Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in cells.

Yunqing Li, Luisa Iamele, Hugo de Jonge, Davide M Ferraris, Hartmut H Niemann, Marina S Dietz, Mike Heilemann, Serena M Arghittu, Gabriel J Hella, Daniel Haße, Petra Freund, Hans-Dieter Barth, Roberto Covino

Journal: Nature communications 2024;15(1):9486

PMID: 39488533

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Abstract

Embedding of cell-surface receptors into a membrane defines their dynamics but also complicates experimental characterization of their signaling complexes. The hepatocyte growth factor receptor MET is a receptor tyrosine kinase involved in cellular processes such as proliferation, migration, and survival. It is also targeted by the pathogen Listeria monocytogenes, whose invasion protein, internalin B (InlB), binds to MET, forming a signaling dimer that triggers pathogen internalization. Here we use an integrative structural biology approach, combining molecular dynamics simulations and single-molecule Förster resonance energy transfer (smFRET) in cells, to investigate the early stages of MET activation. Our simulations show that InlB binding stabilizes MET in a conformation that promotes dimer formation. smFRET reveals that the in situ dimer structure closely resembles one of two previously published crystal structures, though with key differences. This study refines our understanding of MET activation and provides a methodological framework for studying other plasma membrane receptors.

Address: Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, Frankfurt am Main, Germany.; Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, Frankfurt am Main, Germany.; IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, Frankfurt am Main, Germany.; Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, Frankfurt am Main, Germany.; Department of Chemistry, Bielefeld University, Universitaetsstr. 25, Bielefeld, Germany.; Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, Novara, Italy.; Department of Molecular Medicine, University of Pavia, Immunology and General Pathology Section, Via Ferrata 9, Pavia, Italy.; Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, Frankfurt am Main, Germany. [email protected].; IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, Frankfurt am Main, Germany. [email protected].; Institute of Computer Science, Goethe-University Frankfurt, Robert-Mayer-Str. 11-15, Frankfurt am Main, Germany. [email protected].; Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, Frankfurt am Main, Germany. [email protected].; IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, Frankfurt am Main, Germany. [email protected].

DOI: 10.1038/s41467-024-53772-7

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https://assays.cancer.gov/CPTAC-1496

MeSH Terms: Proto-Oncogene Proteins c-met, Molecular Dynamics Simulation, Single Molecule Imaging, Fluorescence Resonance Energy Transfer, Bacterial Proteins, Humans, Membrane Proteins, Listeria monocytogenes, Protein Binding, Signal Transduction, Protein Multimerization