Recent developments in cryo-electron microscopy reconstruction of single particles

Tao, Yizhi Jane; Zhang, Wei

doi:10.1016/s0959-440x(00)00139-1

Cited by 15 publications

(2 citation statements)

References 80 publications

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“…First, cryo-EM allows the visualization of very large macromolecules and their complexes, such as the ribosome or the nuclear pore complex. These giant structures are usually hard to crystallize [69], and even if crystallized, the resolutions of structures solved by X-ray diffraction are comparable to that of cryo-EM [63–66,70]. Second, in cryo-EM experiments data are collected from single molecules or complexes with molecular conformations unaffected by potentially ‘unnatural’ interactions due to the formation of crystal contacts.…”

Section: Integration Of X-ray Crystallography With Other Biophysicmentioning

confidence: 99%

X-ray crystallography over the past decade for novel drug discovery – where are we heading next?

Zheng

Handing

Zimmerman

et al. 2015

Expert Opinion on Drug Discovery

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Introduction Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. Areas covered This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. Expert opinion X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.

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Section: Integration Of X-ray Crystallography With Other Biophysicmentioning

confidence: 99%

X-ray crystallography over the past decade for novel drug discovery – where are we heading next?

Zheng

Handing

Zimmerman

et al. 2015

Expert Opinion on Drug Discovery

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“…Using the Strep•SWNT, we captured a stable protein complex (nucleoid protein HU-DNA complex) (Dame and Goosen 2002;Rouviereyaniv and Gros 1975) on a mica surface and in solution (Liu et al 2012). In order to show that the Strep•SWNT can also be used for the capture of unstable protein complex for the further applications in 3D structural reconstruction using single-particle cryo-EM analysis (Zhou 2008;Frank 2002;van Heel et al 2000;Tao and Zhang 2000), in the current study, we tested the capture of an unstable protein complex (DNA-EcoRI complex) (Sorel et al 2006) on the Strep•SWNT and characterized these complexes with atomic force microscopy (AFM) and electrophoresis gel analysis. For the first time, we show that the unstable protein complexes can indeed be captured on these Strep•SWNT, and this paves the way for the cryo-EM analysis for 3D structural characterization of unstable protein complexes.…”

Section: Introductionmentioning

confidence: 99%

Capture of unstable protein complex on the streptavidin-coated single-walled carbon nanotubes

Liu

Voskamp²,

Zhang

et al. 2013

J Nanopart Res

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Purification of unstable protein complexes is a bottleneck for investigation of their 3D structure and in protein-protein interaction studies. In this paper, we demonstrate that streptavidin-coated single-walled carbon nanotubes (Strep•SWNT) can be used to capture the biotinylated DNA-EcoRI complexes on a 2D surface and in solution using atomic force microscopy and electrophoresis analysis, respectively. The restriction enzyme EcoRI forms unstable complexes with DNA in the absence of Mg 2? . Capturing the EcoRI-DNA complexes on the Strep•SWNT succeeded in the absence of Mg 2? , demonstrating that the Strep•SWNT can be used for purifying unstable protein complexes.

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Construction of Low-Resolution X-Ray Crystallographic Electron Density Maps of the Ribosome

Cate¹

2001

Methods

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Recent developments in cryo-electron microscopy reconstruction of single particles

Cited by 15 publications

References 80 publications

X-ray crystallography over the past decade for novel drug discovery – where are we heading next?

X-ray crystallography over the past decade for novel drug discovery – where are we heading next?

Capture of unstable protein complex on the streptavidin-coated single-walled carbon nanotubes

Construction of Low-Resolution X-Ray Crystallographic Electron Density Maps of the Ribosome

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