicu

Biophys J 2019 Apr 26;116(7):1313-1327. Epub 2019 Feb 26.

Physics Department and Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin. Electronic address:

Quantitative imaging methods based on Förster resonance energy transfer (FRET) rely on the determination of an apparent FRET efficiency (E), as well as donor and acceptor concentrations, to uncover the identity and relative abundance of the supramolecular (or quaternary) structures of associating macromolecules. Theoretical work has provided "structure-based" relationships between E distributions and the quaternary structure models that underlie them. By contrast, the body of work that predicates the "signal-based" dependence of E on directly measurable quantities (i. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451038PMC

A Nondimensional Model Reveals Alterations in Nuclear Mechanics upon Hepatitis C Virus Replication.

Biophys J 2019 Apr 26;116(7):1328-1339. Epub 2019 Feb 26.

BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, Karnataka, India; Mechanical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India. Electronic address:

Morphology of the nucleus is an important regulator of gene expression. Nuclear morphology is in turn a function of the forces acting on it and the mechanical properties of the nuclear envelope. Here, we present a two-parameter, nondimensional mechanical model of the nucleus that reveals a relationship among nuclear shape parameters, such as projected area, surface area, and volume. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451028PMC

Hyaluronan Disrupts Cardiomyocyte Organization within 3D Fibrin-Based Hydrogels.

Biophys J 2019 Apr 26;116(7):1340-1347. Epub 2019 Feb 26.

Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania.

The extracellular matrix in vivo contains variable but often large amounts of glycosaminoglycans that influence cell and tissue function. Hyaluronan (HA) is an abundant glycosaminoglycan within the extracellular matrix of the myocardium during early development and in the aftermath of a myocardial infarction. Its flexible anionic structure has a strong influence on mechanical response and interstitial fluid flow within the matrix. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451035PMC
April 2019
1 Read

Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data.

Biophys J 2019 Apr 26;116(7):1216-1227. Epub 2019 Feb 26.

BioCIS, University Paris-Sud, CNRS UMR 8076, University Paris-Saclay, Châtenay-Malabry, France. Electronic address:

Because of their large conformational heterogeneity, structural characterization of intrinsically disordered proteins (IDPs) is very challenging using classical experimental methods alone. In this study, we use NMR and small-angle x-ray scattering (SAXS) data with multiple molecular dynamics (MD) simulations to describe the conformational ensemble of the fully disordered verprolin homology domain of the neural Aldrich syndrome protein involved in the regulation of actin polymerization. First, we studied several back-calculation software of SAXS scattering intensity and optimized the adjustable parameters to accurately calculate the SAXS intensity from an atomic structure. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451034PMC
April 2019
6 Reads

How Does Cilium Length Affect Beating?

Biophys J 2019 Apr 26;116(7):1292-1304. Epub 2019 Feb 26.

Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri. Electronic address:

The effects of cilium length on the dynamics of cilia motion were investigated by high-speed video microscopy of uniciliated mutants of the swimming alga, Chlamydomonas reinhardtii. Cells with short cilia were obtained by deciliating cells via pH shock and allowing cilia to reassemble for limited times. The frequency of cilia beating was estimated from the motion of the cell body and of the cilium. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451027PMC

Structure and Conformation of Wild-Type Bacterial Lipopolysaccharide Layers at Air-Water Interfaces.

Biophys J 2019 Apr 28;116(7):1259-1269. Epub 2019 Feb 28.

Max Planck Institute of Colloids and Interfaces, Potsdam, Germany. Electronic address:

The outer membrane of Gram-negative bacteria is of great scientific interest because it mediates the action of antimicrobial agents. The membrane surface is composed of lipopolysaccharide (LPS) molecules with negatively charged oligosaccharide headgroups. To a certain fraction, LPSs additionally display linear polysaccharides termed O-side chains (OSCs). Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451063PMC

Power Dissipation in the Cochlea Can Enhance Frequency Selectivity.

Biophys J 2019 Apr 1;116(7):1362-1375. Epub 2019 Mar 1.

Department of Mechanical Engineering, University of Rochester, Rochester, New York; Department of Biomedical Engineering, University of Rochester, Rochester, New York. Electronic address:

The cochlear cavity is filled with viscous fluids, and it is partitioned by a viscoelastic structure called the organ of Corti complex. Acoustic energy propagates toward the apex of the cochlea through vibrations of the organ of Corti complex. The dimensions of the vibrating structures range from a few hundred (e. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451036PMC

A Highly Accurate Pixel-Based FRAP Model Based on Spectral-Domain Numerical Methods.

Biophys J 2019 Apr 1;116(7):1348-1361. Epub 2019 Mar 1.

RISE Research Institutes of Sweden, Bioscience and Materials, Göteborg, Sweden; Department of Physics, Chalmers University of Technology, Göteborg, Sweden.

