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Results: 1 to 10 of 190

Publication Record


Nanoscale architecture of the contractile ring.
McDonald NA, Lind AL, Smith SE, Li R, Gould KL
(2017) Elife 6:
MeSH Terms: Cell Cycle Proteins, Cell Division, Cell Membrane, Cytoplasm, Fluorescence Resonance Energy Transfer, Macromolecular Substances, Microscopy, Fluorescence, Schizosaccharomyces, Schizosaccharomyces pombe Proteins
Show Abstract · Added March 14, 2018
The contractile ring is a complex molecular apparatus which physically divides many eukaryotic cells. Despite knowledge of its protein composition, the molecular architecture of the ring is not known. Here we have applied super-resolution microscopy and FRET to determine the nanoscale spatial organization of contractile ring components relative to the plasma membrane. Similar to other membrane-tethered actin structures, we find proteins localize in specific layers relative to the membrane. The most membrane-proximal layer (0-80 nm) is composed of membrane-binding scaffolds, formin, and the tail of the essential myosin-II. An intermediate layer (80-160 nm) consists of a network of cytokinesis accessory proteins as well as multiple signaling components which influence cell division. Farthest from the membrane (160-350 nm) we find F-actin, the motor domains of myosins, and a major F-actin crosslinker. Circumferentially within the ring, multiple proteins proximal to the membrane form clusters of different sizes, while components farther from the membrane are uniformly distributed. This comprehensive organizational map provides a framework for understanding contractile ring function.
0 Communities
1 Members
0 Resources
9 MeSH Terms
Zebrafish Developmental Models of Skeletal Diseases.
Luderman LN, Unlu G, Knapik EW
(2017) Curr Top Dev Biol 124: 81-124
MeSH Terms: Animals, Bone Diseases, Cartilage, Disease Models, Animal, Extracellular Matrix, Humans, Macromolecular Substances, Zebrafish
Show Abstract · Added April 26, 2017
The zebrafish skeleton shares many similarities with human and other vertebrate skeletons. Over the past years, work in zebrafish has provided an extensive understanding of the basic developmental mechanisms and cellular pathways directing skeletal development and homeostasis. This review will focus on the cell biology of cartilage and bone and how the basic cellular processes within chondrocytes and osteocytes function to assemble the structural frame of a vertebrate body. We will discuss fundamental functions of skeletal cells in production and secretion of extracellular matrix and cellular activities leading to differentiation of progenitors to mature cells that make up the skeleton. We highlight important examples where findings in zebrafish provided direction for the search for genes causing human skeletal defects and also how zebrafish research has proven important for validating candidate human disease genes. The work we cover here illustrates utility of zebrafish in unraveling molecular mechanisms of cellular functions necessary to form and maintain a healthy skeleton.
© 2017 Elsevier Inc. All rights reserved.
1 Communities
1 Members
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8 MeSH Terms
Simple rules for passive diffusion through the nuclear pore complex.
Timney BL, Raveh B, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, Rout MP
(2016) J Cell Biol 215: 57-76
MeSH Terms: Biological Transport, Computer Simulation, Diffusion, Fluorescence Recovery After Photobleaching, Kinetics, Macromolecular Substances, Molecular Weight, Mutation, Nuclear Pore, Nuclear Pore Complex Proteins, Permeability, Protein Domains, Saccharomyces cerevisiae, Substrate Specificity, Thermodynamics, Time Factors
Show Abstract · Added April 14, 2017
Passive macromolecular diffusion through nuclear pore complexes (NPCs) is thought to decrease dramatically beyond a 30-60-kD size threshold. Using thousands of independent time-resolved fluorescence microscopy measurements in vivo, we show that the NPC lacks such a firm size threshold; instead, it forms a soft barrier to passive diffusion that intensifies gradually with increasing molecular mass in both the wild-type and mutant strains with various subsets of phenylalanine-glycine (FG) domains and different levels of baseline passive permeability. Brownian dynamics simulations replicate these findings and indicate that the soft barrier results from the highly dynamic FG repeat domains and the diffusing macromolecules mutually constraining and competing for available volume in the interior of the NPC, setting up entropic repulsion forces. We found that FG domains with exceptionally high net charge and low hydropathy near the cytoplasmic end of the central channel contribute more strongly to obstruction of passive diffusion than to facilitated transport, revealing a compartmentalized functional arrangement within the NPC.
