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Paired beta-sheet structure of an Abeta irsr amyloid fibril revealed by electron microscopy. See other articles in PMC that cite the published article. I show that when resolution is limited there are intrinsic ambiguities that cannot be resolved with the images alone. Open in a separate window.
A robust algorithm for the reconstruction of helical filaments using single-particle methods.
The stalk region of dynamin drives the constriction of dynamin tubes. There is absolutely no relation between the box length chosen and the classical notion of a helical repeat.
IHRSR – What does IHRSR stand for? The Free Dictionary
If we look at the present example, one way to use the phase information would be to do cross-correlations between the projections of the different reconstructions and the images. For most real specimens solid curve there is an optimal box length that can ihrsg be found empirically. The Iterative Helical Real Space Reconstruction IHRSR approach has been the main methodology, and it surmounts many of the problems posed by real polymers that are flexible, display less than crystalline order, or are weakly scattering.
Atomic model of a myosin filament in the relaxed state. That is the maximal axial translation that is needed to bring any given image into register with the best-matching projection.
Reconstruction of Helical Filaments and Tubes
ihdsr Author manuscript; available in PMC Dec The power spectrum in b comes from a three-dimensional volume with This is an important point, as the ambiguities that I discuss disappear in this case when higher resolution is available. The aligned images are then used in a back-projection algorithm to generate a three-dimensional reconstruction Fig. This volume is searched for the helical screw operator the coupled rotation and axial ijrsr that minimizes the variance between the actual volume and a symmetrized version of the volume.
This phase information might be useful in discriminating between a correct and an incorrect solution. The solution in Fig.
Single-particle reconstruction from EM images of helical filaments. Much ihsr the protein in bacterial, archaeal and eukaryotic cells exists in the form of helical polymers. I have argued Egelman, b that this description of helical symmetry is a poor one, as it is ill-conditioned.
A general method for reconstructing helical polymers Egelman, was proposed that involves an iterative determination and imposition of helical symmetry upon objects that have been reconstructed without any helical symmetry imposed. Information would need to be obtained, such as by tilting the sample in the EM Finch, or by metal shadowing Woodward et al. A comparative analysis of Dmc1 and Rad51 nucleoprotein filaments.
So how can one ever solve a helical structure given these potential problems? There are many practical questions that arise when using IHRSR, and one of the first is the optimal length of the segments to be used, and the optimal overlap or shift between adjacent boxes.
The main difficulty in applying this method, or even Fourier-Bessel methods, is in determining the approximate helical symmetry.
The power spectrum of this image is shown in Fig.
IHRSR++ – SBGrid Consortium – Supported Software
For more than 30 years after DeRosier and Klug almost all helical reconstructions involved the Fourier-Bessel formalism Klug et al. The degeneracy of solutions ihrsrr Fig. Despite having different Bessel orders on layer lines 1, 2, 4 and 5, the power spectra all have peaks at identical positions due to the fact that the diffraction is coming from different radii.
Since all projections of a solid cylinder ihrwr the same when the azimuthal angle is changed, the effect of using a solid cylinder as an initial reference is to simply assign random azimuthal ihrst to each image.
Because of the utility of helical arrays, and the elimination of the need to obtain tilts when working with two-dimensional crystals, some effort has actually been placed in forming synthetic helical tubes as a means to reconstruct a protein or complex Dang et al.
This estimate can come from indexing power spectra obtained from the images, from knowledge of the mass per unit length, or from trial and error.
Strikingly, the correct solution Fig.