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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 

The Fall Semester 2021 Program will be available soon. Unless mentioned, attendance is open to all interested people, without registration.

September 7, 2021 (via Zoom) at 10.00

 

SBBS introductory meeting for students

 

Zoom link: https://unibas.zoom.us/j/68704039154

 

September 14, 2021 (via Zoom) at 9.30

Prof. Radostin Danev
University of Tokyo, Japan

Advancing cryo-electron microscopy towards atomic resolution of membrane proteins

Cryo-electron microscopy (cryo-EM) is rapidly gaining popularity as a powerful method for structural studies of biomolecules and their complexes. Over the last decade, the technique experienced a “revolution” in performance that was brought about by direct electron detector technologies and advances in image processing algorithms. Nowadays, cryo-EM routinely determines molecular structures with resolutions in the 2.5 – 3.5 Å range. Such results are adequate for protein modelling but lack fidelity for confident localization of water molecules and hydrogen atoms. Unambiguous elucidation of the biochemistry behind protein function and pharmacology of drugs would require atomic resolution structures, at levels below 1.5 Å. Last year, several groups worldwide demonstrated atomic resolution cryo-EM with a test sample comprising the “easy” soluble protein apoferritin. This was an important technological milestone showcasing the best-case-scenario capabilities of cryo-EM. However, membrane proteins, and other real-world samples, impose numerous experimental challenges, such as small size, heterogeneity, flexibility, preferential orientation, etc. The talk will be about pushing the performance boundaries of cryo-EM for challenging membrane proteins, and in particular, in studies of G protein-coupled receptors.

 

Zoom link: https://unibas.zoom.us/j/3060091905?pwd=bnYzczZuc0VXYy84TnpOOEM0K3ZjQT09

October 5, 2021 (via Zoom) at 9.30

Prof. Mariusz Jaskolski
Mickiewicz University and Polish Academy of Sciences, Poland

“Trust but verify” attitude in structural biology

A number of reports have warned that a growing fraction of biomedical research cannot be reproduced. Structural biology, traditionally viewed as the gold standard in life science, is not without sin as problematic models end up from time to time in the PDB (Protein Data Bank), contaminating the literature and often frustrating other efforts, such as structure-based drug design. The errors are most frequent at the sensitive macro-/small-molecule interface and are manifested by suboptimal/unsatisfactory/or wrong modeling of ligands in the electron density maps. We have analyzed several classes of medicinally important PDB models (including β-lactamases and SARS-CoV-2 proteins) and found errors of various severity, as well as serious ripple effects in the scientific literature. In many cases the models could be significantly corrected and redeposited in the PDB. We always contacted the original authors, with reaction ranging from hostility to fruitful cooperation. The open questions include better quality control, the treatment of the new deposits, and retraction of the invalidated papers.

 

Zoom link: https://unibas.zoom.us/j/3060091905

November 02, 2021 (via Zoom) at 12.15

Prof. Johnjoe McFadden
University of Surrey, UK

The Quantum Underpinnings of Life

Quantum mechanics and molecular biology were the two revolutionary scientific disciplines that grew out of the twentieth century: quantum mechanics and molecular biology. Quantum biology can be said to have been initiated by a physicist, Erwin Schrödinger, in his lecture, essay and book entitled “What in Life” (published in 1944) in which he proposed that that heredity was based on non-trivial aspects of quantum mechanics. The book was very influential to molecular biology pioneers, such as James Watson and Francis Crick, who went on to discover the double-helical structure of DNA. Thereafter the field of quantum biology largely languished. However, the twenty-first century has seen a revival of quantum biology with the arrival of new experimental evidence of quantum mechanical effects in a range of biological phenomena such as photosynthesis and enzyme action. In this talk I will provide an introduction to quantum biology, returning to Schrödinger’s original insight that quantum phenomena may be found in biological processes that involve very numbers of molecules including photosynthesis, enzyme action, avian navigation and mutation.

 

Zoom link: https://unibas.zoom.us/j/66342690166

November 09, 2021 (via Zoom) at 10.00

Prof. John Briggs
Max Planck Institute of Biochemistry, Germany

Structural Biology of Viruses with Cryo-Electron Tomography

We are interested in the structures and lifecycles of pathogenic enveloped viruses. Using a combination of cryo-electron microscopy, cryo-electron tomography and computational image processing we can obtain structures of proteins to high-resolution in-situ within virus particles. By doing so we can learn how viral proteins interact with one another to assemble virus particles, and how they then rearrange to perform or to adapt their functions at different stages of the viral lifecycle. I will present some of our recent data on viruses including influenza A and SARS-CoV-2. I will discuss the techniques used to obtain these data, and their implications for understanding the biology of these viruses.

Zoom link: 

November 16, 2021 (via Zoom) at 16.15

Prof. Mimi Ho
Columbia University, USA

Structural Parasitology of the Malaria Parasite Plasmodium falciparum

While most intracellular pathogens export a limited repertoire of effector proteins to co-opt existing host-cell metabolic machineries, the Malaria-causing parasite Plasmodium falciparum exports more than 10% of its proteome into host human red blood cells, which are highly specialized for carrying hemoglobin and lack the resources to support the active growth and replication of the parasites. The hundreds of proteins in the P. falciparum exportome extensively remodel host erythrocytes, creating the infrastructure needed to import nutrients, export waste, and evade the host immune system. The complexity and breadth of its host-cell remodeling machinery make P. falciparum a rich and exciting system for the study of host-pathogen interfaces. Unfortunately, many of the molecular mechanisms underlying this parasite’s ability to hijack human red blood cells remain enigmatic, as much of the P. falciparum proteome has proven recalcitrant to structural and biochemical characterization using traditional recombinant approaches. This paucity of high resolution structural and functional information is compounded by the fact that 50% of the P. falciparum proteome is novel.

To overcome these barriers to structural study of malaria parasites and address the gaps in our understanding of the molecular mechanisms underpinning host-pathogen interactions in parasite-infected red blood cells, our lab develops and implements methodologies for endogenous structure determination from P. falciparum. We combine CRISPR-Cas9 parasite gene editing, single particle cryoelectron microscopy (cryoEM), and in situ cryoelectron tomography (cryoET) to determine near-atomic resolution structures of previously intractable protein complexes enriched directly from endogenous P. falciparumparasites and directly visualize the host-pathogen interface in intact parasite-infected red blood cells at sub-nanometer resolutions.

 

Zoom link: 

December 7, 2021 (live) at 12.15

Prof. Edward Lemke

Johannes Gutenberg University, Germany

Decoding Molecular Plasticity in the Dark Proteome

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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