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Biophysical Journal

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https://www.readbyqxmd.com/read/29056231/mitochondrial-adp-atp-carrier-in-dodecylphosphocholine-binds-cardiolipins-with-non-native-affinity
#1
François Dehez, Paul Schanda, Martin S King, Edmund R S Kunji, Christophe Chipot
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...
October 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29037600/asymmetric-phosphatidylethanolamine-distribution-controls-fusion-pore-lifetime-and-probability
#2
Alex J B Kreutzberger, Volker Kiessling, Binyong Liang, Sung-Tae Yang, J David Castle, Lukas K Tamm
Little attention has been given to how the asymmetric lipid distribution of the plasma membrane might facilitate fusion pore formation during exocytosis. Phosphatidylethanolamine (PE), a cone-shaped phospholipid, is predominantly located in the inner leaflet of the plasma membrane and has been proposed to promote membrane deformation and stabilize fusion pores during exocytotic events. To explore this possibility, we modeled exocytosis using plasma membrane SNARE-containing planar-supported bilayers and purified neuroendocrine dense core vesicles (DCVs) as fusion partners, and we examined how different PE distributions between the two leaflets of the supported bilayers affected SNARE-mediated fusion...
October 13, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29032961/optimal-quantification-of-contact-inhibition-in-cell-populations
#3
David J Warne, Ruth E Baker, Matthew J Simpson
Contact inhibition refers to a reduction in the rate of cell migration and/or cell proliferation in regions of high cell density. Under normal conditions, contact inhibition is associated with the proper functioning tissues, whereas abnormal regulation of contact inhibition is associated with pathological conditions, such as tumor spreading. Unfortunately, standard mathematical modeling practices mask the importance of parameters that control contact inhibition through scaling arguments. Furthermore, standard experimental protocols are insufficient to quantify the effects of contact inhibition because they focus on data describing early time, low-density dynamics only...
October 12, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29017728/near-infrared-fluorescent-proteins-engineered-from-bacterial-phytochromes-in-neuroimaging
#4
Kiryl D Piatkevich, Ho-Jun Suk, Suhasa B Kodandaramaiah, Fumiaki Yoshida, Ellen M DeGennaro, Mikhail Drobizhev, Thomas E Hughes, Robert Desimone, Edward S Boyden, Vladislav V Verkhusha
Several series of near-infrared (NIR) fluorescent proteins (FPs) were recently engineered from bacterial phytochromes but were not systematically compared in neurons. To fluoresce, NIR FPs utilize an enzymatic derivative of heme, the linear tetrapyrrole biliverdin, as a chromophore whose level in neurons is poorly studied. Here, we evaluated NIR FPs of the iRFP protein family, which were reported to be the brightest in non-neuronal mammalian cells, in primary neuronal culture, in brain slices of mouse and monkey, and in mouse brain in vivo...
October 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28992937/substrate-specificity-of-the-kinase-p-tefb-towards-the-rna-polymerase-ii-c-terminal-domain
#5
Eric B Gibbs, Tatiana N Laremore, Grace A Usher, Bede Portz, Erik C Cook, Scott A Showalter
The positive transcription elongation factor b (P-TEFb) promotes transcription elongation through phosphorylation of the RNA polymerase II C-terminal domain. This process is not well understood, partly due to difficulties in determining the specificity of P-TEFb toward the various heptad repeat motifs within the C-terminal domain. A simple assay using mass spectrometry was developed to identify the substrate specificity of the Drosophila melanogaster P-TEFb (DmP-TEFb) in vitro. This assay demonstrated that DmP-TEFb preferentially phosphorylates Ser5 and, surprisingly, that pre-phosphorylation or conserved amino acid variation at the 7-position in the heptad can alter DmP-TEFb specificity, leading to the creation of distinct double-phosphorylation marks...
October 6, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28988699/disruption-of-ankyrin-b-and-caveolin-1-interaction-sites-alters-na-k-atpase-membrane-diffusion
#6
Cornelia Junghans, Vladana Vukojević, Neslihan N Tavraz, Eugene G Maksimov, Werner Zuschratter, Franz-Josef Schmitt, Thomas Friedrich
The Na(+),K(+)-ATPase is a plasma membrane ion transporter of high physiological importance for ion homeostasis and cellular excitability in electrically active tissues. Mutations in the genes coding for Na(+),K(+)-ATPase α-subunit isoforms lead to severe human pathologies including Familial Hemiplegic Migraine type 2, Alternating Hemiplegia of Childhood, Rapid-onset Dystonia Parkinsonism, or epilepsy. Many of the reported mutations lead to change- or loss-of-function effects, whereas others do not alter the functional properties, but lead to, e...
