Section: Scientific Foundations
Modeling Macro-molecular Assemblies
Macro-molecular assembly, reconstruction by data integration, proteomics, modeling with uncertainties, curved Voronoi diagrams, topological persistence.
Reconstruction by data integration
Large protein assemblies such as the Nuclear Pore Complex (NPC), chaperonin cavities, the proteasome or ATP synthases, to name a few, are key to numerous biological functions. To improve our understanding of these functions, one would ideally like to build and animate atomic models of these molecular machines. However, this task is especially tough, due to their size and their plasticity, but also due to the flexibility of the proteins involved. In a sense, the modeling challenges arising in this context are different from those faced for binary docking, and also from those encountered for intermediate size complexes which are often amenable to a processing mixing (cryo-EM) image analysis and classical docking. To face these new challenges, an emerging paradigm is that of reconstruction by data integration  . In a nutshell, the strategy is reminiscent from NMR and consists of mixing experimental data from a variety of sources, so as to find out the model(s) best complying with the data. This strategy has been in particular used to propose plausible models of the Nuclear Pore Complex  , the largest assembly known to date in the eukaryotic cell, and consisting of 456 protein instances of 30 types.
Modeling with uncertainties and model assessment
Reconstruction by data integration requires three ingredients. First, a parametrized model must be adopted, typically a collection of balls to model a protein with pseudo-atoms. Second, as in NMR, a functional measuring the agreement between a model and the data must be chosen. In  , this functional is based upon restraints, namely penalties associated to the experimental data. Third, an optimization scheme must be selected. The design of restraints is notoriously challenging, due to the ambiguous nature and/or the noise level of the data. For example, Tandem Affinity Purification (TAP) gives access to a pullout i.e. a list of protein types which are known to interact with one tagged protein type, but no information on the number of complexes or on the stoichiometry of proteins types within a complex is provided. In cryo-EM, the envelope enclosing an assembly is often imprecisely defined, in particular in regions of low density. For immuno-EM labelling experiments, positional uncertainties arise from the microscope resolution.
These uncertainties coupled with the complexity of the functional being optimized, which in general is non convex, have two consequences. First, it is impossible to single out a unique reconstruction, and a set of plausible reconstructions must be considered. As an example, 1000 plausible models of the NPC were reported in  . Interestingly, averaging the positions of all balls of a particular protein type across these models resulted in 30 so-called probability density maps, each such map encoding the probability of presence of a particular protein type at a particular location in the NPC. Second, the assessment of all models (individual and averaged) is non trivial. In particular, the lack of straightforward statistical analysis of the individual models and the absence of assessment for the averaged models are detrimental to the mechanistic exploitation of the reconstruction results. At this stage, such models therefore remain qualitative.
As outlined by the previous discussion, a number of methodological developments are called for. On the experimental side, the problem of fostering the interpretation of data is under scrutiny. Of particular interest is the disambiguation of proteomics signals (TAP data, mass spectrometry data), and that of density maps coming from electron microscopy. As for modeling, two classes of developments are particularly stimulating. The first one is concerned with the design of algorithms performing reconstruction by data integration. The second one encompasses assessment tools, in order to single out the reconstructions which best comply with the experimental data.