Unveiling Contacts within Macro-molecular assemblies by solving Minimum Weight Connectivity Inference Problems

Deepesh Agarwal 1 Christelle Caillouet 2 David Coudert 2 Frédéric Cazals 1
1 ABS - Algorithms, Biology, Structure
CRISAM - Inria Sophia Antipolis - Méditerranée
2 COATI - Combinatorics, Optimization and Algorithms for Telecommunications
CRISAM - Inria Sophia Antipolis - Méditerranée , Laboratoire I3S - COMRED - COMmunications, Réseaux, systèmes Embarqués et Distribués
Abstract : Consider a set of oligomers listing the subunits involved in sub-complexes of a macro-molecular assembly, obtained e.g. using native mass spectrometry or affinity purification. Given these oligomers, connectivity inference (CI) consists of finding the most plausible contacts between these subunits, and minimum connectivity inference (MCI) is the variant consisting of finding a set of contacts of smallest cardinality. MCI problems avoid speculating on the total number of contacts, but yield a subset of all contacts and do not allow exploiting a priori information on the likelihood of individual contacts. In this context, we present two novel algorithms, MILP-W and MILP-WB. The former solves the minimum weight connectivity inference (MWCI), an optimization problem whose criterion mixes the number of contacts and their likelihood. The latter uses the former in a bootstrap fashion, to improve the sensitivity and the specificity of solution sets. Experiments on three systems (yeast exosome, yeast proteasome lid, human eiF3), for which reference contacts are known (crystal structure, cryo electron microscopy, cross-linking), show that our algorithms predict contacts with high specificity and sensitivity, yielding a very significant improvement over previous work, typically a twofold increase in sensitivity. The software accompanying this paper is made available, and should prove of ubiquitous interest whenever connectivity inference from oligomers is faced.
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Deepesh Agarwal, Christelle Caillouet, David Coudert, Frédéric Cazals. Unveiling Contacts within Macro-molecular assemblies by solving Minimum Weight Connectivity Inference Problems. Molecular and Cellular Proteomics, American Society for Biochemistry and Molecular Biology, 2015, 14, pp.2274-2284. ⟨10.1074/mcp.M114.047779⟩. ⟨hal-01245401v2⟩

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