Lattice filter for processing image data of three-dimensional protein nanocrystals

Genderen, Eric Van; Li, Y.-W.; Nederlof, Igor; Abrahams, Jan Pieter

doi:10.1107/s205979831502149x

Cited by 9 publications

(9 citation statements)

References 7 publications

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“…By using images, a moderate resolution molecular envelop of the sample within the crystal could be determined, which then could be used to phase the MicroED data. These efforts are currently underway in several laboratories 87, 88 . Heavy metal phasing is another avenue of active research.…”

Section: Opportunities For Future Developmentmentioning

confidence: 99%

The cryo-EM method microcrystal electron diffraction (MicroED)

2019

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In 2013 we established a cryoelectron microscopy (cryo-EM) technique called microcrystal electron diffraction (MicroED). Since that time, data collection and analysis schemes have been fine-tuned, and structures for over 40 different proteins, oligopeptides and organic molecules and been determined. Here, we review the MicroED technique and place it in context with other structure determination methods. We showcase example structures solved by MicroED and provide practical advice to perspective users.

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Section: Opportunities For Future Developmentmentioning

confidence: 99%

The cryo-EM method microcrystal electron diffraction (MicroED)

2019

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“…The images used in Figures d and S15b were enhanced by a filter, based on a Wiener Filter approach . To enhance lattice signal, images were filtered using an in-house algorithm in which the filtered images were used as an overlay with 50% transparency on top of the original non-noise filtered image (Figures d and S15a) using the standard overlay feature in FIJI.…”

Section: Experimental Methodsmentioning

confidence: 99%

Shape-Shifting Peptide Nanomaterials: Surface Asymmetry Enables pH-Dependent Formation and Interconversion of Collagen Tubes and Sheets

et al. 2020

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The fabrication of dynamic, transformable biomaterials that respond to environmental cues represents a significant step forward in the development of synthetic materials that rival their highly functional, natural counterparts. Here, we describe the design and synthesis of crystalline supramolecular architectures from charge-complementary heteromeric pairs of collagen-mimetic peptides (CMPs). Under appropriate conditions, CMP pairs spontaneously assemble into either 1D ultraporous (pore diameter > 100 nm) tubes or 2D bilayer nanosheets due to the structural asymmetry that arises from heteromeric self-association. Crystalline collagen tubes represent a heretofore unobserved morphology of this common biomaterial. In-depth structural characterization from a suite of biophysical methods, including TEM, AFM, high-resolution cryo-EM, and SAXS/WAXS measurements, reveals that the sheet and tube assemblies possess a similar underlying lattice structure. The experimental evidence suggests that the tubular structures are a consequence of the self-scrolling of incipient 2D layers of collagen triple helices, and that the scrolling direction determines the formation of two distinct structural isoforms. Furthermore, we show that nanosheets and tubes can spontaneously interconvert through manipulation of the assembly pH and systematic adjustment of the CMP sequence. Altogether, we establish initial guidelines for the construction of dynamically responsive 1D and 2D assemblies that undergo a structurally programmed morphological transition.

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“…The circle indicates 3 Å resolution. A peak search routine identified potential Bragg spots above background (van Genderen et al, 2016). The average peak height of these spots was plotted as a function of resolution with a solid line.…”

Section: Scattering Events Described By Particle and Wave Modelsmentioning

confidence: 99%

Inelastic scattering and solvent scattering reduce dynamical diffraction in biological crystals

Latychevskaia

Abrahams

2019

Acta Crystallogr B Struct Sci Cryst Eng Mater

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Multi-slice simulations of electron diffraction by three-dimensional protein crystals have indicated that structure solution would be severely impeded by dynamical diffraction, especially when crystals are more than a few unit cells thick. In practice, however, dynamical diffraction turned out to be less of a problem than anticipated on the basis of these simulations. Here it is shown that two scattering phenomena, which are usually omitted from multi-slice simulations, reduce the dynamical effect: solvent scattering reduces the phase differences within the exit beam and inelastic scattering followed by elastic scattering results in diffusion of dynamical scattering out of Bragg peaks. Thus, these independent phenomena provide potential reasons for the apparent discrepancy between theory and practice in protein electron crystallography.

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Lattice filter for processing image data of three-dimensional protein nanocrystals

Cited by 9 publications

References 7 publications

The cryo-EM method microcrystal electron diffraction (MicroED)

The cryo-EM method microcrystal electron diffraction (MicroED)

Shape-Shifting Peptide Nanomaterials: Surface Asymmetry Enables pH-Dependent Formation and Interconversion of Collagen Tubes and Sheets

Inelastic scattering and solvent scattering reduce dynamical diffraction in biological crystals

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