We introduce a new, to our knowledge, numerical model based on spectral methods for analysis of fluorescence recovery after photobleaching data. The model covers pure diffusion and diffusion and binding (reaction-diffusion) with immobile binding sites, as well as arbitrary bleach region shapes. Fitting of the model is supported using both conventional recovery-curve-based estimation and pixel-based estimation, in which all individual pixels in the data are utilized. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451077PMC

A Novel Microscopic Assay Reveals Heterogeneous Regulation of Local Endothelial Barrier Function.

Biophys J 2019 Feb 22. Epub 2019 Feb 22.

Institute of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany. Electronic address:

Blood vessels are covered with endothelial cells on their inner surfaces, forming a selective and semipermeable barrier between the blood and the underlying tissue. Many pathological processes, such as inflammation or cancer metastasis, are accompanied by an increased vascular permeability. Progress in live cell imaging techniques has recently revealed that the structure of endothelial cell contacts is constantly reorganized and that endothelial junctions display high heterogeneities at a subcellular level even within one cell. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.008DOI Listing
February 2019

Biophysics and Structure-Function Relationships of LRRC8-Formed Volume-Regulated Anion Channels.

Biophys J 2019 Apr 26;116(7):1185-1193. Epub 2019 Feb 26.

Freie Universität Berlin, Institute of Chemistry and Biochemistry, Berlin, Germany. Electronic address:

Volume-regulated anion channels (VRACs) are key players in regulatory volume decrease of vertebrate cells by mediating the extrusion of chloride and organic osmolytes. They play additional roles in various physiological processes beyond their role in osmotic volume regulation. VRACs are formed by heteromers of LRRC8 proteins; LRRC8A (also called SWELL1) is an essential subunit that combines with any of its paralogs, LRRC8B-E, to form hexameric VRAC complexes. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451053PMC

Coarse-Grained Simulation of Full-Length Integrin Activation.

Biophys J 2019 Mar 22;116(6):1000-1010. Epub 2019 Feb 22.

Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois. Electronic address:

Integrin conformational dynamics are critical to their receptor and signaling functions in many cellular processes, including spreading, adhesion, and migration. However, assessing integrin conformations is both experimentally and computationally challenging because of limitations in resolution and dynamic sampling. Thus, structural changes that underlie transitions between conformations are largely unknown. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6428961PMC
March 2019
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Physical Properties of Bacterial Outer Membrane Models: Neutron Reflectometry & Molecular Simulation.

Biophys J 2019 Mar 10;116(6):1095-1104. Epub 2019 Feb 10.

Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania. Electronic address:

The outer membrane (OM) of Gram-negative bacteria is an asymmetric bilayer having phospholipids in the inner leaflet and lipopolysaccharides in the outer leaflet. This unique asymmetry and the complex carbohydrates in lipopolysaccharides make it a daunting task to study the asymmetrical OM structure and dynamics, its interactions with OM proteins, and its roles in translocation of substrates, including antibiotics. In this study, we combine neutron reflectometry and molecular simulation to explore the physical properties of OM mimetics. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6428969PMC

A Bidomain Model for Lens Microcirculation.

Biophys J 2019 Mar 20;116(6):1171-1184. Epub 2019 Feb 20.

Department of Mathematics and Statistics, York University, Toronto, Ontario, Canada; Centre for Quantitative Analysis and Modelling, Fields Institute for Research in Mathematical Sciences, Toronto, Ontario, Canada.

There exists a large body of research on the lens of the mammalian eye over the past several decades. The objective of this work is to provide a link between the most recent computational models and some of the pioneering work in the 1970s and 80s. We introduce a general nonelectroneutral model to study the microcirculation in the lens of the eye. Read More

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http://dx.doi.org/10.1016/j.bpj.2019.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6428941PMC

Response to: Thick Filament Length Changes in Muscle Have Both Elastic and Structural Components.

Biophys J 2019 Mar 5;116(6):985-986. Epub 2019 Mar 5.

Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2019.02.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6428942PMC

Controlling Anomalous Diffusion in Lipid Membranes.

Biophys J 2019 Mar 16;116(6):1085-1094. Epub 2019 Jan 16.

Department of Chemistry, King's College London, London, United Kingdom. Electronic address:

Diffusion in cell membranes is not just simple two-dimensional Brownian motion but typically depends on the timescale of the observation. The physical origins of this anomalous subdiffusion are unresolved, and model systems capable of quantitative and reproducible control of membrane diffusion have been recognized as a key experimental bottleneck. Here, we control anomalous diffusion using supported lipid bilayers containing lipids derivatized with polyethylene glycol (PEG) headgroups. Read More

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http://dx.doi.org/10.1016/j.bpj.2018.12.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6428747PMC
March 2019
4 Reads