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Biophysical Journal

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https://www.readbyqxmd.com/read/28648754/what-can-human-guided-simulations-bring-to-rna-folding
#1
Liuba Mazzanti, Sébastien Doutreligne, Cedric Gageat, Philippe Derreumaux, Antoine Taly, Marc Baaden, Samuela Pasquali
Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures...
June 22, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28647061/vesicle-fusion-mediated-by-solanesol-anchored-dna
#2
Kristina M Flavier, Steven G Boxer
Fusion between two lipid bilayers is one of the central processes in cell biology, playing a key role in endocytosis, exocytosis, and vesicle transport. We have previously developed a model system that uses the hybridization of complementary DNA strands to model the formation of the SNARE four-helix bundle that mediates synaptic vesicle fusion and used it to study vesicle fusion to a tethered lipid bilayer. Using single vesicle assays, 70% of observed fusion events in the DNA-lipid system are arrested at the hemifusion stage, whereas only 5% eventually go to full fusion...
June 21, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28647060/lipid-droplets-can-spontaneously-bud-off-from-a-symmetric-bilayer
#3
François Deslandes, Abdou Rachid Thiam, Lionel Forêt
Lipid droplets (LDs) are cytosolic organelles that protrude from the endoplasmic reticulum membrane under energy-rich conditions. How an LD buds off from the endoplasmic reticulum bilayer is still elusive. By using a continuous media description, we computed the morphology of a lipid droplet embedded in between two identical monolayers of a bilayer. We found that beyond a critical volume, the droplet morphology abruptly transits from a symmetrical elongated lens to a spherical protrusion. This budding transition does not require any energy-consuming machinery, or curvature-inducing agent, or intrinsic asymmetry of the bilayer; it is solely driven by the large interfacial energy of the LD, as opposed to the bilayer surface tension...
June 21, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28633759/martini-coarse-grained-force-field-extension-to-rna
#4
Jaakko J Uusitalo, Helgi I Ingólfsson, Siewert J Marrink, Ignacio Faustino
RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain molecular dynamics simulations are a key tool to that end. Here, we have extended the coarse-grain Martini force field to include RNA after our recent extension to DNA. In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network...
June 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28629620/effects-of-inhibiting-vps4-support-a-general-role-for-escrts-in-extracellular-vesicle-biogenesis
#5
Charles E Jackson, Benjamin S Scruggs, Jean E Schaffer, Phyllis I Hanson
Extracellular vesicles (EVs) are proposed to play important roles in intercellular communication. Two classes of EVs can be distinguished based on their intracellular origin. Exosomes are generated within endosomes and released when these fuse with the plasma membrane, whereas ectosomes bud directly from the plasma membrane. Studies of EV function have been hindered by limited understanding of their biogenesis. Components of the endosomal sorting complex required for transport (ESCRT) machinery play essential roles in topologically equivalent processes at both the endosome and the plasma membrane and are consistently recovered in EVs, but whether they are generally required to produce EVs is still debated...
June 16, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28629619/slow-interconversion-in-a-heterogeneous-unfolded-state-ensemble-of-outer-membrane-phospholipase-a
#6
Georg Krainer, Pablo Gracia, Erik Frotscher, Andreas Hartmann, Philip Gröger, Sandro Keller, Michael Schlierf
Structural and dynamic investigations of unfolded proteins are important for understanding protein-folding mechanisms as well as the interactions of unfolded polypeptide chains with other cell components. In the case of outer-membrane proteins (OMPs), unfolded-state properties are of particular physiological relevance, because these proteins remain unfolded for extended periods of time during their biogenesis and rely on interactions with binding partners to support proper folding. Using a combination of ensemble and single-molecule spectroscopy, we have scrutinized the unfolded state of outer-membrane phospholipase A (OmpLA) to provide a detailed view of its structural dynamics on timescales from nanoseconds to milliseconds...
