Assessing the reconstruction of macromolecular assemblies with toleranced models

作者：Dreyfus Tom; Doye Valerie; Cazals Frederic^*

来源：Proteins: Structure, Function, and Genetics , 2012, 80(9): 2125-2136.

DOI：10.1002/prot.24092

• protein complex
• macromolecular assembly
• nuclear pore complex
• model assessment
• curved Voronoi diagram
• curved a-complex
• uncertain models

We introduce toleranced models (TOMs), a generic and versatile framework meant to handle models of macromolecular assemblies featuring uncertainties on the shapes and the positions of proteins. A TOM being a continuum of nested shapes, the inner (resp. outer) ones representing high (low) confidence regions, we present topological and geometric statistics assessing features of this continuum at multiple scales. While the topological statistics qualify contacts between instances of protein types and complexes involving prescribed protein types, the geometric statistics scale the geometric accuracy of these complexes. We validate the TOM framework on recent average models of the entire nuclear pore complex (NPC) obtained from reconstruction by data integration, and confront our quantitative analysis against experimental findings related to complexes of the NPC, namely the Y-complex, the T-complex, and the Nsp1Nup82Nup159 complex. In the three cases, our analysis bridges the gap between global qualitative models of the entire NPC, and atomic resolution models or putative models of the aforementioned complexes. In a broader perspective, the quantitative assessments provided by the TOM framework should prove instrumental to implement a virtuous loop model reconstructionmodel selection, in the context of reconstruction by data integration.

• 出版日期2012-8
• 单位INRIA