February 21st, 2023 at 12:15

SBBS introductory meeting for students

March 14th, 2023 at 14:15, by ZOOM

ATTENTION: NEW TALK TIME

Title: Defining How Sequence and Local Chromatin Context Regulate Gene Expression

RNA polymerase (Pol) II is regulated during all stages of transcription to ensure appropriate gene expression. This regulation involves interaction with various factors that modulate Pol II activity as it traverses across genes. I will discuss recent cryo-electron microscopy(EM) work that has uncovered how Pol II is both negatively and positively regulated by transcription elongation factors. Pol II activity is also influenced by the organization of the genome. Genome organization is regulated at multiple levels ranging from the underlying DNA sequence to large scale interactions between chromosomes. Our recent efforts to understand how these multiple levels of genome organisation are used to regulate gene expression will be discussed.  Finally, I will show new computational tools we are developing to improve cryo-EM data collection to make cryo-EM more accessible to the broader community.

Prof. Seychelle Vos
Massachusetts Institute of Technology (MIT) - USA

March 21st, 2023 at 12:15, room U1.197

Title: The kinetochore: an intrinsically divisive molecular machine

Chromosome bi-orientation is the pre-condition for successful cell division, but how it is achieved on the molecular level in settings as diverse as mitosis and meiosis remains poorly understood. Kinetochores play a decisive role in promoting chromosome bi-orientation and in imparting fidelity to the chromosome segregation process. In addition to binding microtubules, they recognize and correct improper microtubule attachments, and act as control centers to make the timing of cell division contingent on completion of bi-orientation through the spindle assembly checkpoint. How are these different activities regulated and integrated within the kinetochore’s structure? To answer this question, our laboratory took up the long-term goal of reconstituting kinetochores and their functions in vitro, focusing on human kinetochores as model system. The reconstitution is challenging, because kinetochores consist collectively of ~35 core subunits [1], and several additional regulatory subunits, for a total of ~100 different polypeptides. The challenge is compounded by the embedding of kinetochores in the complex and incompletely understood environment of the centromere, a specialized chromatin domain whose organization promotes epigenetic propagation of the kinetochore assembly site through cell generations. As a summary of our work so far, I will present three large reconstitutions, comprising two major stable kinetochore sub-complexes (each with molecular mass ³ 1 MDa), and the signaling ensemble of the spindle assembly checkpoint. I will illustrate what organizational principles have emerged from this work, often through parallel structural work. All three reconstitutions reflect stable interactions at thermodynamic equilibrium, and therefore cannot be considered “alive”. The ultimate challenge for future in vitro work on the kinetochore, and a more general challenge for any in vitro reconstitution, is to ignite the energy-dissipating reactions that promote functional regulation and informational processing. We would like to build particles that, like their cellular counterparts, sense bi-orientation (or lack thereof) and turn the checkpoint on or off depending on context. This will require the addition of enzymes, most notably mitotic kinases and phosphatases, whose opposing regulation determines, at any given time, appropriate context-dependent signaling outcomes.

Prof. Andrea Musacchio
Max Planck Institute of Molecular Physiology - Germany

April 25th, 2023 at 12:15, room U1.197

Title: Structural basis for drug and metabolite uptake via Solute Carrier (SLC) Transporters

Recent advances in single particle cryo-EM have accelerated research in membrane proteins. However, small membrane proteins remain a challenge due to their dynamic nature and featureless structures outside the membrane. One strategy has been to use single chain nanobodies to overcome these challenges. In this seminar I will present our strategy for the selection of high affinity synthetic nanobodies against small (50kDa) solute carrier transporters. My group focuses on understanding how nutrient transporters recognise and transport drugs and xenobiotic compounds in the body. I will present our latest insights into several pharmaceutically important SLC transporters involved in vitamin and metabolite transport and how insights into their structure and function can be used to develop more targeted therapeutics.

Prof. Simon Newstead
University of Oxford - UK

May 2nd, 2023 at 12:15, room U1.197

Title: Solving 3D puzzles of biomolecular interactions by integrative modelling

The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modelling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process.

We have developed for this purpose a versatile information-driven docking approach HADDOCK (https://www.bonvinlab.org/software) available as a web portal from https://wenmr.science.uu.nl . HADDOCK can integrate information derived from biochemical, biophysical or bioinformatics methods to enhance sampling, scoring, or both. The information that can be integrated is quite diverse: Interface restraints from e.g. NMR, mutagenesis experiments, or bioinformatics predictions; shape data from small-angle X-ray scattering and cryo-electron microscopy experiments.

In my talk, I will introduce HADDOCK and illustrate its capabilities with various examples including among others recent work on the inclusion of shape information to drive the modelling process.

Prof. Alexandre Bonvin
University of Utrecht - Netherlands

May 9th, 2023 at 12:15, room U1.197

Title: The architecture of organelle contact sites

Organelles interact through close apposition of their membranes. Such contact sites serve the exchange of lipid molecules, calcium transport and organelle biogenesis. The mechanisms by which lipids are transferred across organelle contact sites are poorly understood because little is known about the underpinning supramolecular structure. We aim to reveal the architecture composed of proteins and apposing membranes and thereby shed light on how these microenvironments facilitate the transport of lipid molecules between organelles. Towards this goal, we employ correlative light and electron microscopy approaches including electron cryo-tomography as well as live fluorescence imaging.

Prof. Wanda Kukulski
University of Bern - Switzerland

May 30th, 2023 at 12:15, room U1.197

Title: Structural studies of co-translational protein folding and misfolding on the ribosome

During protein biosynthesis, nascent polypeptide chains emerge from the ribosome’s exit tunnel and face a branch-point in which they have their first opportunity to either fold productively to adopt their 3D structure or misfold and form aberrant structure. In some cases, the latter is implicated to the onset of a growing number of human diseases.  Although the links between protein folding and misfolding have been described within in vitro studies of isolated proteins, very little is understood of these processes as they occur during protein biosynthesis.   NMR spectroscopy and cryoEM studies on ribosome-nascent chain complexes (RNCs) are providing detailed structural and dynamic insights in the folding pathways sampled by emerging nascent polypeptide chains. The ribosome is also the first place where misfolding can occur, and we will describe emerging studies which explore the co-translational folding-misfolding competition during biosynthesis and its relationship to human disease.

Prof. Lisa Cabrita
University College of London - UK