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NMR in structural biology: methods development for protein structure determination

Applicant Wider Gerhard
Number 100399
Funding scheme Project funding
Research institution Institut für Molekularbiologie und Biophysik ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Biophysics
Start/End 01.10.2003 - 31.12.2006
Approved amount 176'118.00
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Keywords (6)

NMR spectroscopy in solution; NMR structures of proteins; Structural biology; Hydration ; Trosy Crinept; SAR by NMR

Lay Summary (English)

Lead
Lay summary
For the detailed understanding of the processes of live, a picture at atomic resolution of the molecules involved in this processes is required. Nuclear magnetic resonance (NMR) spectroscopy has become a powerful tool that can provide the necessary information. In this project we develop new techniques and apply NMR to biological systems. For the analysis of NMR spectra each signal has to be assigned to an atom in the molecule under investigation. Conventionally, this task requires for proteins fully 13C and 15N isotope labeling; however, 13C labeling can be become very expensive. Since many more protein structures were/are determined by X-ray crystallography than by NMR, the X-ray structure is often available when e.g., dynamic properties of proteins or molecular interactions shall be studied. For some of these investigations NMR is very well suited and often only 15N-labeled proteins are necessary. We developed a resonance assignment method based on NOE (nuclear Overhauser effect) spectra of only 15N labeled proteins and their known X-ray structure. In collaboration with the research group of Prof. Wüthrich we developed a new procedure for obtaining efficient sequence specific assignments of fully 13C,15N labeled proteins based on an automated analysis of projections of high-dimensional NMR spectra (APSY: automated projection spectroscopy). Measurement of protein concentrations by NMR spectroscopy requires an internal reference compound which is highly undesirable when working with biological macromolecules. We developed a method, PULCON, which permits the determination of concentrations by NMR without the addition of an internal reference compound. In addition to the above technical developments we applied NMR spectroscopy to biological questions in the following two ongoing, collaborative projects. “Characterization of novel ubiquitin-binding domains in Y-family polymerases”: upon DNA damage the replication machinery is directed into the translesion synthesis (TLS) pathway. Using NMR spectroscopy we are studying novel ubiquitin-binding domains in TLS polymerases to get further insight into the nature of their interactions. “Studies of FimA as a basis for a structure determination of a type 1 pilus rod”: we are determining the structure, dynamics and interactions of the protein FimA by NMR. FimA forms the pili of uropathogenic E.coli strains. Based on the NMR data of FimA we will try to deduce the whole pilus rod assembly.More details on all projects can be found on www.mol.biol.ethz.ch/groups/wider_group.
Direct link to Lay Summary Last update: 21.02.2013

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Associated projects

Number Title Start Funding scheme
113730 NMR in structural biology: protein structure determination and studies of protein-protein interactions 01.01.2007 Project funding
66427 NMR in structural biology: methods development for structural genomics and protein structure determination, in particular prionproteins 01.04.2002 Project funding

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