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Biophysical Journal

Mitsuhiro Hirai, Satoshi Ajito, Masaaki Sugiyama, Hiroki Iwase, Shin-Ichi Takata, Nobutaka Shimizu, Noriyuki Igarashi, Anne Martel, Lionel Porcar
No abstract text is available yet for this article.
August 1, 2018: Biophysical Journal
Mike Zhang, Thasin Peyear, Ilias Patmanidis, Denise V Greathouse, Siewert J Marrink, Olaf S Andersen, Helgi I Ingólfsson
Fluorinated alcohols (fluoroalcohols) have physicochemical properties that make them excellent solvents of peptides, proteins, and other compounds. Like other alcohols, fluoroalcohols also alter membrane protein function and lipid bilayer properties and stability. Thus, the questions arise: how potent are fluoroalcohols as lipid-bilayer-perturbing compounds, could small residual amounts that remain after adding compounds dissolved in fluoroalcohols alter lipid bilayer properties sufficiently to affect membranes and membrane protein function, and do they behave like other alcohols? To address these questions, we used a gramicidin-based fluorescence assay to determine the bilayer-modifying potency of selected fluoroalcohols: trifluoroethanol (TFE), HFIP, and perfluoro-tert-butanol (PFTB)...
August 1, 2018: Biophysical Journal
Sarafina M Kimø, Ida Friis, Ilia A Solov'yov
It is striking that the mechanism by which birds sense geomagnetic fields during the biannual migration seasons is not entirely understood. A protein believed to be responsible for avian magnetoreception is the flavoprotein cryptochrome (CRY), which fulfills many of the criteria for a magnetic field sensor. Some experiments, however, indicate that magnetoreception in birds may be disturbed by extremely weak radio frequency fields, an effect that likely cannot be described by an isolated CRY protein. An explanation can possibly be delivered if CRY binds to another protein inside a cell that would possess certain biochemical properties, and it is, therefore, important to identify possible intracellular CRY interaction partners...
July 30, 2018: Biophysical Journal
Alexander W Mauney, Joshua M Tokuda, Lisa M Gloss, Oscar Gonzalez, Lois Pollack
DNA is tightly wrapped around histone proteins in nucleosome core particles (NCPs) yet must become accessible for processing in the cell. This accessibility, a key component of transcription regulation, is influenced by the properties of both the histone proteins and the DNA itself. Small angle x-ray scattering with contrast variation is used to examine how sequence variations affect DNA unwrapping from NCPs at different salt concentrations. Salt destabilizes NCPs, populating multiple unwrapped states as many possible unwrapping pathways are explored by the complexes...
July 30, 2018: Biophysical Journal
Van Tran, Christian Stricker
Not only the amplitude but also the time course of a presynaptic Ca2+ transient determine multiple aspects of synaptic transmission. In small bouton-type synapses, the mechanisms underlying the Ca2+ decay kinetics have not been fully investigated. Here, factors that shape an action-potential-evoked Ca2+ transient were quantitatively studied in synaptic boutons of neocortical layer 5 pyramidal neurons. Ca2+ transients were measured with different concentrations of fluorescent Ca2+ indicators and analyzed based on a single-compartment model...
July 26, 2018: Biophysical Journal
Tsung-Jen Liao, Hyunbum Jang, David Fushman, Ruth Nussinov
Membrane-anchored Ras family proteins are activated by guanine nucleotide exchange factors such as SOS1. The CDC25 domain of SOS1 catalyzes GDP-to-GTP exchange, thereby activating Ras. Here, we aim to decipher the activation mechanism of KRas4B, a significantly mutated oncogene. We perform large-scale molecular dynamics simulations on 12 SOS1 systems, scrutinizing each step in two possible KRas4B activation cycles, fast and slow. To activate KRas4B at the CDC25 catalytic site, the allosteric site in the Ras exchanger motif (REM) domain of SOS1 needs to recruit a (nucleotide-bound) KRas4B molecule...