October 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28988026/quantitative-image-restoration-in-bright-field-optical-microscopy
#7
Braulio Gutiérrez-Medina, Manuel de Jesús Sánchez Miranda
Bright field (BF) optical microscopy is regarded as a poor method to observe unstained biological samples due to intrinsic low image contrast. We introduce quantitative image restoration in bright field (QRBF), a digital image processing method that restores out-of-focus BF images of unstained cells. Our procedure is based on deconvolution, using a point spread function modeled from theory. By comparing with reference images of bacteria observed in fluorescence, we show that QRBF faithfully recovers shape and enables quantify size of individual cells, even from a single input image...
October 4, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28939194/modification-of-c-terminus-provides-new-insights-into-the-mechanism-of-%C3%AE-synuclein-aggregation
#8
Kseniia Afitska, Anna Fucikova, Volodymyr V Shvadchak, Dmytro A Yushchenko
Aggregation of neuronal protein α-synuclein leads to the formation of amyloid fibrils, which are associated with the development of Parkinson's disease. The mechanism of α-synuclein pathology is not fully understood and is a subject of active research in the field. To tackle this problem, the fusions of fluorescent proteins to α-synuclein C-terminus are often used in cellular and animal studies. The effects induced by such α-synuclein sequence extension on α-synuclein aggregation propensity are, however, not systematically examined despite the evidence that the negatively charged C-terminus plays a critical role in the regulation of α-synuclein aggregation...
September 19, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28935134/sites-contributing-to-trpa1-activation-by-the-anesthetic-propofol-identified-by-photoaffinity-labeling
#9
Kellie A Woll, Kenneth A Skinner, Eleonora Gianti, Natarajan V Bhanu, Benjamin A Garcia, Vincenzo Carnevale, Roderic G Eckenhoff, Rachelle Gaudet
In addition to inducing anesthesia, propofol activates a key component of the pain pathway, the transient receptor potential ankyrin 1 ion channel (TRPA1). Recent mutagenesis studies suggested a potential activation site within the transmembrane domain, near the A-967079 cavity. However, mutagenesis cannot distinguish between protein-based and ligand-based mechanisms, nor can this site explain the complex modulation by propofol. Thus more direct approaches are required to reveal potentially druggable binding sites...
September 19, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28935133/functional-validation-of-heteromeric-kainate-receptor-models
#10
Teresa Paramo, Patricia M G E Brown, Maria Musgaard, Derek Bowie, Philip C Biggin
Kainate receptors require the presence of external ions for gating. Most work thus far has been performed on homomeric GluK2 but, in vivo, kainate receptors are likely heterotetramers. Agonists bind to the ligand-binding domain (LBD) which is arranged as a dimer of dimers as exemplified in homomeric structures, but no high-resolution structure currently exists of heteromeric kainate receptors. In a full-length heterotetramer, the LBDs could potentially be arranged either as a GluK2 homomer alongside a GluK5 homomer or as two GluK2/K5 heterodimers...
September 19, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28916386/molecular-mechanisms-of-the-r61t-mutation-in-apolipoprotein-e4-a-dynamic-rescue
#11
Benfeard Williams, Marino Convertino, Jhuma Das, Nikolay V Dokholyan
The apolipoprotein E4 (ApoE4) gene is the strongest genetic risk factor for Alzheimer's disease (AD). With respect to the other common isoforms of this protein (ApoE2 and ApoE3), ApoE4 is characterized by lower stability that underlies the formation of a stable interaction between the protein's N- and C-terminal domains. AD-related cellular dysfunctions have been linked to this ApoE4 misfolded state. In this regard, it has been reported that the mutation R61T is able to rescue the deleterious cellular effects of ApoE4 by preventing the formation of the misfolded intermediate state...
