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Structural Biology and Biophysics Seminar (SBBS)


D6: Structural Biology and Biophysics I – 22827 (Fall 2021)
D7: Structural Biology and Biophysics II – 24284 (Spring 2021)

(2 hrs/week; 1 CP) 

Stephan Grzesiek, Sebastian Hiller, Rod Lim, Timm Maier

The Structural Biology and Biophysics Seminar series (SBBS) is organized by PhD students of the Biozentrum, University of Basel since 2009. World-leading scientists are invited to present their current work to an audience of students, researchers and PIs. Typical lectures in this series describe applications of advanced structural biology and biophysics methods to solve biological problems. Methods include NMR spectroscopy, X-ray crystallography, cryo-electron microscopy, surface plasmon resonance and atomic force microscopy, but not only. The list of the past SBBS speakers is accessible here.

The talks take place on Tuesdays, the time will depend on speaker, via the Zoom videoconferencing platform (Intranet ↗).

Check the current program below for more information. Unless mentioned, attendance is open to all interested people, without registration.

March 1, 2021 (via Zoom) at 16.00

 

SBBS introductory meeting for students

 

March 9, 2021 (via Zoom) at 16.15

Prof. Enrico Gratton
University of California, Irvine

Ultrafast Nanocamera fluctuation measurement and analysis

The availability of the nanocamera Airyscan detector in the Zeiss LSM 880 has made possible the development of a new concept in fluctuation correlation spectroscopy using super-resolution. The Airyscan unit acquires data simultaneously on 32 detectors arranged in a hexagonal array. This detector opens up the possibility to use fluctuation methods based on time correlation at single points or at a number of points simultaneously, as well as methods based on spatial correlation in the area covered by the detector. Given the frame rate of this detector, millions of frames can be acquired in seconds, providing a robust statistical basis for fluctuation data. We apply the comprehensive analysis to the molecular fluctuations of free GFP diffusing in live cells at different subcellular compartments to show that at the nanoscale different cell environments can be distinguished by the comprehensive fluctuation analysis.

 

Zoom link: https://unibas.zoom.us/j/91536194105?pwd=ZVg2eTRuRzVELzFXTGNXdTlUallodz09

 

April 13, 2021 (via Zoom) at 9.30

Prof. Patrick Sexton
Monash University, Melbourne

Using cryo-electron microscopy to probe G protein-coupled receptor function

 

G protein-coupled receptors (GPCRs) are the largest family of cell surface drug targets. Consequently, there is high interest in understanding the structure of members of this receptor superfamily and molecular detail of how ligands and transducer proteins interact with the receptors. While x-ray crystallography has been the mainstay for GPCR structure determination, this method requires modification of receptors to limit flexibility and to enable crystal packing, and has been refractory to capturing fully active, transducer (G protein) complexed receptor structure. Our laboratory has been applying single particle cryo-EM to determination of active GPCR structures, using minimally modified receptors. We have now solved >80 structures of 17 unique receptors, with a focus on class B1 peptide hormone GPCRs; many at high resolution (<2.5 Å). Moreover, unlike x-ray crystallography that captures a single receptor conformation, cryo-EM can access the spectrum of conformations present during vitrification allowing 3D reconstruction of conformational dynamics of GPCR complexes along principal components. This new insight into receptor dynamics has been critical to understanding differences in the pharmacology of different ligands that can interact with the same receptor or receptor family.

 

Zoom link:  https://unibas.zoom.us/j/92551250507

 

April 20, 2021 (via Zoom) at 12.15

Prof. Christoph von Ballmoos
University of Bern, Bern

Bottom-up assembly of a respiratory chain from purified components

Membrane proteins are the windows and doors of living cells, e.g. for the controlled influx and efflux of substrates across biological membranes. To reduce the complexity of native membranes, the proteins are extracted and purified and reconstituted back into liposomes to allow investigations of the molecular mechanism. An important, but relatively unaddressed problem during reconstitution is the orientation of the protein, as its incorporation into vesicles is not aided by cellular chaperones but driven by unknown mechanisms. Orientation however can be of crucial impact for the outcome of measurements, especially when several membrane proteins are embedded in the same membrane. 

