title: Topological models of heteromeric protein assemblies from mass spectrometry: application to the yeast eIF3:eIF5 complex.
abstract: Describing, understanding, and modulating the function of the cell require elucidation of the structures of macromolecular assemblies. Here, we describe an integrative method for modeling heteromeric complexes using as a starting point disassembly pathways determined by native mass spectrometry (MS). In this method, the pathway data and other available information are encoded as a scoring function on the positions of the subunits of the complex. The method was assessed on its ability to reproduce the native contacts in five benchmark cases with simulated MS data and two cases with real MS data. To illustrate the power of our method, we purified the yeast initiation factor 3 (eIF3) complex and characterized it by native MS and chemical crosslinking MS. We established substoichiometric binding of eIF5 and derived a model for the five-subunit eIF3 complex, at domain level, consistent with its role as a scaffold for other initiation factors.
authors.affiliation: Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK; Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK.
authors.forename: Argyris
authors.initials: A
authors.lastname: Politis
authors.affiliation: Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
authors.forename: Carla
authors.initials: C
authors.lastname: Schmidt
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
authors.forename: Elina
authors.initials: E
authors.lastname: Tjioe
authors.affiliation: Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
authors.forename: Alan M
authors.initials: AM
authors.lastname: Sandercock
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
authors.forename: Keren
authors.initials: K
authors.lastname: Lasker
authors.affiliation: Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
authors.forename: Yuliya
authors.initials: Y
authors.lastname: Gordiyenko
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Russel
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA. Electronic address: sali@salilab.org.
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
authors.affiliation: Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK. Electronic address: carol.robinson@chem.ox.ac.uk.
authors.forename: Carol V
authors.initials: CV
authors.lastname: Robinson
mesh_terms: D039621:Eukaryotic Initiation Factor-3 / Q000032:analysis* / Q000378:metabolism; D008958:Models, Molecular; D010448:Peptide Initiation Factors / Q000032:analysis* / Q000378:metabolism; D011485:Protein Binding; D012372:ROC Curve; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis* / Q000378:metabolism; D053719:Tandem Mass Spectrometry
chemical_list: D039621:Eukaryotic Initiation Factor-3; D010448:Peptide Initiation Factors; D029701:Saccharomyces cerevisiae Proteins