© 2016 Timney et al.
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1 Members
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16 MeSH Terms
Data publication with the structural biology data grid supports live analysis.
Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P
(2016) Nat Commun 7: 10882
MeSH Terms: Crystallography, X-Ray, Databases, Genetic, Internet, Macromolecular Substances, Publications, Software
Show Abstract · Added April 7, 2017
Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.
1 Communities
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6 MeSH Terms
Molecular and Structural Analysis of the Helicobacter pylori cag Type IV Secretion System Core Complex.
Frick-Cheng AE, Pyburn TM, Voss BJ, McDonald WH, Ohi MD, Cover TL
(2016) MBio 7: e02001-15
MeSH Terms: Helicobacter pylori, Humans, Immunohistochemistry, Macromolecular Substances, Microscopy, Electron, Type IV Secretion Systems
Show Abstract · Added January 26, 2016
UNLABELLED - Bacterial type IV secretion systems (T4SSs) can function to export or import DNA, and can deliver effector proteins into a wide range of target cells. Relatively little is known about the structural organization of T4SSs that secrete effector proteins. In this report, we describe the isolation and analysis of a membrane-spanning core complex from the Helicobacter pylori cag T4SS, which has an important role in the pathogenesis of gastric cancer. We show that this complex contains five H. pylori proteins, CagM, CagT, Cag3, CagX, and CagY, each of which is required for cag T4SS activity. CagX and CagY are orthologous to the VirB9 and VirB10 components of T4SSs in other bacterial species, and the other three Cag proteins are unique to H. pylori. Negative stain single-particle electron microscopy revealed complexes 41 nm in diameter, characterized by a 19-nm-diameter central ring linked to an outer ring by spoke-like linkers. Incomplete complexes formed by Δcag3 or ΔcagT mutants retain the 19-nm-diameter ring but lack an organized outer ring. Immunogold labeling studies confirm that Cag3 is a peripheral component of the complex. The cag T4SS core complex has an overall diameter and structural organization that differ considerably from the corresponding features of conjugative T4SSs. These results highlight specialized features of the H. pylori cag T4SS that are optimized for function in the human gastric mucosal environment.
IMPORTANCE - Type IV secretion systems (T4SSs) are versatile macromolecular machines that are present in many bacterial species. In this study, we investigated a T4SS found in the bacterium Helicobacter pylori. H. pylori is an important cause of stomach cancer, and the H. pylori T4SS contributes to cancer pathogenesis by mediating entry of CagA (an effector protein regarded as a "bacterial oncoprotein") into gastric epithelial cells. We isolated and analyzed the membrane-spanning core complex of the H. pylori T4SS and showed that it contains unique proteins unrelated to components of T4SSs in other bacterial species. These results constitute the first structural analysis of the core complex from this important secretion system.
Copyright © 2016 Frick-Cheng et al.
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3 Members
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6 MeSH Terms
ω-Alkynyl lipid surrogates for polyunsaturated fatty acids: free radical and enzymatic oxidations.
