Rainer-Rudolph-Awards Session at the Mosbacher Kolloquium 2024
The Arsenal of a Bacterial Predator Revealed by Cryo-Electron Microscopy
Davide Amendola
ETH Zürich
Ixotrophy is a bacterial predation strategy observed in a subset of multicellular, filamentous bacteria of the phylum Bacteroidota and is characterized by their ability to catch prey cells on their surface - like flies on flypaper - and subsequently lyse them to supplement their own nutritional needs. Accordingly, it has been proposed to be an elegant solution to the problem of low nutrient availability in aquatic environments, as well as an important mechanism regulating the dynamics of various microbial communities. The exact mechanisms that mediate ixotrophy, however, have remained largely elusive.
Here, we employed a state-of-the-art multi-scale imaging workflow to visualize and identify the macromolecular protein complexes involved in ixotrophy. We combined cryo-electron tomography and subtomogram averaging with single-particle cryo-electron microscopy to determine the structure of a novel grappling hook-like adhesin responsible for the catching of flagellated prey. By determining the primary amino acid sequence directly from the high-resolution density maps, we identified grappling hooks as the heptameric assembly of a single giant protein. Further, we used various bioinformatic analyses to show that its N-terminal domain resembles other bacterial adhesins, whereas its C-terminal domain directs secretion to the outer membrane via the Type IX Secretion System.
Rainer-Rudolph-Awards Session at the Mosbacher Kolloquium 2024
Designing triosephosphate isomerases using generative language models
Alexander Braun
University Bayreuth
Enzymes are wonderful biocatalysts that increase reaction rates by several orders of magnitude. The ability to catalyze reactions in aqueous solution at atmospheric pressure and at ambient temperatures makes these biomolecules an environmentally friendly and cost-effective alternative to synthetic catalysts used in industry. However, enzymes are mostly restricted to reactions occurring in the context of cellular life. The ability to design tailor-made enzymes is therefore of great interest for biotechnology and chemical industry. Methods to create proteins that catalyze a desired reaction have been mostly based on physics-based heuristics or built on improving promiscuous activity in natural proteins. These methodologies are highly time-consuming and in need of extensive screening. As a shift of paradigm, recent successes in the application of language models based on the transformer architecture in protein sciences inspired the development of unconditional and conditional language models, such as ZymCTRL, to design new protein sequences. Being trained on the BRENDA database of enzymes, ZymCTRL generates putative enzyme sequences according to the enzyme commission number used as input. We assess experimentally the performance of this language model to generate triosephosphate isomerases (TIM), an obligatory oligomeric well-researched enzyme class catalyzing its reaction near the diffusion limit. Shallow filtering of generated putative enzyme sequences resulted in three out of twelve de novo TIMs being active in vivo and able to complement a TIM deficient E. coli strain. In depth characterization of the best performing
artificial enzyme shows in vitro activity just two orders of magnitude below its natural counterparts. Based on the results we propose a filtering mechanism to increase experimental success rates of artificially generated proteins even further. This study highlights the potential of protein language models as tools for the generation of tailored enzymes directly from sequence.
Rainer-Rudolph-Awards Session at the Mosbacher Kolloquium 2024
Engineering of single domain antibody-based Bispecifics
Britta Lipinski
Merck KGaA, Darmstadt
Bispecific antibodies offer a targeted approach for cancer treatments by simultaneously engaging two different antigens. The ability to recruit and conditionally activate a targeted immune cell population enhances specificity and efficacy while minimising off-target effects in the absence of the tumour-associated antigen. The use of camelid-derived single-domain antibodies (VHHs) offer several advantages, such as their small size and high stability, but more importantly, in the context of complex multi-specific antibodies, they allow the possibility of multiple ‘plug-and-play’ reformatting options and easy combination with Fab-based paratopes, as they do not require an additional light chain. The main master thesis project focuses on the generation of potent NKCE (natural killer cell engagers) formats that bridge NKp46 on NK cells with EGFR on tumor cells to redirect NK cell cytotoxicity against EGFR-positive tumor cells (Lipinski et al 2023, NKp46-specific single domain antibodies enable facile engineering of various potent NK cell engager formats). In an additional project, single domain antibodies were used as surrogate agonists to mimic the cytokine functionality of IL-18 (Lipinski et al 2023, Generation and engineering of potent single domain antibody-based bispecific IL-18 mimetics resistant to IL-18BP decoy receptor inhibition.). For both projects the impact of valencies and the spatial orientation of individual paratopes within the overall design architecture were further explored by antibody engineering to augment the desired functionality.