September 12, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28866426/biophysics-of-biochemical-signaling-in-dendritic-spines-implications-in-synaptic-plasticity
#12
REVIEW
Ryohei Yasuda
Dendritic spines are mushroom-shaped postsynaptic compartments that host biochemical signal cascades important for synaptic plasticity and, ultimately, learning and memory. Signaling events in spines involve a signaling network composed of hundreds of signaling proteins interacting with each other extensively. Synaptic plasticity is typically induced by Ca(2+) elevation in spines, which activates a variety of signaling pathways. This leads to changes in the actin cytoskeleton and membrane dynamics, which in turn causes structural and functional changes of the spine...
August 30, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28863864/two-pools-of-vesicles-associated-with-synaptic-ribbons-are-molecularly-prepared-for-release
#13
Proleta Datta, Jared Gilliam, Wallace B Thoreson, Roger Janz, Ruth Heidelberger
Neurons that form ribbon-style synapses are specialized for continuous exocytosis. To this end, their synaptic terminals contain numerous synaptic vesicles, some of which are ribbon associated, that have difference susceptibilities for undergoing Ca(2+)-dependent exocytosis. In this study, we probed the relationship between previously defined vesicle populations and determined their fusion competency with respect to SNARE complex formation. We found that both the rapidly releasing vesicle pool and the releasable vesicle pool of the retinal bipolar cell are situated at the ribbon-style active zones, where they functionally interact...
August 29, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28863863/unitary-properties-of-ampa-receptors-with-reduced-desensitization
#14
Wei Zhang, Clarissa Eibl, Autumn M Weeks, Irene Riva, Yan-Jun Li, Andrew J R Plested, James R Howe
Wild-type AMPA receptors display a characteristic rapidly desensitizing phenotype. Many studies point to the dimer interface between pairs of extracellular ligand binding domains as the key region controlling the rate at which the receptors desensitize. However, mutations at the extracellular end of the pore-forming regions (near the putative ion channel gate) have also been shown to alter desensitization. Here we report the behavior of single GluA4 receptors carrying one of two mutations that greatly reduce desensitization at the level of ensemble currents: the dimer interface mutation L484Y and the Lurcher mutation (A623T, GluA4-Lc) in the extracellular end of M3 (the second true transmembrane helix)...
August 29, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28844473/the-challenge-of-interpreting-glutamate-receptor-ion-channel-structures
#15
REVIEW
Mark L Mayer
Ion channels activated by glutamate mediate excitatory synaptic transmission in the central nervous system. Similar to other ligand-gated ion channels, their gating cycle begins with transitions from a ligand-free closed state to glutamate-bound active and desensitized states. In an attempt to reveal the molecular mechanisms underlying gating, numerous structures for glutamate receptors have been solved in complexes with agonists, antagonists, allosteric modulators, and auxiliary proteins. The embarrassingly rich library of structures emerging from this work reveals very dynamic molecules with a more complex conformational spectrum than anticipated from functional studies...
August 24, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29045882/untangling-the-hairball-fitness-based-asymptotic-reduction-of-biological-networks
#16
Félix Proulx-Giraldeau, Thomas J Rademaker, Paul François
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. The ϕ¯ algorithm works by putting parameters or combination of parameters to some asymptotic limit, while keeping (or slightly improving) the model performance, and requires parameter symmetry breaking for more complex models...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29045881/confocal-rheology-probes-the-structure-and-mechanics-of-collagen-through-the-sol-gel-transition
#17
Khanh-Hoa Tran-Ba, Daniel J Lee, Jieling Zhu, Keewook Paeng, Laura J Kaufman
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...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29045880/a-model-for-link-pruning-to-establish-correctly-polarized-and-oriented-tip-links-in-hair-bundles
#18
Nathan Tompkins, Kateri J Spinelli, Dongseok Choi, Peter G Barr-Gillespie
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...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29045879/probing-cell-adhesion-profiles-with-a-microscale-adhesive-choice-assay
#19
Harsha Kittur, Andy Tay, Avery Hua, Min Yu, Dino Di Carlo
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. Here, we demonstrate a method to quantify the transhesive properties of cells that relies on the microscale juxtaposition of two extracellular matrix-coated surfaces...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29045878/homodimeric-kinesin-2-kif3cc-promotes-microtubule-dynamics
#20
Stephanie Guzik-Lendrum, Ivan Rayment, Susan P Gilbert
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...
October 17, 2017: Biophysical Journal
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