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Biophysical Journal

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https://www.readbyqxmd.com/read/28522140/membrane-fusion-stalks-and-lipid-rafts-a-love-hate-relationship
#1
Herre Jelger Risselada
Coarse-grained molecular dynamics simulations are applied to explore the experimentally observed ability of the liquid-ordered (lo)/liquid-disordered (ld) phase boundary to facilitate viral membrane fusion. Surprisingly, a formed fusion stalk can be both attracted (i.e., stalkophilic) and repelled (i.e., stalkophobic) by the lo/ld phase boundary. The phase boundary becomes stalkophilic if the lo phase constituents have the larger negative spontaneous curvature. In such a case, location of the highly curved stalk near the less-ordered and thus (relatively) softer boundary region becomes energetically favorable...
May 15, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28506526/molecular-simulation-and-biochemical-studies-support-an-elevator-type-transport-mechanism-in%C3%A2-eiic
#2
Jumin Lee, Zhenning Ren, Ming Zhou, Wonpil Im
Enzyme IIC (EIIC) is a membrane-embedded sugar transport protein that is part of the phosphoenolpyruvate-dependent phosphotransferases. Crystal structures of two members of the glucose EIIC superfamily, bcChbC in the inward-facing conformation and bcMalT in the outward-facing conformation, were previously solved. Comparing the two structures led us to the hypothesis that sugar translocation could be achieved by an elevator-type transport mechanism in which a transport domain binds to the substrate and, through rigid body motions, transports it across the membrane...
May 13, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28506527/ancestral-interactions-of-ribosomal-rna-and-ribosomal-proteins
#3
Kathryn A Lanier, Poorna Roy, Dana M Schneider, Loren Dean Williams
We have proposed that the ancient ribosome increased in size during early evolution by addition of small folding-competent RNAs. In this Accretion Model, small RNAs and peptides were subsumed onto subunit surfaces, gradually encasing and freezing previously acquired components. The model predicts that appropriate rRNA fragments have inherited local autonomy of folding and local autonomy of assembly with ribosomal proteins (rProteins), and that the rProtein and rRNA are co-chaperones. To test these predictions, we investigate the rRNA interactions of rProtein uL23 and its tail, uL23(tail), which is a β-hairpin that penetrates deep into the core of the large ribosomal subunit...
May 12, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28506525/how-does-mg-2-modulate-the-rna-folding-mechanism-a-case-study-of-the-g-c-w-w-trans-basepair
#4
Antarip Halder, Rohit Roy, Dhananjay Bhattacharyya, Abhijit Mitra
Reverse Watson-Crick G:C basepairs (G:C W:W Trans) occur frequently in different functional RNAs. This is one of the few basepairs whose gas-phase-optimized isolated geometry is inconsistent with the corresponding experimental geometry. Several earlier studies indicate that through post-transcriptional modification, direct protonation, or coordination with Mg(2+), accumulation of positive charge near N7 of guanine can stabilize the experimental geometry. Interestingly, recent studies reveal significant variation in the position of putatively bound Mg(2+)...
May 12, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28456331/complexin-binding-to-membranes-and-acceptor-t-snares-explains-its-clamping-effect-on-fusion
#5
Rafal Zdanowicz, Alex Kreutzberger, Binyong Liang, Volker Kiessling, Lukas K Tamm, David S Cafiso
Complexin-1 is a SNARE effector protein that decreases spontaneous neurotransmitter release and enhances evoked release. Complexin binds to the fully assembled four-helical neuronal SNARE core complex as revealed in competing molecular models derived from x-ray crystallography. Presently, it is unclear how complexin binding to the postfusion complex accounts for its effects upon spontaneous and evoked release in vivo. Using a combination of spectroscopic and imaging methods, we characterize in molecular detail how complexin binds to the 1:1 plasma membrane t-SNARE complex of syntaxin-1a and SNAP-25 while simultaneously binding the lipid bilayer at both its N- and C-terminal ends...
April 26, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28454841/assisted-and-unassisted-protein-insertion-into-liposomes
#6
REVIEW
Andreas Kuhn, Maximilian Haase, Sebastian Leptihn
The insertion of newly synthesized membrane proteins is a well-regulated and fascinating process occurring in every living cell. Several translocases and insertases have been found in prokaryotic and eukaryotic cells, the Sec61 complex and the Get complex in the endoplasmic reticulum and the SecYEG complex and YidC in bacteria and archaea. In mitochondria, TOM and TIM complexes transport nuclear-encoded proteins, whereas the Oxa1 is required for the insertion of mitochondria-encoded membrane proteins. Related to the bacterial YidC and the mitochondrial Oxa1 are the Alb3 and Alb4 proteins in chloroplasts...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28450130/from-gene-to-function-cell-free-electrophysiological-and-optical-analysis-of-ion-pumps-in-nanodiscs
#7
Erik Henrich, Janina Sörmann, Peter Eberhardt, Oliver Peetz, Julija Mezhyrova, Nina Morgner, Klaus Fendler, Volker Dötsch, Josef Wachtveitl, Frank Bernhard, Christian Bamann
Nanodiscs that hold a lipid bilayer surrounded by a boundary of scaffold proteins have emerged as a powerful tool for membrane protein solubilization and analysis. By combining nanodiscs and cell-free expression technologies, even completely detergent-free membrane protein characterization protocols can be designed. Nanodiscs are compatible with various techniques, and due to their bilayer environment and increased stability, they are often superior to detergent micelles or liposomes for membrane protein solubilization...