July 24, 2018: Biophysical Journal
Natalie E Stenzoski, Bowu Luan, Alex S Holehouse, Daniel P Raleigh
The temperature dependence of the overall dimensions of the denatured state ensemble (DSE) of proteins remains unclear. Some studies indicate compaction of the DSE at high temperatures, whereas others argue that dimensions do not decrease. The degree of compaction or expansion in the cold-denatured state has been less studied. To investigate the temperature dependence of unfolded state dimensions, small angle x-ray scattering measurements were performed in native buffer in the absence of denaturant for a designed point mutant of the C-terminal domain of L9, a small cooperatively folded α-β protein, at 14 different temperatures over the range of 5-60°C...
July 23, 2018: Biophysical Journal
Roxanne Glazier, Khalid Salaita
No abstract text is available yet for this article.
July 23, 2018: Biophysical Journal
Meimei Dong, Dawn P Spelke, Young Kwang Lee, Jean K Chung, Cheng-Han Yu, David V Schaffer, Jay T Groves
Interactions between EphB4 receptor tyrosine kinases and their membrane-bound ephrin-B2 ligands on apposed cells play a regulatory role in neural stem cell differentiation. With both receptor and ligand constrained to move within the membranes of their respective cells, this signaling system inevitably experiences spatial confinement and mechanical forces in conjunction with receptor-ligand binding. In this study, we reconstitute the EphB4-ephrin-B2 juxtacrine signaling geometry using a supported-lipid-bilayer system presenting laterally mobile and monomeric ephrin-B2 ligands to live neural stem cells...
July 23, 2018: Biophysical Journal
Alexey K Mazur, Eugene Gladyshev
In some fungi, a premeiotic process known as repeat-induced point mutation (RIP) can accurately identify and mutate nearly all gene-sized DNA repeats present in the haploid germline nuclei. Studies in Neurospora crassa have suggested that RIP detects sequence homology directly between intact DNA double helices, without strand separation and without the participation of RecA-like proteins. Those studies used the aggregated number of RIP mutations as a simple quantitative measure of RIP activity. Additional structural information about homologous DNA-DNA pairing during RIP can be extracted by analyzing spatial distributions of RIP mutations converted into profiles of partitioned RIP propensity (PRP)...
July 21, 2018: Biophysical Journal
Edward Lyman, Chia-Lung Hsieh, Christian Eggeling
New experimental techniques, especially in the context of observing molecular dynamics, reveal the plasma membrane to be heterogeneous and "scale rich," from nanometers to microns and from microseconds to seconds. This is critical information, which shows that scale-dependent transport governs the molecular encounters that underlie cellular signaling. The data are rich and reaffirm the importance of the cortical cytoskeleton, protein aggregates, and lipidomic complexity on the statistics of molecular encounters...
July 21, 2018: Biophysical Journal
Qing Wang, Erwin London
Using Förster resonance energy transfer, raft/liquid-ordered-domain formation was assessed in asymmetric vesicles containing outer leaflets composed of high-Tm (melting temperature) saturated phosphatidylcholines (diC18:0 PC, diC16:0 PC, diC15:0 PC, or diC14:0 PC), low-Tm unsaturated dioleoylphosphatidylcholine (DOPC) and cholesterol, and inner leaflets composed of lipids that by themselves would not form ordered domains (DOPC and cholesterol). Ordered-domain formation in the outer leaflet was compared to that in symmetric vesicles with the same lipid composition as the asymmetric vesicle outer leaflets...
July 19, 2018: Biophysical Journal
Dylan Johnson, C William Angus, Joseph M Chalovich
Activation of striated muscle contraction occurs in response to Ca2+ binding to troponin C. The resulting reorganization of troponin repositions tropomyosin on actin and permits activation of myosin-catalyzed ATP hydrolysis. It now appears that the C-terminal 14 amino acids of cardiac troponin T (TnT) control the level of activity at both low and high Ca2+ . We made a series of C-terminal truncation mutants of human cardiac troponin T, isoform 2, to determine if the same residues of TnT are involved in the low and high Ca2+ effects...
July 12, 2018: Biophysical Journal
Sampada P Mutalik, Joby Joseph, Pramod A Pullarkat, Aurnab Ghose
Mechanotransduction is likely to be an important mechanism of signaling in thin, elongated cells such as neurons. Maintenance of prestress or rest tension may facilitate mechanotransduction in these cells. In recent years, functional roles for mechanical tension in neuronal development and physiology are beginning to emerge, but the cellular mechanisms regulating neurite tension remain poorly understood. Active contraction of neurites is a potential mechanism of tension regulation. In this study, we have explored cytoskeletal mechanisms mediating active contractility of neuronal axons...