Beavers WN, Serwa R, Shimozu Y, Tallman KA, Vaught M, Dalvie ED, Marnett LJ, Porter NA
(2014) J Am Chem Soc 136: 11529-39
MeSH Terms: Animals, Arachidonate 15-Lipoxygenase, Arachidonic Acid, Carbon, Cell Line, Chromatography, High Pressure Liquid, Cyclooxygenase 1, Cyclooxygenase 2, Fatty Acids, Fatty Acids, Unsaturated, Free Radicals, Hydroxyeicosatetraenoic Acids, Linoleic Acid, Lipids, Lipoxygenases, Macromolecular Substances, Macrophages, Mice, Oxygen, Soybeans, Spectrophotometry, Ultraviolet, Tandem Mass Spectrometry
Show Abstract · Added February 22, 2016
Lipid and lipid metabolite profiling are important parameters in understanding the pathogenesis of many diseases. Alkynylated polyunsaturated fatty acids are potentially useful probes for tracking the fate of fatty acid metabolites. The nonenzymatic and enzymatic oxidations of ω-alkynyl linoleic acid and ω-alkynyl arachidonic acid were compared to that of linoleic and arachidonic acid. There was no detectable difference in the primary products of nonenzymatic oxidation, which comprised cis,trans-hydroxy fatty acids. Similar hydroxy fatty acid products were formed when ω-alkynyl linoleic acid and ω-alkynyl arachidonic acid were reacted with lipoxygenase enzymes that introduce oxygen at different positions in the carbon chains. The rates of oxidation of ω-alkynylated fatty acids were reduced compared to those of the natural fatty acids. Cyclooxygenase-1 and -2 did not oxidize alkynyl linoleic but efficiently oxidized alkynyl arachidonic acid. The products were identified as alkynyl 11-hydroxy-eicosatetraenoic acid, alkynyl 11-hydroxy-8,9-epoxy-eicosatrienoic acid, and alkynyl prostaglandins. This deviation from the metabolic profile of arachidonic acid may limit the utility of alkynyl arachidonic acid in the tracking of cyclooxygenase-based lipid oxidation. The formation of alkynyl 11-hydroxy-8,9-epoxy-eicosatrienoic acid compared to alkynyl prostaglandins suggests that the ω-alkyne group causes a conformational change in the fatty acid bound to the enzyme, which reduces the efficiency of cyclization of dioxalanyl intermediates to endoperoxide intermediates. Overall, ω-alkynyl linoleic acid and ω-alkynyl arachidonic acid appear to be metabolically competent surrogates for tracking the fate of polyunsaturated fatty acids when looking at models involving autoxidation and oxidation by lipoxygenases.
0 Communities
1 Members
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22 MeSH Terms
Exchange-mediated contrast in CEST and spin-lock imaging.
Cobb JG, Li K, Xie J, Gochberg DF, Gore JC
(2014) Magn Reson Imaging 32: 28-40
MeSH Terms: Amides, Carbohydrates, Computer Simulation, Contrast Media, Dextrans, Image Enhancement, Macromolecular Substances, Magnetic Resonance Imaging, Peptides, Polylysine, Protons, Water
Show Abstract · Added March 7, 2014
PURPOSE - Magnetic resonance images of biological media based on chemical exchange saturation transfer (CEST) show contrast that depends on chemical exchange between water and other protons. In addition, spin-lattice relaxation rates in the rotating frame (R1ρ) are also affected by exchange, especially at high fields, and can be exploited to provide novel, exchange-dependent contrast. Here, we evaluate and compare the factors that modulate the exchange contrast for these methods using simulations and experiments on simple, biologically relevant samples.
METHODS - Simulations and experimental measurements at 9.4 T of rotating frame relaxation rate dispersion and CEST contrast were performed on solutions of macromolecules containing amide and hydroxyl exchanging protons.
RESULTS - The simulations and experimental measurements confirm that both CEST and R1ρ measurements depend on similar exchange parameters, but they manifest themselves differently in their effects on contrast. CEST contrast may be larger in the slow and intermediate exchange regimes for protons with large resonant frequency offsets (e.g. >2 ppm). Spin-locking techniques can produce larger contrast enhancement when resonant frequency offsets are small (<2 ppm) and exchange is in the intermediate-to-fast regime. The image contrasts scale differently with field strength, exchange rate and concentration.
CONCLUSION - CEST and R1ρ measurements provide different and somewhat complementary information about exchange in tissues. Whereas CEST can depict exchange of protons with specific chemical shifts, appropriate R1ρ-dependent acquisitions can be employed to selectively portray protons of specific exchange rates.
© 2013.
0 Communities
1 Members
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12 MeSH Terms
Effects of pressure and electrical charge on macromolecular transport across bovine lens basement membrane.