June 16, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28629618/conditioning-and-robustness-of-rna-boltzmann-sampling-under-thermodynamic-parameter-perturbations
#7
Emily Rogers, David Murrugarra, Christine Heitsch
Understanding how RNA secondary structure prediction methods depend on the underlying nearest-neighbor thermodynamic model remains a fundamental challenge in the field. Minimum free energy (MFE) predictions are known to be "ill conditioned" in that small changes to the thermodynamic model can result in significantly different optimal structures. Hence, the best practice is now to sample from the Boltzmann distribution, which generates a set of suboptimal structures. Although the structural signal of this Boltzmann sample is known to be robust to stochastic noise, the conditioning and robustness under thermodynamic perturbations have yet to be addressed...
June 16, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28625696/comparative-visualization-of-the-rna-suboptimal-conformational-ensemble-in%C3%A2-vivo
#8
Chanin T Woods, Lela Lackey, Benfeard Williams, Nikolay V Dokholyan, David Gotz, Alain Laederach
When a ribonucleic acid (RNA) molecule folds, it often does not adopt a single, well-defined conformation. The folding energy landscape of an RNA is highly dependent on its nucleotide sequence and molecular environment. Cellular molecules sometimes alter the energy landscape, thereby changing the ensemble of likely low-energy conformations. The effects of these energy landscape changes on the conformational ensemble are particularly challenging to visualize for large RNAs. We have created a robust approach for visualizing the conformational ensemble of RNAs that is well suited for in vitro versus in vivo comparisons...
June 15, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28554481/zebrafish-keep-their-cool
#9
Aurelia R Honerkamp-Smith
No abstract text is available yet for this article.
May 26, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28552311/miscibility-transition-temperature-scales-with-growth-temperature-in-a-zebrafish-cell-line
#10
Margaret Burns, Kathleen Wisser, Jing Wu, Ilya Levental, Sarah L Veatch
Cells can alter the lipid content of their plasma membranes upon changes in their environment to maintain and adjust membrane function. Recent work suggests that some membrane functions arise because cellular plasma membranes are poised close to a miscibility transition under growth conditions. Here we report experiments utilizing giant plasma membrane vesicles (GPMVs) to explore how membrane transition temperature varies with growth temperature in a zebrafish cell line (ZF4) that can be adapted for growth between 20 and 32°C...
May 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28506527/ancestral-interactions-of-ribosomal-rna-and-ribosomal-proteins
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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/28636925/achievements-and-challenges-for-our-society-s-journal
#18
EDITORIAL
Leslie M Loew
No abstract text is available yet for this article.
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636924/epithelial-folding-driven-by-apical-or-basal-lateral-modulation-geometric-features-mechanical-inference-and-boundary-effects
#19
Fu-Lai Wen, Yu-Chiun Wang, Tatsuo Shibata
During embryonic development, epithelial sheets fold into complex structures required for tissue and organ functions. Although substantial efforts have been devoted to identifying molecular mechanisms underlying epithelial folding, far less is understood about how forces deform individual cells to sculpt the overall sheet morphology. Here we describe a simple and general theoretical model for the autonomous folding of monolayered epithelial sheets. We show that active modulation of intracellular mechanics along the basal-lateral as well as the apical surfaces is capable of inducing fold formation in the absence of buckling instability...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636923/mechanosensitive-adhesion-explains-stepping-motility-in-amoeboid-cells
#20
Calina A Copos, Sam Walcott, Juan C Del Álamo, Effie Bastounis, Alex Mogilner, Robert D Guy
Cells employing amoeboid motility exhibit repetitive cycles of rapid expansion and contraction and apply coordinated traction forces to their environment. Although aspects of this process are well studied, it is unclear how the cell controls the coordination of cell length changes with adhesion to the surface. Here, we develop a simple model to mechanistically explain the emergence of periodic changes in length and spatiotemporal dynamics of traction forces measured in chemotaxing unicellular amoeba, Dictyostelium discoideum...
June 20, 2017: Biophysical Journal
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