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6. Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry

Author

Leitner, Alexander, Bonvin, Alexandre M. J. J., Borchers, Christoph H., Chalkley, Robert J., Chamot-Rooke, Julia, Combe, Colin W., Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C., Heck, Albert J. R., Hoopmann, Michael R., Huang, Lan, Ishihama, Yasushi, Jones, Andrew R., Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L., Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A., Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaino, Juan A., Wilkins, Marc R., and Rappsilber, Juri

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination, conformation analysis and mapping protein interactions in complex mixtures. Crosslinking MS has become a much-appreciated and routinely applied tool especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Crosslinking MS for which guidelines should be developed as part of a Crosslinking MS standards initiative., Comment: 26 pages, 1 figure

Published
2020

10. First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study

Author

Iacobucci, Claudio, Piotrowski, Christine, Aebersold, Ruedi, Amaral, Bruno C, Andrews, Philip, Bernfur, Katja, Borchers, Christoph, Brodie, Nicolas I, Bruce, James E, Cao, Yong, Chaignepain, Stéphane, Chavez, Juan D, Claverol, Stéphane, Cox, Jürgen, Davis, Trisha, Degliesposti, Gianluca, Dong, Meng-Qiu, Edinger, Nufar, Emanuelsson, Cecilia, Gay, Marina, Götze, Michael, Gomes-Neto, Francisco, Gozzo, Fabio C, Gutierrez, Craig, Haupt, Caroline, Heck, Albert JR, Herzog, Franz, Huang, Lan, Hoopmann, Michael R, Kalisman, Nir, Klykov, Oleg, Kukačka, Zdeněk, Liu, Fan, MacCoss, Michael J, Mechtler, Karl, Mesika, Ravit, Moritz, Robert L, Nagaraj, Nagarjuna, Nesati, Victor, Neves-Ferreira, Ana GC, Ninnis, Robert, Novák, Petr, O’Reilly, Francis J, Pelzing, Matthias, Petrotchenko, Evgeniy, Piersimoni, Lolita, Plasencia, Manolo, Pukala, Tara, Rand, Kasper D, Rappsilber, Juri, Reichmann, Dana, Sailer, Carolin, Sarnowski, Chris P, Scheltema, Richard A, Schmidt, Carla, Schriemer, David C, Shi, Yi, Skehel, J Mark, Slavin, Moriya, Sobott, Frank, Solis-Mezarino, Victor, Stephanowitz, Heike, Stengel, Florian, Stieger, Christian E, Trabjerg, Esben, Trnka, Michael, Vilaseca, Marta, Viner, Rosa, Xiang, Yufei, Yilmaz, Sule, Zelter, Alex, Ziemianowicz, Daniel, Leitner, Alexander, and Sinz, Andrea

Subjects
Generic health relevance, Cross-Linking Reagents, Laboratories, Mass Spectrometry, Reproducibility of Results, Serum Albumin, Bovine, Analytical Chemistry, Other Chemical Sciences
Abstract

The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

Published
2019

12. Positively charged specificity site in cyclin B1 is essential for mitotic fidelity.

Author

Heinzle, Christian, Höfler, Anna, Yu, Jun, Heid, Peter, Kremer, Nora, Schunk, Rebecca, Stengel, Florian, Bange, Tanja, Boland, Andreas, and Mayer, Thomas U.

Subjects
CYCLIN-dependent kinases, LIFE sciences, SPINDLE apparatus, BIOCHEMICAL substrates, UBIQUITIN ligases
Abstract

Phosphorylation of substrates by cyclin-dependent kinases (CDKs) is the driving force of cell cycle progression. Several CDK-activating cyclins are involved, yet how they contribute to substrate specificity is still poorly understood. Here, we discover that a positively charged pocket in cyclin B1, which is exclusively conserved within B-type cyclins and binds phosphorylated serine- or threonine-residues, is essential for correct execution of mitosis. HeLa cells expressing pocket mutant cyclin B1 are strongly delayed in anaphase onset due to multiple defects in mitotic spindle function and timely activation of the E3 ligase APC/C. Pocket integrity is essential for APC/C phosphorylation particularly at non-consensus CDK1 sites and full in vitro ubiquitylation activity. Our results support a model in which cyclin B1's pocket facilitates sequential substrate phosphorylations involving initial priming events that assist subsequent pocket-dependent phosphorylations even at non-consensus CDK1 motifs. How cyclins contribute to CDK1 substrate specificity during cell division is poorly understood. Here, the authors show that a phosphate-binding pocket in cyclin B1 is critical for accurate CDK1 substrate phosphorylation ensuring mitotic fidelity. [ABSTRACT FROM AUTHOR]

Published
2025
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17. Kinetic principles of chemical cross-link formation for protein-protein interactions.

