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A S Frangakis

Publications and source records attributed to A S Frangakis.

5 recordsLinked to original sources

FhuA-mediated phage genome transfer into liposomes: a cryo-electron tomography study.

BACKGROUND: The transfer of phage genomes into host cells is a well established but only dimly understood process. Following the irreversible phage binding to a receptor in the bacterial outer membrane, the DNA is ejected from the viral capsid and transferred across the bacterial cell envelope. In Escherichia coli, the mere interaction of the phage T5 with its outer membrane receptor, the ferrichrome transporter FhuA, is sufficient to trigger the release of the DNA from the phage capsid. Although the structure of FhuA has been determined at atomic resolution, the understanding of the respective roles of phage and bacterial proteins in DNA channeling and the mechanisms by which the transfer of the DNA is mediated remains fragmentary. RESULTS: We report on the use of cryo-electron tomography to analyze, at a molecular level, the interactions of T5 phages bound to FhuA-containing proteoliposomes. The resolution of the three-dimensional reconstructions allowed us to visualize the phage-proteoliposome interaction before and after release of the genome into the vesicles. After binding to its receptor, the straight fiber of the phage T5 (the "tip" of the viral tail made of pb2 proteins) traverses the lipid bilayer, allowing the transfer of its double-stranded DNA (121,000 bp) into the proteoliposome. Concomitantly, the tip of the tail undergoes a major conformational change; it shrinks in length (from 50 to 23 nm), while its diameter increases (from 2 to 4 nm). CONCLUSIONS: Taking into account the crystal structure of FhuA, we conclude that FhuA is only used as a docking site for the phage. The tip of the phage tail acts like an "injection needle," creating a passageway at the periphery of FhuA, through which the DNA crosses the membrane. A possible mechanistic scenario for the transfer of the viral genome into bacteria is discussed.

Bacterial Outer Membrane Proteins↗

Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion.

Electron tomography is a powerful technique capable of giving unique insights into the three-dimensional structural organization of pleomorphic biological objects. However, visualization and interpretation of the resulting volumetric data are hampered by an extremely low signal-to-noise ratio, especially when ice-embedded biological specimens are investigated. Usually, isosurface representation or volume rendering of such data is hindered without any further signal enhancement. We propose a novel technique for noise reduction based on nonlinear anisotropic diffusion. The approach combines efficient noise reduction with excellent signal preservation and is clearly superior to conventional methods (e.g., low-pass and median filtering) and invariant wavelet transform filtering. The gain in the signal-to-noise ratio is verified and demonstrated by means of Fourier shell correlation. Improved visualization performance after processing the 3D images is demonstrated with two examples, tomographic reconstructions of chromatin and of a mitochondrion. Parameter settings and discretization stencils are presented in detail.

Anisotropy↗

Wavelet transform filtering and nonlinear anisotropic diffusion assessed for signal reconstruction performance on multidimensional biomedical data.

Computer tomography (CT) techniques are the most widely applicable noninvasive methods for obtaining two- and three-dimensional insights into biological objects. They comprise CT for medical applications, as well as electron tomography used for investigating macromolecular and cellular specimens. Recent advances in the recording schemes improve the speed and resolution frontiers and provide new insights into structural organizations of different objects. However, many data sets suffer from a poor signal-to-noise ratio, which severely hinders the application of methods for automated data analysis, such as feature extraction, segmentation, and visualization. We propose the multidimensional implementation of two powerful signal reconstruction techniques, namely invariant wavelet filtering and nonlinear anisotropic diffusion. We establish quantitative measures to assess the signal reconstruction performance on synthetic data and biomedical images. The appropriate multidimensional implementations of wavelet and diffusion techniques allow for a superior performance over conventional noise-reduction methods. We derive the conditions for the choice between wavelet and diffusion techniques with respect to an optimal signal reconstruction performance. Results of applying the proposed methods in two very different imaging domains-molecular biology and clinical research-are provided.

Anisotropy↗

Toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomograms.

Electron tomography is the only technique available that allows us to visualize the three-dimensional structure of unfixed and unstained cells currently with a resolution of 6-8 nm, but with the prospect to reach 2-4 nm. This raises the possibility of detecting and identifying specific macromolecular complexes within their cellular context by virtue of their structural signature. Templates derived from the high-resolution structure of the molecule under scrutiny are used to search the reconstructed volume. Here we outline and test a computationally feasible two-step procedure: In a first step, mean-curvature motion is used for segmentation, yielding subvolumes that contain with a high probability macromolecules in the expected size range. Subsequently, the particles contained in the subvolumes are identified by cross-correlation, using a set of three-dimensional templates. With simulated and real tomographic data we demonstrate that such an approach is feasible and we explore the detection limits. Even structurally similar particles, such as the thermosome, GroEL, and the 20S proteasome can be identified with high fidelity. This opens up exciting prospects for mapping the territorial distribution of macromolecules and for analyzing molecular interactions in situ.

Algorithms↗

Cryo-electron tomography of neurospora mitochondria.

Cryo-electron tomography was used to study the structural organization of whole frozen-hydrated mitochondria from Neurospora crassa. Unlike mitochondria from many other species and tissues, in this case the cristae form a three-dimensional network of interconnected lamellae. Basically, the three-dimensional structure of ice-embedded mitochondria from this species is consistent with previous descriptions of mitochondria prepared by chemical fixation and resin embedding. Nonetheless, ice-embedded mitochondria display some important differences: the outer surface of the mitochondria was found to be rather smooth, the intermembrane space was constant in width, and distinct contact sites between the membranes were clearly revealed. Furthermore ATP synthase particles on the outer surface of an "inside-out vesicle" were visible in 3-D reconstructions. Thus, cryo-electron tomography can provide detailed insights into these organelles with minimal perturbations of the physiological state. This indicates that it is a realistic goal to achieve "molecular resolution" with rather large biological specimens in the near future, ultimately allowing the identification and localization of macromolecules in their cellular context.

Cryoelectron Microscopy↗