Our research revolves around the reconstitution of respiratory chain enzymes found in bacteria and mitochondria to produce the cellular energy currency ATP. In my talk, I would like to cover current efforts to assemble respiratory chains from purified components, and to measure and manipulate orientation of membrane proteins during reconstitution. In addition, I present a recent project, where we used the technique to investigate the effect of mitochondrial cristae on oxidative phosphorylation.

 

Zoom link:  https://unibas.zoom.us/j/69516533927

 

April 27, 2021 (via Zoom) at 16.15

Prof. Loren Hough
University of Colorado, Boulder

Selective transport through biopolymer barriers

In biological systems, polymeric materials block the movement of some macromolecules while allowing the selective passage of others. In some cases, binding enables selective transport, while in others the most inert particles appear to transit most rapidly. I’ll discuss my lab’s efforts to study the general principles of filtering by polymeric materials motivated by transport through the nuclear pore complex. Our efforts have combined experimental work, including NMR spectroscopy, to determine the behavior of disordered proteins in cells, and with theoretical work to understand the role of flexibility in biopolymer barriers. I’ll describe our efforts to characterize the motion arising from binding to flexible filaments, both active and passive. Remarkably, this motion is sufficient to give selective transport similar to that observed, in some cases, through the nuclear pore complex.

 

Zoom link: https://unibas.zoom.us/j/61641706937

 

May 11, 2021 (via Zoom) at 12.15

Prof. Jason Chin
MRC Laboratory of Molecular Biology, Cambridge

Reprogramming the Genetic Code

In terrestrial life, DNA is copied to messenger RNA, and the 64 triplet codons in messenger
RNAs are decoded – in the process of translation – to synthesize proteins. Cellular protein
translation provides the ultimate paradigm for the synthesis of long polymers of defined
sequence and composition, but is commonly limited to polymerizing the 20 canonical amino
acids. I will describe our progress towards the encoded synthesis of non-canonical
biopolymers. These advances may form a basis for new classes of genetically encoded
polymeric materials and medicines. To realize our goals we are re-imagining some of the
most conserved features of the cell; we have created new ribosomes, new aminoacyl-tRNA
synthetase/tRNA pairs, and organisms with entirely synthetic genomes in which we have rewritten
the genetic code.

 Zoom link: https://unibas.zoom.us/j/66956412478

May 18, 2021 (via Zoom) at 12.15

Prof. Brenda Schulman
Max Planck Institute of Biochemistry

How a ubiquitin-like protein brings E3 ubiquitin ligases to life

A predominant form of eukaryotic regulation involves post-translational modification by ubiquitin and ubiquitin-like proteins.  Much of this regulation is mediated by the large family of cullin-RING E3 ubiquitin ligases (CRLs).  CRLs direct ≈20% of all proteasome-dependent degradation, regulate virtually all eukaryotic processes, and serve as one of the hottest drug discovery platforms in pharma and biotech.  The more than 250 human CRL family members regulate processes including the immune response, transcription, signal transduction, cell division, cell death, development, and numerous facets of neurobiology.  Moreover, many CRLs are mutated in diseases, including cancers, heart diseases, and developmental disorders.  A variety of CRLs are usurped by HIV to suppress immunity and promote infectivity.  And due to revolutionary cancer treatments modulating CRL targeting, CRLs are the focus of a billion-dollar drug discovery industry aimed at eliciting ubiquitylation of disease-causing proteins.

 Numerous facets of CRL activation – from E3 ligase assembly to catalysis of ubiquitylation to subsequent processing of ubiquitylated substrates – depend on the dynamic linkage and removal of the distinctive UBL NEDD8. NEDD8 is nearly 60% identical to ubiquitin, yet it predominantly regulates CRLs. In my talk, I will describe our findings that reveal the marvellous ways NEDD8 uniquely brings CRLs – and a large fraction of all ubiquitylation - to life.

 Zoom link: https://unibas.zoom.us/j/67715875646

Important information for students enrolled at the University of Basel:

  • You can earn one credit point (CP) by registering to the course.
  • To get the CP for this course, all of the proposed seminars have to be attended from start to finish and a written exam in the form of an essay must be passed.
  • It is your responsibility to check this website for eventual updates/changes to the program.
  • Each in-person seminar is followed by a lunch with the speaker. Contact the host if you are interested in participating.

 

 

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