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Structural Biology and Biophysics Seminar (SBBS)


D6: Structural Biology and Biophysics I – 22827 (Fall 2023)
D7: Structural Biology and Biophysics II – 24284 (Spring 2024)

(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, room U1.197

Unless mentioned, attendance is open to all interested people, without registration. The Fall Semester 2023 is the following:

September 19, 2023 at 12:15

 

SBBS introductory meeting for students

 

 

October 10, 2023 at 12:15, room U1.197

Title: Understanding the role of intrinsic disorder in MAPK cell signaling by NMR spectroscopy

 

The mitogen-activated protein kinase (MAPK) cell signaling pathways are essential components of eukaryotic signal transduction networks that enable cells to respond appropriately to extracellular stimuli. These signalling pathways generally feature a signalling module composed of a small GTPase and three protein kinases that are sequentially activated by phosphorylation. Intrinsically disordered scaffold proteins play crucial roles in ensuring signalling specificity by mediating the assembly of specific signalling modules. Our research group is interested in revealing the mechanism of action of these disordered scaffolds at atomic resolution using NMR spectroscopy. This includes revealing the structural and dynamic basis of the recruitment of GTPases and kinases onto the scaffolds and studying how phosphorylation of the scaffold proteins modulates complex assembly. The presentation will focus on scaffold proteins within the stress-activated JNK signalling pathway and, in particular, on the recruitment of the small GTPase Rac1 to the disordered scaffold protein POSH. Using a combination of NMR and X-ray crystallography, we show that POSH adopts a novel fold in complex with Rac1 by exploiting two separate molecular recognition elements (MRE1 and MRE2) that fold upon binding to Rac1. Using NMR exchange experiments, we map the kinetic details of the folding trajectory of POSH revealing that the interaction initially proceeds through binding and instantaneous folding of MRE1 followed by a reversible folding event of MRE2 on the second time scale on the surface of Rac1. Our work provides insight into the complexity of binding mechanisms employed by intrinsically disordered proteins and offers novel structural insight into effector recruitment by Rac1.

Research Director Dr. Malene Ringkjøbing Jensen
Institut de Biologie Structurale (IBS) Grenoble - France

October 24, 2023 at 12:15, room U1.197

Title: Structure of membrane proteins in native membranes by cryo-EM

 

Subtomogram averaging from cryo electron tomograms is a powerful method to determine structures of macromolecules in their native state. Outstanding applications to protein lattices, coats and ribosomes provided unique insights into their functions and even revealed interactions with small molecules in situ. For other macromolecules, such as membrane proteins, which are present in tomograms in limited numbers, the throughput of data processing and the processing time are key bottlenecks in obtaining high-resolution reconstructions. This is particularly the case for membrane proteins that are typically present in tomograms in moderate amounts.

I will introduce the tools that we developed in our lab for in situ structural biology with a focus on a large ion channel RyR1 which is a part of the excitation-contraction coupling in muscle. TomoBEAR is a workflow for processing of tomographic data utilizing common cryo-EM tools and original code that allows transparent near-automated tomographic pre-processing, alignment, reconstruction and particle identification followed by structural analysis.

In the second part of the talk I will show our recent results on understanding molecular architecture of synapstic vesicles. We imaged neurons grown on EM grids and purified synaptic vesicles by cryo electron tomography. We could identify individual proteins important for the function of synaptic vesicles and study their distribution on the surface.


Prof. Dr. Misha Kudryashev
Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin - Germany

November 21, 2023 at 12:15, room U1.197

Title: Integrative structural biology to understand epigenetic mechanisms in Drosophila dosage compensation

 

Dosage compensation in fruit flies provides an ideal model system to study the contribution of RNA– protein interactions and the role of lncRNAs in epigenetic regulation. Integrative structural biology approaches are needed to understand the mechanism involved in transcription regulation (male dosage compensation) and translation regulation (female dosage compensation).

In males, maleless (MLE), an evolutionarily conserved RNA helicase is best known for its role in remodelling roX (roX1 and roX2) lncRNAs during male dosage compensation. This remodelling is required for the assembly of the functional dosage compensation complex on the male X chromosome.

DHX9, the ortholog of MLE in humans, has been implicated in multiple diseases and its potential as a therapeutic target has been noted. However, how this multi-domain RNA helicase recognizesand processes its target RNA remains unknown.

Here, we present a series of cryo-EM structures of MLE in complex with RNA at different stages of the helicase cycle. Together with our NMR studies, these structures provide snapshots of the steps required for the recognition and remodelling of lncRNAs. Structure-based mutations change the ability of MLE to integrate roX2 RNA into the dosage compensation complex and affect localization of MLE to the X territory, thereby validating our structures. Our data provide new insights into how DExH-type helicases and RNA chaperones remodel their target lncRNAs to modulate gene regulation.


Prof. Janosch Hennig
University of Bayreuth and EMBL Heidelberg - Germany

November 28, 2023 at 12:15, room U1.197

Title: Dynamic Remodeling of Cellular Proteomes via the Ubiquitin Proteasome System

 

Proteolysis stands as a cornerstone of cellular regulation, with the ubiquitin proteasome system (UPS) being pivotal, accounting for the degradation of up to 80% of cellular proteins. The versatility of the UPS is essential, as it ensures precise protein turnover tailored to the diverse demands of different cellular states, particularly during critical phases such as development and differentiation. This adaptability is achieved through modulation of both the function and localization of its components.

In this presentation, I will highlight our recent discovery of Akirin2, a novel player essential for the nuclear import of proteasomes in mammalian cells. By integrating functional genetics with cryo-electron microscopy (cryo-EM), we have delineated a previously uncharted pathway for proteasome import.

Furthermore, I will discuss our innovative use of time-resolved EM to dissect the mechanism by which the proteasome identifies and processes ubiquitinated substrates. This investigation serendipitously unveiled PITHD1 as an intrinsic inhibitor, which maintains proteasomes in a quiescent state until the initiation of differentiation programs is required.

Our findings not only expand the understanding of the UPS but also illuminate the intricate regulatory networks that govern cellular proteostasis and its impact on cellular fate determination.


Dr. David Haselbach
Vienna BioCenter - Austria

December 19, 2023 at 12:15, room U1.197

Title: Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference

 

Converting cryo-electron microscopy (cryo-EM) data into high-quality structural models is a challenging problem of outstanding importance. Current refinement methods often generate unbalanced models in which physico-chemical quality is sacrificed for excellent fit to the data. Furthermore, these techniques struggle to represent the conformational heterogeneity averaged out in low-resolution regions of density maps. Here we introduce EMMIVox, a Bayesian inference approach to determine single-structure models as well as structural ensembles from cryo-EM maps. EMMIVox automatically balances experimental information with accurate physico-chemical models of the system and the surrounding environment, including waters, lipids, and ions. Explicit treatment of data correlation and noise as well as inference of accurate B-factors enable determination of structural models and ensembles with both excellent fit to the data and high stereochemical quality, thus outperforming state-of-the-art refinement techniques. EMMIVox represents a flexible approach to determine high-quality structural models that will contribute to advancing our understanding of the molecular mechanisms underlying biological functions.


Dr. Max Bonomi
Institut Pasteur - France

January TBA, 2024 at 12:15, room U1.197

Title: TBA

Speaker TBA

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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