Putting structure into context: fitting of atomic models into electron microscopic and electron tomographic reconstructions

Abstract

A complete understanding of complex dynamic cellular processes such as cell migration or cell adhesion requires the integration of atomic level structural information into the larger cellular context. While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale. Atomic-resolution information obtained by other means can be combined with this data to obtain three-dimensional models of large macromolecular assemblies in their cellular context. This article summarizes some recent advances in this field.

Piecing it together: Unraveling the elusive structure-function relationship in single-pass membrane receptors

“…The incorporation of electron multiplying CCD or CMOS cameras [126,127] have led to the emergence of single molecule imaging, enabling the fluorescence-based imaging of individual receptor molecules within the membrane [128]. Furthermore, advances in data collection and image processing have enabled high-throughput methods in electron microscopy resulting in nanometer-scale reconstructions of large biological assemblies by incorporating crystal structural data [129,130]. Single molecule imaging provides a novel link between structural and cellular biology by contextualizing models of receptor interactions within the dynamic cellular environment.…”

Electron crystallography — the waking beauty of structural biology

“…Clearly, resolution will likely be limited and significantly lower than needed to resolve near-atomic detail. However, routine electron crystallographic reconstruction of macromolecular complexes at subnanometer resolutions would have a tremendous impact because fitting of available subunit crystal structures into the subnanometer molecular envelopes would allow the construction of pseudo atomic models [44], which in turn would enable informed biochemical and cell biological studies. That prospect alone appears sufficient to advocate for further development of electron crystallography.…”

Efficient Extraction of Macromolecular Complexes from Electron Tomograms Based on Reduced Representation Templates

“…While there have been substantial efforts during the last few years [15–18], progress has been much slower than in related fields. One of the prime reasons for this is that image and signal processing methods developed for other domains are not straightforward to apply to electron tomography data owing to its special characteristics:…”