Ferrell N, Cameron KO, Groszek JJ, Hofmann CL, Li L, Smith RA, Bian A, Shintani A, Zydney AL, Fissell WH
(2013) Biophys J 104: 1476-84
MeSH Terms: Animals, Basement Membrane, Biological Transport, Cattle, Electric Conductivity, Lens, Crystalline, Macromolecular Substances, Permeability, Pressure
Show Abstract · Added August 21, 2013
Molecular transport through the basement membrane is important for a number of physiological functions, and dysregulation of basement membrane architecture can have serious pathological consequences. The structure-function relationships that govern molecular transport in basement membranes are not fully understood. The basement membrane from the lens capsule of the eye is a collagen IV-rich matrix that can easily be extracted and manipulated in vitro. As such, it provides a convenient model for studying the functional relationships that govern molecular transport in basement membranes. Here we investigate the effects of increased transmembrane pressure and solute electrical charge on the transport properties of the lens basement membrane (LBM) from the bovine eye. Pressure-permeability relationships in LBM transport were governed primarily by changes in diffusive and convective contributions to solute flux and not by pressure-dependent changes in intrinsic membrane properties. The solute electrical charge had a minimal but statistically significant effect on solute transport through the LBM that was opposite of the expected electrokinetic behavior. The observed transport characteristics of the LBM are discussed in the context of established membrane transport modeling and previous work on the effects of pressure and electrical charge in other basement membrane systems.
Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.
0 Communities
1 Members
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9 MeSH Terms
Ex vivo red blood cell hemolysis assay for the evaluation of pH-responsive endosomolytic agents for cytosolic delivery of biomacromolecular drugs.
Evans BC, Nelson CE, Yu SS, Beavers KR, Kim AJ, Li H, Nelson HM, Giorgio TD, Duvall CL
(2013) J Vis Exp : e50166
MeSH Terms: Cytosol, Drug Carriers, Drug Delivery Systems, Endosomes, Erythrocyte Membrane, Erythrocytes, Hemolysis, Humans, Hydrogen-Ion Concentration, Lipid Bilayers, Lysosomes, Macromolecular Substances
Show Abstract · Added August 29, 2013
Phospholipid bilayers that constitute endo-lysosomal vesicles can pose a barrier to delivery of biologic drugs to intracellular targets. To overcome this barrier, a number of synthetic drug carriers have been engineered to actively disrupt the endosomal membrane and deliver cargo into the cytoplasm. Here, we describe the hemolysis assay, which can be used as rapid, high-throughput screen for the cytocompatibility and endosomolytic activity of intracellular drug delivery systems. In the hemolysis assay, human red blood cells and test materials are co-incubated in buffers at defined pHs that mimic extracellular, early endosomal, and late endo-lysosomal environments. Following a centrifugation step to pellet intact red blood cells, the amount of hemoglobin released into the medium is spectrophotometrically measured (405 nm for best dynamic range). The percent red blood cell disruption is then quantified relative to positive control samples lysed with a detergent. In this model system the erythrocyte membrane serves as a surrogate for the lipid bilayer membrane that enclose endo-lysosomal vesicles. The desired result is negligible hemolysis at physiologic pH (7.4) and robust hemolysis in the endo-lysosomal pH range from approximately pH 5-6.8.
1 Communities
2 Members
0 Resources
12 MeSH Terms
EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.
Lindert S, Alexander N, Wötzel N, Karakaş M, Stewart PL, Meiler J
(2012) Structure 20: 464-78
MeSH Terms: Algorithms, Cryoelectron Microscopy, Crystallography, X-Ray, Macromolecular Substances, Membrane Proteins, Models, Molecular, Molecular Biology, Protein Conformation, Protein Folding, Software
Show Abstract · Added January 24, 2015
Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy or X-ray crystallography. In these density maps, the general arrangement of secondary structure elements (SSEs) is revealed, whereas their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the SSEs de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins, the protocol consistently and reproducibly achieves models with root mean square deviation values <3 Å.
Copyright © 2012 Elsevier Ltd. All rights reserved.
1 Communities
1 Members
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10 MeSH Terms