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David Jones
University College London [UK]
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Matthias Rarey
/Hamburg [DE]
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Andrea Volkamer
/Saarbrücken [DE]
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Artificial Intelligence deciphers the code of life written in proteins?
Burkhard Rost
Technical University of Munich, School of Computation, Information and Technology, München [DE]
The objective of our group is to predict aspects of protein function and structure from sequence. The wealth of evolutionary information available through comparing the whole bio-diversity of species makes such an ambitious goal achievable. Our particular niche is the combination of evolutionary information (EI) with machine learning (ML) and artificial intelligence (AI). 30 years ago, the marriage of machine learning and evolutionary information (in the form of Multiple Sequence Alignments) allowed a breakthrough in secondary structure prediction. The same principle has been underlying all state-of-the-art predictions of protein structure and function and is also the root for the program that broke through in protein structure prediction, namely AlphaFold2.
Over the last two years, it has become possible to deep learn the language of life written in proteins through protein Language Models (pLMs). The information extracted is transfer learned to supervise learn protein prediction with annotations. I will present three particular new methods predicting protein structure (1D: secondary structure, membrane regions, & disorder, 2D: inter-residue distances/contacts, 3D: co-ordinates) and protein function (sub-cellular location, binding residues, GO terms), and the effects of sequence variation using pLMs. These embeddings allow for some applications to reach for others to surpass the state-of-the-art without using evolutionary information.
Crucial in all of this is the understanding of the AI and the control of database bias. For both computational biology could serve as a sandbox to prepare more sensitive applications of AI in society.
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Sergey Ovchinnikov
/Cambridge [USA]
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Optimizing proteins with reinforcement learning
Noelia Ferruz
/Barcelona [ES]
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Martin Steinegger
/Seoul [KR]
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Feodor Lynen Lecture:
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Tanja Kortemme
/San Francisco [USA]
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Yang Zhang
/Ann Arbor [USA]
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AI-based integrative structural modeling
Jan Kosinski
/Hamburg [DE]
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Possu Huang
/Stanford [USA]
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Bruno Correia
/Lausanne [CH]
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What can we learn from incorrect AlphaFold2 models? (the case of signal transduction)
Stanislaw Dunin-Horkawicz
/Tübingen [DE]
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Jens Meiler
/Leipzig [DE]
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Eduard Buchner Prize
The Protein Dance – from Experiments to AI Predictions
Dorothee Kern
/La Jolla [USA]
not submitted yet
sponsored by:
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Otto Warburg Medal
From Otto Warburg to Riboregulation: a 100 year journey in metabolism
Matthias Hentze
European Molecular Biology Laboratory (EMBL), Heidelberg
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sponsored by:
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Mining cryo-electron tomography data with self-supervised deep learning models
Judith Zaugg
/Heidelberg [DE]
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Alexander Rives
/New York [USA]
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Programmable generative protein design: from molecules to medicines
Gevorg Grigoryan
/Somerville [USA]
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Andrea Thorn
/Hamburg [DE]
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Big data from wet-lab biochemistry and dry-lab biophysics to advance AI protein design
Maximilian Fürst
/Groningen [NL]
not submitted yet
Industrial Workshop
Demonstrating eLabFTW: A Free and Open-Source Electronic Laboratory Notebook
In this session, we will explore eLabFTW, an open-source Electronic Laboratory Notebook (ELN) designed to meet the diverse needs of research groups across a range of disciplines, including chemistry, biology, physics, and more. eLabFTW provides secure storage and management of scientific data, ensuring the integrity, confidentiality, and probity of results through advanced features such as qualified timestamping, cryptographic signatures, and comprehensive audit logs.
