Modeling protein assemblies in the proteome

Guray Kuzu, Ozlem Keskin, Ruth Nussinov, Attila Gursoy*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)887-896
Number of pages10
JournalMolecular and Cellular Proteomics
Volume13
Issue number3
DOIs
StatePublished - Mar 2014

Funding

FundersFunder number
National Institute of General Medical SciencesP41-GM103311
National Cancer InstituteZIABC010441

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