Universität zu Köln

Cappelletti, Valentina, Hauser, Thomas, Piazza, Ilaria ORCID: 0000-0001-5895-6134, Pepelnjak, Monika, Malinovska, Liliana ORCID: 0000-0002-8514-4569, Fuhrer, Tobias, Li, Yaozong ORCID: 0000-0002-5796-2644, Doerig, Christian, Boersema, Paul, Gillet, Ludovic, Grossbach, Jan, Dugourd, Aurelien, Saez-Rodriguez, Julio ORCID: 0000-0002-8552-8976, Beyer, Andreas ORCID: 0000-0002-3891-2123, Zamboni, Nicola ORCID: 0000-0003-1271-1021, Caflisch, Amedeo, de Souza, Natalie and Picotti, Paola ORCID: 0000-0002-4109-3552 (2021). Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell, 184 (2). S. 545 - 582. CAMBRIDGE: CELL PRESS. ISSN 1097-4172

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Abstract

Biological processes are regulated by intermolecular interactions and chemical modifications that do not affect protein levels, thus escaping detection in classical proteomic screens. We demonstrate here that a global protein structural readout based on limited proteolysis-mass spectrometry (LiP-MS) detects many such functional alterations, simultaneously and in situ, in bacteria undergoing nutrient adaptation and in yeast responding to acute stress. The structural readout, visualized as structural barcodes, captured enzyme activity changes, phosphorylation, protein aggregation, and complex formation, with the resolution of individual regulated functional sites such as binding and active sites. Comparison with prior knowledge, including other 'omics data, showed that LiP-MS detects many known functional alterations within well-studied pathways. It suggested distinct metabolite-protein interactions and enabled identification of a fructose-1,6-bisphosphate-based regulatory mechanism of glucose uptake in E coli. The structural readout dramatically increases classical proteomics coverage, generates mechanistic hypotheses, and paves the way for in situ structural systems biology.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Cappelletti, Valentina UNSPECIFIED UNSPECIFIED UNSPECIFIED Hauser, Thomas UNSPECIFIED UNSPECIFIED UNSPECIFIED Piazza, Ilaria UNSPECIFIED orcid.org/0000-0001-5895-6134 UNSPECIFIED Pepelnjak, Monika UNSPECIFIED UNSPECIFIED UNSPECIFIED Malinovska, Liliana UNSPECIFIED orcid.org/0000-0002-8514-4569 UNSPECIFIED Fuhrer, Tobias UNSPECIFIED UNSPECIFIED UNSPECIFIED Li, Yaozong UNSPECIFIED orcid.org/0000-0002-5796-2644 UNSPECIFIED Doerig, Christian UNSPECIFIED UNSPECIFIED UNSPECIFIED Boersema, Paul UNSPECIFIED UNSPECIFIED UNSPECIFIED Gillet, Ludovic UNSPECIFIED UNSPECIFIED UNSPECIFIED Grossbach, Jan UNSPECIFIED UNSPECIFIED UNSPECIFIED Dugourd, Aurelien UNSPECIFIED UNSPECIFIED UNSPECIFIED Saez-Rodriguez, Julio UNSPECIFIED orcid.org/0000-0002-8552-8976 UNSPECIFIED Beyer, Andreas UNSPECIFIED orcid.org/0000-0002-3891-2123 UNSPECIFIED Zamboni, Nicola UNSPECIFIED orcid.org/0000-0003-1271-1021 UNSPECIFIED Caflisch, Amedeo UNSPECIFIED UNSPECIFIED UNSPECIFIED de Souza, Natalie UNSPECIFIED UNSPECIFIED UNSPECIFIED Picotti, Paola UNSPECIFIED orcid.org/0000-0002-4109-3552 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-592537
DOI:	10.1016/j.cell.2020.12.021
Journal or Publication Title:	Cell
Volume:	184
Number:	2
Page Range:	S. 545 - 582
Date:	2021
Publisher:	CELL PRESS
Place of Publication:	CAMBRIDGE
ISSN:	1097-4172
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language ENZYME-I; MOLECULAR-DYNAMICS; ESCHERICHIA-COLI; HIGH-THROUGHPUT; HEAT-SHOCK; ALLOSTERIC REGULATION; SOMATIC MUTATIONS; FORCE-FIELD; YEAST; COMPLEX Multiple languages Biochemistry & Molecular Biology; Cell Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/59253