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MPI für Biochemie  

Molecular Structural Biology
Wolfgang Baumeister

Visual Proteomics

 

Members

Dr. Stephan Nickell

Phone: +49 - 89 - 8578 2231

Overview

ViPromed

By help of the cryo-EM technique described in the section Cryo-Electron Tomography we are able to do molecular mapping of whole cells. This can tells us, where different proteins are located, and even when and where new proteins are built up and others are degraded.

High resolution cryoelectron tomograms are essentially 3D images of the cells entire proteome and they depict the network of interactions that orchestrates higher cellular functions.

However, it is not a trivial task to retrieve this information, because of the poor signal-to-noise ratio of the tomograms and the crowded nature of the cytoplasm.

This protein interaction research takes place as a part of INTERACTION PROTEOME, which is an integrated project to establish Europe as the international scientific leader in the analysis of protein-protein interactions. Major objectives include the establishment of a broadly applicable platform of routine methods for the analysis of protein interaction networks.

Molecular interpretation by template matching

template

Single particle analysis of proteins can provide their structure with very high resolution. Electron crystallography achieves a resolution down to 2 nanometers, X-ray crystallography even shows atomic resolution.

These protein models we use as templates for searching tomograms. By parallel computation the reference molecule is compared with the molecules detected inside the cell. The rate of success can be slightly different for various proteins, in case of the 20S proteasome template with 2 nm resolution we achieve correct identification of 97%.

For a systematic and exhaustive interrogation of tomograms a comprehensive library of template structures is needed. EM “single particle analysis” could contribute to such a library in a major way if we succeed in developing high throughput tactics.

The image on the right shows the reconstruction of a Tricorn protease, in the background you see the very noisy original tomography data.

Detection and identification strategy

detect

Publications

  1. Nickell S, Förster F, Linaroudis A, Net WD, Beck F, Hegerl R, Baumeister W, Plitzko JM. TOM software toolbox: acquisition and analysis for electron tomography. J Struct Biol, 2005. 149(3): p. 227-34.
  2. Nickell S, Kofler C, Leis AP, Baumeister W. A visual approach to proteomics. Nat Rev Mol Cell Biol, 2006. 7(3): 225-30.
  3. Sun N, Beck F, Knispel RW, Siedler F, Scheffer B, Nickell S, Baumeister W, Nagy I. Proteomics analysis of Thermoplasma acidophilum with a focus on protein complexes. Mol Cell Proteomics, 2007. 6(3): p. 492-502.