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Location: Room 411, Biozentrum; Klingelbergstr. 50-70, Basel
Using RNAi screens and phosphoproteomics to gain a systems understanding of Shigella infection.
Prof. Cécile Arrieumerlou, Biozentrum, Basel
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Location: HS 2, Pharmazentrum; Klingelbergstr. 50-70, Basel
Protein Structure and Dynamics from Low-Resolution Data
Dr. Gunnar Schroeder, Forschungszentrum Jülich, Jülich
Structure determination of large proteins and protein assemblies is a major challenge in molecular biology. Experiments, such as X-ray crystallography or single-particle Cryo-EM, on such complex systems often yield only low resolution (> 4Å) data, which are not sufficient to
fully determine atomistic structures. The refinement of approximate initial models is typically significantly harder than at high resolution. The Deformable Elastic Network (DEN) approach is presented that makes use of additional prior information on homologous structures which guides the refinement and dramatically improves the obtained structures. Furthermore, this approach can also be applied in combinations with molecular dynamics simulations to refine homology models in the absence of experimental information. Single-particle Cryo-EM yields images of individual proteins in potentially different conformations and therefore yields a wealth of information on structural dynamics. This information is however very difficult to extract since each image is extremely noisy. The common
approaches to reconstruct three-dimensional density maps average out any structural heterogeneity and the information on the dynamics is lost. We show how principal protein motions can be reconstructed from the variation contained in the single particle images.
Host: Tiziano Gallo Cassarino, Biozentrum
Email: tiziano.gallocassarino@unibas.ch
Phone: 061 267 15 80
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Location: Room 104, Biozentrum; Klingelbergstr. 50-70, Basel
Exploring protein energy landscapes by NMR.
Prof. Jochen Balbach, Naturwissenschaftliche Fakultät II, Fachbereich Physik, Halle / Saale, Deutschland
The energy landscape of a protein predetermines its folding reaction and its function. We investigated several examples, where the molecular folding mechanism is directly coupled to the function of the protein. NMR provides several tools to explore these landscapes at equilibrium and during kinetic experiments at high molecular resolution. The following examples will be discussed: (A) The cold shock protein CspB shows a smooth energy landscape, which we could explore with residue resolution in a complete pressure – temperature phase diagram between –13 to 57 °C and 1 to 2200 bar including complete heat and cold denaturation using a ceramic high pressure NMR cell. (B) For the gene-3-protein at the tip of fd phage, we could characterize the infectious state by 2D real time and H/D exchange competition NMR, which is a local minimum at the energy landscape of the protein. The global minimum is not infectious. (C) In the case of ankyrin repeat proteins controlling the human cell cycle, the cell uses their ragged protein folding landscape to control their inhibitory function. By employing the concept of conformational selection, a high energy intermediate state becomes accessible upon phosphorylation, which can be characterized at residue resolution. A second phosphorylation is required for subsequent ubiquitination and proteasome degradation. (D) A low-energy folding intermediate of RNase T1 is the target of the metallochaperone and prolyl isomerase SlyD, where we could characterize the Michaelis-Menten complex by 2D and 3D real time NMR using the BEST approach for fast data acquisition. A combination of dynamic and real-time NMR with other biophysical methods including single-molecule FRET allows a molecular interpretation of the Michaelis-Menten parameter KM and kcat.
Host: Ricardo Adaixo, Biozentrum