Author

Kammer, Kai-Michael, Eisgruber, Terese, Heid, Peter, Pellarin, Riccardo, and Stengel, Florian

Subjects
CHEMICAL kinetics, CHEMICAL processes, PROTEIN crosslinking, PROTEIN-protein interactions, PROTEIN structure
Abstract

Proteins play a central role in most biological processes within the cell, and deciphering how they interact is key to understand their function. Cross-linking coupled with mass spectrometry is an essential tool for elucidating protein-protein interactions (PPIs). Despite its importance, we still know surprisingly little about the principles that underlie the process of chemical cross-link formation itself and how it is influenced by different physicochemical factors. To understand the molecular details of cross-link formation, we have set up a comprehensive kinetic model and carried out simulations of protein cross-linking on large protein complexes. We dissect the contribution on the cross-link yield of parameters such as amino acid reactivity, cross-linker concentration, and hydrolysis rate. Our model can compute cross-link formation based solely on the structure of a protein complex, thereby enabling realistic predictions for a diverse set of systems. We quantitatively show how cross-links and mono-links are in direct competition and how the hydrolysis rate and abundance of cross-linker and proteins directly influence their relative formation. We show how cross-links and mono-links exist in an "all-against-all" competition due to their simultaneous formation, resulting in a nonintuitive network of interdependence. We show that this interdependence is locally confined and mainly limited to direct neighbors or residues in direct vicinity. These results enable us to identify the optimal cross-linker concentration at which the maximal number of cross-links is formed. Taken together, our study establishes a comprehensive kinetic model to quantitatively describe cross-link formation for PPIs. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Cell‐Permeable Nicotinamide Adenine Dinucleotides for Exploration of Cellular Protein ADP‐Ribosylation.

Author

Kasprzyk, Renata, Rieth, Sonja, Heid, Peter, Stengel, Florian, and Marx, Andreas

Subjects
POST-translational modification, PROTEIN synthesis, ORGANELLE formation, ADP-ribosylation, DNA repair, POLY ADP ribose
Abstract

Posttranslational modifications (PTMs) greatly enhance the functional diversity of proteins, surpassing the number of gene‐encoded variations. One intriguing PTM is ADP‐ribosylation, which utilizes nicotinamide adenine dinucleotide (NAD+) as a substrate and is essential in cell signaling pathways regulating cellular responses. Here, we report the first cell‐permeable NAD+ analogs and demonstrate their utility for investigating cellular ADP‐ribosylation. Using a desthiobiotin‐labelled analog for affinity enrichment of proteins that are ADP‐ribosylated in living cells under oxidative stress, we identified protein targets associated with host‐virus interactions, DNA damage and repair, protein biosynthesis, and ribosome biogenesis. Most of these targets have been noted in various literature sources, highlighting the potential of our probes for cellular ADP‐ribosylome studies. [ABSTRACT FROM AUTHOR]

Published
2024
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31. Molecular Architecture of the ATP-Dependent Chromatin-Remodeling Complex SWR1

Author

Nguyen, Vu Q, Ranjan, Anand, Stengel, Florian, Wei, Debbie, Aebersold, Ruedi, Wu, Carl, and Leschziner, Andres E

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Adenosine Triphosphatases, Chromatin Assembly and Disassembly, DNA Helicases, Dimerization, Multiprotein Complexes, Nucleosomes, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This localization of H2A.Z is conserved throughout eukaryotes. SWR1 is a 1 megadalton complex containing 14 different polypeptides, including the AAA+ ATPases Rvb1 and Rvb2. Using electron microscopy, we obtained the three-dimensional structure of SWR1 and mapped its major functional components. Our data show that SWR1 contains a single heterohexameric Rvb1/Rvb2 ring that, together with the catalytic subunit Swr1, brackets two independently assembled multisubunit modules. We also show that SWR1 undergoes a large conformational change upon engaging a limited region of the nucleosome core particle. Our work suggests an important structural role for the Rvbs and a distinct substrate-handling mode by SWR1, thereby providing a structural framework for understanding the complex dimer-exchange reaction.

Published
2013

34. Non-canonical BIM-regulated energy metabolism determines drug-induced liver necrosis

Author

Lambrecht, Rebekka, primary, Rudolf, Franziska, additional, Ückert, Anna-Katharina, additional, Sladky, Valentina C., additional, Phan, Truong San, additional, Jansen, Jasmin, additional, Naim, Samara, additional, Kaufmann, Thomas, additional, Keogh, Adrian, additional, Kirschnek, Susanne, additional, Mangerich, Aswin, additional, Stengel, Florian, additional, Leist, Marcel, additional, Villunger, Andreas, additional, and Brunner, Thomas, additional

Published
2023
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36. Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5

Author

Obayashi, Eiji, Luna, Rafael E., Nagata, Takashi, Martin-Marcos, Pilar, Hiraishi, Hiroyuki, Singh, Chingakham Ranjit, Erzberger, Jan Peter, Zhang, Fan, Arthanari, Haribabu, Morris, Jacob, Pellarin, Riccardo, Moore, Chelsea, Harmon, Ian, Papadopoulos, Evangelos, Yoshida, Hisashi, Nasr, Mahmoud L., Unzai, Satoru, Thompson, Bryttney, Aube, Eric, Hustak, Samantha, Stengel, Florian, Dagraca, Eddie, Ananbandam, Asokan, Gao, Philip, Urano, Takeshi, Hinnebusch, Alan G., Wagner, Gerhard, and Asano, Katsura

Published
2024
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48. Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity

Author

Goretzki, Benedikt, primary, Wiedemann, Christoph, additional, McCray, Brett A., additional, Schäfer, Stefan L., additional, Jansen, Jasmin, additional, Tebbe, Frederike, additional, Mitrovic, Sarah-Ana, additional, Nöth, Julia, additional, Donohue, Jack K., additional, Jeffries, Cy M., additional, Steinchen, Wieland, additional, Stengel, Florian, additional, Sumner, Charlotte J., additional, Hummer, Gerhard, additional, and Hellmich, Ute A., additional

Published
2022
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