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The diverse and expanding role of mass spectrometry in structural and molecular biology

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Mass Spectrometry based proteomics plays a pivotal role in revealing the plethora of protein interactions that take place inside a cell, wherein proteins form protein assemblies and/or signalling networks. Especially using affinity purification of tagged proteins followed by mass spectrometric analysis of its binding partners a wealth of data has been gathered. A next step will be to gather more in-depth structural and functional information on all these individual assemblies. This may come from in-depth high-resolution structural models, as well as detailed information on how they function and dynamically evolve during cellular perturbations. Mass spectrometry can also contribute to this next level of protein interaction analysis although it does require partly different and novel approaches. To contribute to this emerging new area in structural proteomics, our group is developing new methods using native mass spectrometry and cross-linking mass spectrometry with the aim to bridge the gap between interaction proteomics and structural biology. These new innovations and applications of them in interaction proteomics will be central in my presentation.

In the first part of the talk native mass spectrometry and its applications in probing large and dynamic protein assemblies and protein interactions will be described, focusing on the analysis of ribosomal particles, viruses and complexes involved in our immune response. We aim to expand the boundaries of mass spectrometry in mass range up to several million Da, sensitivity and mass resolution, and are now able to detect and analyse single particles/molecules.

In the second part I will highlight recent work on cross-linking mass spectrometry. We have developed XL-MS methods aimed at probing protein interactions at the proteome wide level. We demonstrate the power of our novel strategy to organelles such as mitochondria and nuclei. In each of these studies we successfully identified thousands of cross-links. Many of the identified cross-links could be validated by mapping them on available high-resolution structures, but the data also provide information on assemblies for which no high-resolution structures are available, and even reveal new protein interaction networks.

In the final part of my talk I will briefly describe a new view at the plasma proteome, whereby I will address the questions; Are our plasma proteomes all unique? and ultimately What is a protein?

This talk is part of the MRC LMB Seminar Series series.

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