July 12, 2018: Biophysical Journal
Erik T Garbacik, Maria Sanz-Paz, Kyra J E Borgman, Felix Campelo, Maria F Garcia-Parajo
Standard fluorescence microscopy relies on filter-based detection of emitted photons after fluorophore excitation at the appropriate wavelength. Although of enormous utility to the biological community, the implementation of approaches for simultaneous multicolor fluorescence imaging is commonly challenged by the large spectral overlap between different fluorophores. Here, we describe an alternative multicolor fluorescence imaging methodology that exclusively relies on the absorption spectra of the fluorophores instead of their fluorescence emissions...
July 12, 2018: Biophysical Journal
Caitlin E Cornell, Allison D Skinkle, Shushan He, Ilya Levental, Kandice R Levental, Sarah L Keller
Micron-scale, coexisting liquid-ordered (Lo ) and liquid-disordered (Ld ) phases are straightforward to observe in giant unilamellar vesicles (GUVs) composed of ternary lipid mixtures. Experimentally, uniform membranes undergo demixing when temperature is decreased: domains subsequently nucleate, diffuse, collide, and coalesce until only one domain of each phase remains. The sizes of these two domains are limited only by the size of the system. Under different conditions, vesicles exhibit smaller-scale domains of fixed sizes, leading to the question of what sets the length scale...
July 11, 2018: Biophysical Journal
Jia Gou, Lin Lin, Hans G Othmer
Although significant progress has been made toward understanding morphogen-mediated patterning in development, control of the size and shape of tissues via local and global signaling is poorly understood. In particular, little is known about how cell-cell interactions are involved in the control of tissue size. The Hippo pathway in the Drosophila wing disc involves cell-cell interactions via cadherins, which lead to modulation of Yorkie, a cotranscriptional factor that affects control of the cell cycle and growth, and studies involving over- and underexpression of components of this pathway reveal conditions that lead to tissue over- or undergrowth...
July 11, 2018: Biophysical Journal
Iain D Nicholl, Tsutomu Matsui, Thomas M Weiss, Christopher B Stanley, William T Heller, Anne Martel, Bela Farago, David J E Callaway, Zimei Bu
As a core component of the adherens junction, α-catenin stabilizes the cadherin/catenin complexes to the actin cytoskeleton for the mechanical coupling of cell-cell adhesion. α-catenin also modulates actin dynamics, cell polarity, and cell-migration functions that are independent of the adherens junction. We have determined the solution structures of the α-catenin monomer and dimer using in-line size-exclusion chromatography small-angle X-ray scattering, as well as the structure of α-catenin dimer in complex to F-actin filament using selective deuteration and contrast-matching small angle neutron scattering...
July 11, 2018: Biophysical Journal
Romain Gautier, Amélie Bacle, Marion L Tiberti, Patrick F Fuchs, Stefano Vanni, Bruno Antonny
The analysis of the structural organization of lipid bilayers is generally performed across the direction normal to the bilayer/water interface, whereas the surface properties of the bilayer at the interface with water are often neglected. Here, we present PackMem, a bioinformatic tool that performs a topographic analysis of the bilayer surface from various molecular dynamics simulations. PackMem unifies and rationalizes previous analyses based on a Cartesian grid. The grid allows identification of surface regions defined as lipid-packing defects where lipids are loosely packed, leading to cavities in which aliphatic carbons are exposed to the solvent, either deep inside or close to the membrane surface...
July 5, 2018: Biophysical Journal
Anton V Sinitskiy, Vijay S Pande
N-methyl-D-aspartate receptors (NMDARs)-i.e., transmembrane proteins expressed in neurons-play a central role in the molecular mechanisms of learning and memory formation. It is unclear how the known atomic structures of NMDARs determined by x-ray crystallography and electron cryomicroscopy (18 published Protein Data Bank entries) relate to the functional states of NMDARs inferred from electrophysiological recordings (multiple closed, open, preopen, etc. states). We address this problem by using molecular dynamics simulations at atomic resolution, a method successfully applied in the past to much smaller biomolecules...
June 28, 2018: Biophysical Journal
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