Adopted by leading research institutions like the CNRS, Institut Curie, Vrije Universiteit Brussel, and IRD, eLabFTW has undergone rigorous security audits and risk analyses. The platform offers flexible deployment options, including SecNumCloud-qualified secure hosting, as well as local installation for complete control.
During this demonstration, attendees will learn how to use eLabFTW and explore customization options to enhance their research workflow. We will discuss the laboratory inventory system, scheduler, and other features. We will also consider ways in which eLabFTW can support the goals of the open science movement via the .ELN file format, encourage compliance with data integrity standards, and facilitate the generation of FAIR data. Join us to learn how this free and open-source solution can transform the way research labs manage and protect their scientific data.
Speaker:
Sydney Koke (Sydney@deltablot.email, Deltablot)
Time/Location:
Thursday, March 20, 13:30-14:00
Lecture hall
Introduction to the Rainer-Rudolph-Awards Session at the Mosbacher Kolloquium 2024
The Rainer Rudolph Foundation promotes and supports basic and applied research in protein biochemistry and biotechnology. Every year awards are given to young scientists who have made outstanding advances in these fields. In this session, the awardees of the Rainer Rudolph Prize will present their work in short lectures.
Davide Amendola /Zürich [DE]
The Arsenal of a Bacterial Predator Revealed by Cryo-Electron Microscopy
Alexander Braun /Bayreuth [DE]
Designing triosephosphate isomerases using generative language models
Britta Lipinski /Darmstadt [DE]
Engineering of single domain antibody-based Bispecifics
Panel Discussion: Big Data, Big Challenges - How do we manage research data?
The GBM working group “Young Investigators” invites you to a workshop on “Big Data, Big Challenges - How do we manage research data?”.
Do you want to organize and store your research data efficiently?
Do you wonder how to ensure the reproducibility and integrity of your data?
Do you ask yourself how to comply with data management policies and best practices?
Join us to explore these questions and more with experts from both academia and industry, and learn how to manage your research data effectively!
Panel participants:
Nikolas Carpi, elabFTW
Sydney Koke, elabFTW
Michael Jendrusch, EMBL Heidelberg
Kersten Rabe / KIT
Thursday, March 20, 2025, 12:15-13:30 (Lecture Hall)
Open for all conference participants.
Meet the X
Meet the Prof
(For students only)
Once again the Junior GBM will organize the established event „Meet the Prof“ with distinguished speakers from science and research.
In an informal atmosphere you will get the chance to ask the questions that keep you up at night - e.g. how do I make a career in science? Did the speaker have fun on his/her scientific path and which experiences were decisive?
You are welcome to join and ask further questions.
Thursday, March 20, 12:00 - 13:00 (Room: Darre)
Chair:
Guest: N.N.
Registration is required.
Friday, March 21, 12:00 - 13:00 (Room: Darre)
Chair:
Guest: N.N.
Registration is required.
The number of participants is limited, registration is required. All conference participants will receive a link for a doodle registration in due time.
Meet the X
Meet the industrial Scientist
(For students only)
Analogous to the well-known format "Meet the Prof", this is about research in the pharmaceutical industry.
What are the differences between industrial and university research? How do the ways of thinking, approaches and focal points differ? Other topics include publications, patents, job security and career opportunities in a pharmaceutical environment compared to universities.
Guest: N.N.
Chair:
Date/Location:
Thursday, March 20, 12:00 - 12:45 /Tenne
The number of participants is limited, registration is required. All conference participants will receive a link for a doodle registration in due time.