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Mol Cell Proteomics. 2018 Dec;17(12):2387-2401. doi: 10.1074/mcp.RA118.000892. Epub 2018 Sep 4.

Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes.

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From the ‡KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium.
§European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
§§Technical University of Berlin, Berlin, Germany.
¶Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands.
‖Netherlands Proteomics Centre, Utrecht, The Netherlands.
¶¶Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
From the ‡KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium;
**Leiden University, Institute of Biology Leiden, Leiden, The Netherlands.


Protein post-translational modifications (PTMs) have an indispensable role in living cells as they expand chemical diversity of the proteome, providing a fine regulatory layer that can govern protein-protein interactions in changing environmental conditions. Here we investigated the effects of acetylation and phosphorylation on the stability of subunit interactions in purified Saccharomyces cerevisiae complexes, namely exosome, RNA polymerase II and proteasome. We propose a computational framework that consists of conformational sampling of the complexes by molecular dynamics simulations, followed by Gibbs energy calculation by MM/GBSA. After benchmarking against published tools such as FoldX and Mechismo, we could apply the framework for the first time on large protein assemblies with the aim of predicting the effects of PTMs located on interfaces of subunits on binding stability. We discovered that acetylation predominantly contributes to subunits' interactions in a locally stabilizing manner, while phosphorylation shows the opposite effect. Even though the local binding contributions of PTMs may be predictable to an extent, the long range effects and overall impact on subunits' binding were only captured because of our dynamical approach. Employing the developed, widely applicable workflow on other large systems will shed more light on the roles of PTMs in protein complex formation.


Acetylation; Binding Affinity; Computational Biology; Exosome; Phosphorylation; Proteasome; Proteomics; RNA polymerase II; Structural Biology; Yeast

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