Max Planck Institute for Molecular Genetics

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Collaborations:

X-ray crystallography:

Prof. Shigeyuki Yokoyama is the project director of the RIKEN Genomic Sciences Centre (Japan).
We have established a collaboration with the ribosome group of Prof. Yokoyama, supervised by Dr. Chie Hori-Takemoto to develop the crystallization of 30S and 70S functional complexes.

Prof. Dr Yuji Kobayashi at the graduate school of pharmaceutical sciences at Osaka University, Japan, has, in the past 5 years, solved the structure of five different RRF by X-ray crystallography and NMR and specifically, constructed and characterized a domain I-RRF construct from E. coli.
Recently, we have determined the crystal structure of domain I of RRF bound to the 50S subunit of D. radiodurans at 3.3 Å resolution.

Dr. Sigurd Wilbanks, at the Otago University, New Zealand , is a structural biochemist, whose group has extensive knowledge of the methods associated with purification of a variety of molecular chaperones. We have recently crystallized the D. radiodurans trigger factor binding domain in complex with the D. radiodurans 50S subunit.

Dr. Hideji Yoshida at the Department of Physics, Osaka Medical College, in Japan, working together with Prof. Akira Wada, has extensively characterized the properties and binding site of the ribosome modulation factor (RMF) on the E. coli ribosome. We are working in collaboration to determine the binding site of this factor on the large ribosomal subunit .

We are appreciative to Dr. Clemens Schulze-Briese and Dr. Takashi Tomizaki at the Swiss Light Source (at the Paul Scherrer Institute in Villigen) for exert assistance and technical support.

NMR:

In collaboration with the group of Prof. Chris Dobson , we are interested in analyzing functional ribosome complexes using NMR. Previously we have characterized the dynamics of the stalk proteins bound to the ribosome .

Mass Spectrometry:

In collaboration with the group of Prof. Carol Robinson, mass spectrometry has been used to analyse the stability of intact 70S ribosomes. The results show that emerging mass spectrometric techniques can be used to characterize a fully functional biological assembly as well as its isolated components .

We also collaborate with Dr. Joachim Klose and the in-house group of Dr. Johan Gobom to analyse the composition of ribosomes from different species. Recently we revealed the complexity of the 80S cytoplasmic ribosomes from the model flowering plant Arabidopsis thaliana.

Cryo-electron microscopy:

The analysis of stalled ribosome complex using cryo-electron microscopy has been performed in collaboration with the group of Prof. Chris Dobson and Prof. David Stuart (Wellcome Trust Centre, University of Oxford). The results of these studies suggest that folding of the nascent chain may occur before it emerges from the ribosomal tunnel.

Recently, we have determined the binding site of the highly conserved GTPase Era on the 30S subunit in collaboration with Prof. Shigeyuki Yokoyama and the cryo-EM group of Dr. Rajendra Agrawal.

As part of the Ultra structure network in Berlin we are analyzing many ribosome-functional complexes in collaboration with the cryo-EM group of Prof. Dr. Christian Spahn.

Functional Studies

Prof. Knud H. Nierhaus has over 30 years experience studying functional aspects of the ribosome and protein synthesis.
We work closely with his group on a variety of different projects.

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