title: Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry.
abstract: Mitochondrial protein interactions and complexes facilitate mitochondrial function. These complexes range from simple dimers to the respirasome supercomplex consisting of oxidative phosphorylation complexes I, III, and IV. To improve understanding of mitochondrial function, we used chemical cross-linking mass spectrometry to identify 2,427 cross-linked peptide pairs from 327 mitochondrial proteins in whole, respiring murine mitochondria. In situ interactions were observed in proteins throughout the electron transport chain membrane complexes, ATP synthase, and the mitochondrial contact site and cristae organizing system (MICOS) complex. Cross-linked sites showed excellent agreement with empirical protein structures and delivered complementary constraints for in silico protein docking. These data established direct physical evidence of the assembly of the complex I-III respirasome and enabled prediction of in situ interfacial regions of the complexes. Finally, we established a database and tools to harness the cross-linked interactions we observed as molecular probes, allowing quantification of conformation-dependent protein interfaces and dynamic protein complex assembly.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98105.
authors.forename: Devin K
authors.initials: DK
authors.lastname: Schweppe
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98105.
authors.forename: Juan D
authors.initials: JD
authors.lastname: Chavez
authors.affiliation: Department of Bioengineering, University of Washington, Seattle, WA 98105.|Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105.|Mitochondria and Metabolism Center, University of Washington, Seattle WA 98105.
authors.forename: Chi Fung
authors.initials: CF
authors.lastname: Lee
authors.affiliation: Department of Bioengineering, University of Washington, Seattle, WA 98105.|Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105.|Mitochondria and Metabolism Center, University of Washington, Seattle WA 98105.
authors.forename: Arianne
authors.initials: A
authors.lastname: Caudal
authors.affiliation: Department of Radiology, University of Washington, Seattle, WA 98105.
authors.forename: Shane E
authors.initials: SE
authors.lastname: Kruse
authors.affiliation: Department of Radiology, University of Washington, Seattle, WA 98105.
authors.forename: Rudy
authors.initials: R
authors.lastname: Stuppard
authors.affiliation: Department of Radiology, University of Washington, Seattle, WA 98105.
authors.forename: David J
authors.initials: DJ
authors.lastname: Marcinek
authors.affiliation: Department of Pathology Yale School of Medicine, New Haven, CT 06510.|Department of Genetics, Yale School of Medicine, New Haven, CT 06510.
authors.forename: Gerald S
authors.initials: GS
authors.lastname: Shadel
authors.affiliation: Department of Bioengineering, University of Washington, Seattle, WA 98105.|Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105.|Mitochondria and Metabolism Center, University of Washington, Seattle WA 98105.
authors.forename: Rong
authors.initials: R
authors.lastname: Tian
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98105; jimbruce@uw.edu.
authors.forename: James E
authors.initials: JE
authors.lastname: Bruce
mesh_terms: D000818:Animals; D003432:Cross-Linking Reagents / Q000737:chemistry; D045222:Electron Transport Chain Complex Proteins / Q000737:chemistry* / Q000378:metabolism; D013058:Mass Spectrometry / Q000379:methods*; D051379:Mice; D008928:Mitochondria / Q000378:metabolism; D024101:Mitochondrial Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D010085:Oxidative Phosphorylation; D011485:Protein Binding; D011487:Protein Conformation; D060066:Protein Interaction Maps
chemical_list: D003432:Cross-Linking Reagents; D045222:Electron Transport Chain Complex Proteins; D024101:Mitochondrial Proteins
keywords: cross-linking; interactome; mass spectrometry; mitochondria; protein interaction reporter