Publications
78 results found
Beeby M, 2014, Evolution of Novel Components of the Bacterial Flagellar Motor, 28th Annual Symposium of the Protein-Society, Publisher: WILEY-BLACKWELL, Pages: 61-61, ISSN: 0961-8368
Gumbart JC, Beeby M, Jensen GJ, et al., 2014, Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale aimulations, PLOS Computational Biology, Vol: 10, ISSN: 1553-734X
Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgorpressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterialcell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid,yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by themolecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is notknown. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in adisordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as knownexperimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other featuressuch as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting thedisordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure andbehavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of allatomsimulations to reproduce a range of macroscopic observables for extended polymer meshes.
Beeby M, Gumbart JC, Roux B, et al., 2013, Architecture and assembly of the Gram-positive cell wall, Molecular Microbiology, Vol: 88, Pages: 664-672, ISSN: 0950-382X
Jensen G, Briegel A, Beeby M, 2013, Visualizing large macromolecular assemblies in vivo with electron cryotomography, 245th National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Abrusci P, Vergara-Irigaray M, Johnson S, et al., 2013, Architecture of the major component of the type III secretion system export apparatus, NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol: 20, Pages: 99-U126, ISSN: 1545-9993
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- Citations: 164
Beeby M, Cho M, Stubbe J, et al., 2012, Growth and localization of polyhydroxybutyrate granules in Ralstonia eutropha, J. Bacteriol., Vol: 194, Pages: 1092-1099
Briegel A, Beeby M, Thanbichler M, et al., 2011, Activated chemoreceptor arrays remain intact and hexagonally packed, Mol. Microbiol., Vol: 82, Pages: 748-757
Chen S, Beeby M, Murphy GE, et al., 2011, Structural diversity of bacterial flagellar motors, EMBO J., Vol: 30, Pages: 2972-2981
Chen S, McDowall A, Dobro MJ, et al., 2010, Electron cryotomography of bacterial cells, Jove-Journal of Visualized Experiments, Vol: 39, ISSN: 1940-087X
While much is already known about the basic metabolism of bacterial cells, many fundamental questions are still surprisingly unanswered,including for instance how they generate and maintain specific cell shapes, establish polarity, segregate their genomes, and divide. In orderto understand these phenomena, imaging technologies are needed that bridge the resolution gap between fluorescence light microscopy andhigher-resolution methods such as X-ray crystallography and NMR spectroscopy.Electron cryotomography (ECT) is an emerging technology that does just this, allowing the ultrastructure of cells to be visualized in a near-nativestate, in three dimensions (3D), with "macromolecular" resolution (~4nm).1, 2 In ECT, cells are imaged in a vitreous, "frozen-hydrated" state ina cryo transmission electron microscope (cryoTEM) at low temperature (< -180°C). For slender cells (up to ~500 nm in thickness3), intact cellsare plunge-frozen within media across EM grids in cryogens such as ethane or ethane/propane mixtures. Thicker cells and biofilms can alsobe imaged in a vitreous state by first "high-pressure freezing" and then, "cryo-sectioning" them. A series of two-dimensional projection imagesare then collected through the sample as it is incrementally tilted along one or two axes. A three-dimensional reconstruction, or "tomogram" canthen be calculated from the images. While ECT requires expensive instrumentation, in recent years, it has been used in a few labs to reveal thestructures of various external appendages, the structures of different cell envelopes, the positions and structures of cytoskeletal filaments, andthe locations and architectures of large macromolecular assemblies such as flagellar motors, internal compartments and chemoreceptor arrays.1,2In this video article we illustrate how to image cells with ECT, including the processes of sample preparation, data collection, tomogramreconstruction, and interpre
Chim N, McMath LM, Beeby M, et al., 2009, Advances in Mycobacterium tuberculosis structural genomics: investigating potential chinks in the armor of a deadly pathogen, Infect Disord Drug Targets, Vol: 9, Pages: 475-492
Beeby M, Bobik TA, Yeates TO, 2009, Exploiting genomic patterns to discover new supramolecular protein assemblies, Protein Sci., Vol: 18, Pages: 69-79
Yeates TO, Beeby M, 2006, Proteins in a small world, SCIENCE, Vol: 314, Pages: 1882-1883, ISSN: 0036-8075
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- Citations: 8
Yeates TO, Beeby M, 2006, Biochemistry. Proteins in a small world, Science, Vol: 314, Pages: 1882-1883
Beeby M, O'Connor BD, Ryttersgaard C, et al., 2005, The Genomics of disulfide bonding and protein stabilization in thermophiles, PLOS BIOLOGY, Vol: 3, Pages: 1549-1558, ISSN: 1544-9173
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- Citations: 156
Beeby M, O Connor BD, Ryttersgaard C, et al., 2005, The genomics of disulfide bonding and protein stabilization in thermophiles, PLoS Biol., Vol: 3, Pages: e309-e309
Kerfeld CA, Sawaya MR, Tanaka S, et al., 2005, Protein structures forming the shell of primitive bacterial organelles, Science, Vol: 309, Pages: 936-938
Strong M, Graeber TG, Beeby M, et al., 2003, Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps, Nucleic Acids Res., Vol: 31, Pages: 7099-7109
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