Modeling Protein Assemblies in the Proteome

Abstract

Most (if not all) proteins function when associated in multimolecular assemblies. Attaining the structures of protein assemblies at the atomic scale is an important aim of structural biology. Experimentally, structures are increasingly available, and computations can help bridge the resolution gap between high-and low-resolution scales. Existing computational methods have made substantial progress toward this aim; however, current approaches are still limited. Some involve manual adjustment of experimental data; some are automated docking methods, which are computationally expensive and not applicable to large-scale proteome studies; and still others exploit the symmetry of the complexes and thus are not applicable to nonsymmetrical complexes. Our study aims to take steps toward overcoming these limitations. We have developed a strategy for the construction of protein assemblies computationally based on binary interactions predicted by a motif-based protein interaction prediction tool, PRISM (Protein Interactions by Structural Matching). Previously, we have shown its power in predicting pairwise interactions. Here we take a step toward multimolecular assemblies, reflecting the more prevalent cellular scenarios. With this method we are able to construct homo-/ hetero-complexes and symmetric/asymmetric complexes without a limitation on the number of components. The method considers conformational changes and is applicable to large-scale studies. We also exploit electron microscopy density maps to select a solution from among the predictions. Here we present the method, illustrate its results, and highlight its current limitations. Molecular &

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps

“…Another limitation comes from the rigid-body treatment of the structures. Exploiting alternative conformations available in the PDB may include a certain extent of protein flexibility (Kuzu et al, 2014(Kuzu et al, , 2013, which however is limited by the richness of the PDB. Conformational changes upon binding and allostery may affect the final research papers structures of the assemblies.…”

“…FiberDock mainly reorients side chains and slightly reorients the backbones of the proteins and calculates the energy. The binding energy score (BES) threshold was chosen as À10 as in our previous studies (Kuzu et al, 2013(Kuzu et al, , 2014Kar et al, 2012).…”

“…A general method which does not require any additional information would be helpful in constructing protein assemblies in cases where such data are unavailable. In an earlier effort to address this problem, we presented a method to construct protein assemblies starting from binary interactions (Kuzu et al, 2014). There, only PDB structures (and models if the PDB structures were unavailable) were exploited in the construction, and the model of the complex was obtained based on the predicted interfaces.…”

“…In this approach, one can use computational docking methods (Pierce et al, 2005;Schneidman-Duhovny et al, 2005a,b;Karaca et al, 2010;Inbar et al, 2005;Kuzu et al, 2014) to first construct a large number of protein-assembly models by exploiting existing highresolution structural information from X-ray crystallography and NMR spectroscopy. Using this as a basis set, it is possible to use lower resolution 3DEM density maps to evaluate, rank and select the best models that are both structurally plausible and consistent with the experimental density maps.…”

The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology

“…In another work, homology modeling techniques have been integrated with EM maps to model a high resolution molecular model of the auxillin-clathrin complex. Further, the PRISM algorithm integrated with conformational ensembles of protein monomers and EM maps performed well in modeling large protein assemblies [22]. Integrative modeling has been also applied to the yeast RNA exosome where the spatial restraints from MS data and computational docking of the subunits have been used (as reviewed in [3]).…”