April 24, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28410623/impact-of-gm1-on-membrane-mediated-aggregation-oligomerization-of-%C3%AE-amyloid-unifying-view
#8
REVIEW
Marek Cebecauer, Martin Hof, Mariana Amaro
In this perspective we summarize current knowledge of the effect of monosialoganglioside GM1 on the membrane-mediated aggregation of the β-amyloid (Aβ) peptide. GM1 has been suggested to be actively involved in the development of Alzheimer's disease due to its ability to seed the aggregation of Aβ. However, GM1 is known to be neuroprotective against Aβ-induced toxicity. Here we suggest that the two scenarios are not mutually exclusive but rather complementary, and might depend on the organization of GM1 in membranes...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28400045/rapid-snare-mediated-fusion-of-liposomes-and-chromaffin-granules-with-giant-unilamellar-vesicles
#9
Agata Witkowska, Reinhard Jahn
Soluble N-ethylmaleimide-sensitive factor activating protein receptor (SNARE) proteins are the main catalysts for membrane fusion in the secretory pathway of eukaryotic cells. In vitro, SNAREs are sufficient to mediate effective fusion of both native and artificial membranes. Here we have established, to our knowledge, a new platform for monitoring SNARE-mediated docking and fusion between giant unilamellar vesicles (GUVs) and smaller liposomes or purified secretory granules with high temporal and spatial resolution...
April 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538159/long-term-stochastic-editing-of-regenerative-anatomy-via-targeting-endogenous-bioelectric-gradients
#10
Fallon Durant, Junji Morokuma, Christopher Fields, Katherine Williams, Dany Spencer Adams, Michael Levin
We show that regenerating planarians' normal anterior-posterior pattern can be permanently rewritten by a brief perturbation of endogenous bioelectrical networks. Temporary modulation of regenerative bioelectric dynamics in amputated trunk fragments of planaria stochastically results in a constant ratio of regenerates with two heads to regenerates with normal morphology. Remarkably, this is shown to be due not to partial penetrance of treatment, but a profound yet hidden alteration to the animals' patterning circuitry...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538158/glnk-facilitates-the-dynamic-regulation-of-bacterial-nitrogen-assimilation
#11
Adam Gosztolai, Jörg Schumacher, Volker Behrends, Jacob G Bundy, Franziska Heydenreich, Mark H Bennett, Martin Buck, Mauricio Barahona
Ammonium assimilation in Escherichia coli is regulated by two paralogous proteins (GlnB and GlnK), which orchestrate interactions with regulators of gene expression, transport proteins, and metabolic pathways. Yet how they conjointly modulate the activity of glutamine synthetase, the key enzyme for nitrogen assimilation, is poorly understood. We combine experiments and theory to study the dynamic roles of GlnB and GlnK during nitrogen starvation and upshift. We measure time-resolved in vivo concentrations of metabolites, total and posttranslationally modified proteins, and develop a concise biochemical model of GlnB and GlnK that incorporates competition for active and allosteric sites, as well as functional sequestration of GlnK...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538157/cell-and-tissue-scale-forces-coregulate-fgfr2-dependent-tetrads-and-rosettes-in-the-mouse-embryo
#12
Jun Wen, Hirotaka Tao, Kimberly Lau, Haijiao Liu, Craig A Simmons, Yu Sun, Sevan Hopyan
What motivates animal cells to intercalate is a longstanding question that is fundamental to morphogenesis. A basic mode of cell rearrangement involves dynamic multicellular structures called tetrads and rosettes. The contribution of cell-intrinsic and tissue-scale forces to the formation and resolution of these structures remains unclear, especially in vertebrates. Here, we show that Fgfr2 regulates both the formation and resolution of tetrads and rosettes in the mouse embryo, possibly in part by spatially restricting atypical protein kinase C, a negative regulator of non-muscle myosin IIB...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538156/a-simple-marker-assisted-3d-nanometer-drift-correction-method-for-superresolution-microscopy
#13
Hongqiang Ma, Jianquan Xu, Jingyi Jin, Yi Huang, Yang Liu
High-precision fluorescence microscopy such as superresolution imaging or single-particle tracking often requires an online drift correction method to maintain the stability of the three-dimensional (3D) position of the sample at a nanometer precision throughout the entire data acquisition process. Current online drift correction methods require modification of the existing two-dimensional (2D) fluorescence microscope with additional optics and detectors, which can be cumbersome and limit its use in many biological laboratories...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538155/structure-and-intermolecular-interactions-between-l-type-straight-flagellar-filaments
#14
Daniel Louzon, Avi Ginsburg, Walter Schwenger, Tom Dvir, Zvonimir Dogic, Uri Raviv
