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Chem Biol. 2015 Jan 22;22(1):117-28. doi: 10.1016/j.chembiol.2014.11.010. Epub 2014 Dec 24.

Topological models of heteromeric protein assemblies from mass spectrometry: application to the yeast eIF3:eIF5 complex.

Author information

1
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.
2
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
3
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.
4
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
5
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.
6
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK. Electronic address: carol.robinson@chem.ox.ac.uk.

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.

PMID:
25544043
PMCID:
PMC4306531
DOI:
10.1016/j.chembiol.2014.11.010
[Indexed for MEDLINE]
Free PMC Article

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