Protein structure determined in living cells

March 05, 2009

The function of a protein is determined both by its structure and by its interaction partners in the cell. Until now, proteins had to be isolated for analyzing them. An international team of researchers from Tokyo Metropolitan University, Goethe University, and the Frankfurt Institute for Advanced Studies (FIAS) has, for the first time, determined the structure of a protein in its natural environment, the living cell. Using nuclear magnetic resonance (NMR) spectroscopy, the researchers solved the structure of a protein within the bacterium Escherichia coli. "We have reached an important goal of molecular biology", says Prof. Peter Güntert from the Goethe University's Biomolecular Magnetic Resonance Center. (BMRZ) of The research results will be published by the scientific journal Nature on March 5, 2009.

Conventionally, proteins are extracted from the cell, purified, and analyzed in single crystals or in solution. NMR spectroscopy detects signals from the nuclei of hydrogen atoms that are ubiquitous in organic molecules. Measurements in the living cell are challenging because it is difficult to distinguish between the protein of interest and the many other proteins in the cytoplasm. The Japanese researchers around Prof. Yutaka Ito solved this problem by introducing the gene of a putative heavy-metal-binding protein into the model system Escherichia coli, where the protein was in high concentration.

The success of the measurements relies on the method of "in-cell" NMR spectroscopy that was developed a few years ago by Prof. Volker Dötsch from BMRZ at Goethe University. Dötsch was able to attribute signals from living cells to specific proteins that he had labeled with the stable nitrogen isotope N-15. However, it was not possible to calculate a three-dimensional structure. "About two days of measurement time are required to measure a multidimensional NMR spectrum", says Peter Güntert. "Unfortunately, the cells survive for only a 5-6 hours without supply of oxygen and nutrients. Güntert and his colleagues compensated for the concomitant drastic reduction of the measurement time by computational reconstruction of the complete spectrum. Then, they calculated a detailed three-dimensional structure of the protein within E. coli cells using software that was developed in their research group.

The structure determination of proteins by in-cell NMR spectroscopy opens new avenues to investigate at atomic resolution how proteins participate in biological processes in living systems. In-cell NMR spectroscopy advances our understanding of the molecular basis of life, and can contribute to the development of new, better targeted pharmaceuticals.
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Since July 2007 Prof. Peter Güntert is leading the Lichtenberg professorship for NMR-based Computational Structural Biology at Goethe University that is supported with more than 1.4 million Euro by the VolkswagenFoundation.

Publication: Sakakibara, D., Sasaki, A., Ikeya, T., Hamatsu, J., Hanashima, T., Mishima, M., Yoshimasu, M., Hayashi, N., Mikawa, T., Wälchli, M., Smith, B. O., Shirakawa, M., Güntert, P. & Ito, Y. Protein structure determination in living cells by in-cell NMR spectroscopy. Nature (March 5, 2009).

Goethe University Frankfurt

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