Bacterial mobility is powered by rotation of helical flagellar filaments driven by rotary motors. Flagellin isolated from the Salmonella Typhimurium SJW1660 strain, which differs by a point mutation from the wild-type strain, assembles into straight filaments in which flagellin monomers are arranged in a left-handed helix. Using small-angle x-ray scattering and osmotic stress methods, we investigated the structure of SJW1660 flagellar filaments as well as the intermolecular forces that govern their assembly into dense hexagonal bundles...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538154/effect-of-ca-2-to-sphingomyelin-investigated-by-sum-frequency-generation-vibrational-spectroscopy
#15
Rong-Juan Feng, Lu Lin, Yi-Yi Li, Ming-Hua Liu, Yuan Guo, Zhen Zhang
The interactions between Ca(2+) ions and sphingomyelin play crucial roles in a wide range of cellular activities. However, little is known about the molecular details of the interactions at interfaces. In this work, we investigated the interactions between Ca(2+) ions and egg sphingomyelin (ESM) Langmuir monolayers at the air/water interface by subwavenumber high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS). We show that Ca(2+) ions can induce ordering of the acyl chains in the ESM monolayer...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538153/new-continuum-approaches-for-determining-protein-induced-membrane-deformations
#16
David Argudo, Neville P Bethel, Frank V Marcoline, Charles W Wolgemuth, Michael Grabe
The influence of the membrane on transmembrane proteins is central to a number of biological phenomena, notably the gating of stretch activated ion channels. Conversely, membrane proteins can influence the bilayer, leading to the stabilization of particular membrane shapes, topological changes that occur during vesicle fission and fusion, and shape-dependent protein aggregation. Continuum elastic models of the membrane have been widely used to study protein-membrane interactions. These mathematical approaches produce physically interpretable membrane shapes, energy estimates for the cost of deformation, and a snapshot of the equilibrium configuration...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538152/apoptotic-bax-at-oxidatively-stressed-mitochondrial-membranes-lipid-dynamics-and-permeabilization
#17
Artur Peter Günther Dingeldein, Šárka Pokorná, Martin Lidman, Tobias Sparrman, Radek Šachl, Martin Hof, Gerhard Gröbner
Mitochondria are crucial compartments of eukaryotic cells because they function as the cellular power plant and play a central role in the early stages of programmed cell death (apoptosis). To avoid undesired cell death, this apoptotic pathway is tightly regulated by members of the Bcl-2 protein family, which interact on the external surface of the mitochondria, i.e., the mitochondrial outer membrane (MOM), and modulate its permeability to apoptotic factors, controlling their release into the cytosol. A growing body of evidence suggests that the MOM lipids play active roles in this permeabilization process...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538151/mapping-interpuff-interval-distribution-to-the-properties-of-inositol-trisphosphate-receptors
#18
Pengxing Cao, Martin Falcke, James Sneyd
Tightly clustered inositol trisphosphate receptors (IP3Rs) control localized Ca(2+) liberation from the endoplasmic reticulum to generate repetitive Ca(2+) puffs. Distributions of the interpuff interval (IPI), i.e., the waiting time between successive puffs, are found to be well characterized by a probability density function involving only two parameters, λ and ξ, which represent the basal rate of puff generation and the recovery rate from refractoriness, respectively. However, how the two parameters depend on the kinetic parameters of single IP3Rs in a cluster is still unclear...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538150/lanthanides-report-calcium-sensor-in-the-vestibule-of-ryanodine-receptor
#19
Sándor Sárközi, István Komáromi, István Jóna, János Almássy
Ca(2+) regulates ryanodine receptor's (RyR) activity through an activating and an inhibiting Ca(2+)-binding site located on the cytoplasmic side of the RyR channel. Their altered sensitivity plays an important role in the pathology of malignant hyperthermia and heart failure. We used lanthanide ions (Ln(3+)) as probes to investigate the Ca(2+) sensors of RyR, because they specifically bind to Ca(2+)-binding proteins and they are impermeable to the channel. Eu(3+)'s and Sm(3+)'s action was tested on single RyR1 channels reconstituted into planar lipid bilayers...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538149/icon-an-adaptation-of-infinite-hmms-for-time-traces-with-drift
#20
Ioannis Sgouralis, Steve Pressé
Bayesian nonparametric methods have recently transformed emerging areas within data science. One such promising method, the infinite hidden Markov model (iHMM), generalizes the HMM that itself has become a workhorse in single molecule data analysis. The iHMM goes beyond the HMM by self-consistently learning all parameters learned by the HMM in addition to learning the number of states without recourse to any model selection steps. Despite its generality, simple features (such as drift), common to single molecule time traces, result in an overinterpretation of drift and the introduction of artifact states...
May 23, 2017: Biophysical Journal
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