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

Abstract

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 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.

Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

“…Similarly to our previous results on a smaller dataset [24], the comparison of the binding energy decomposition between non-modified and modified complexes revealed that lysine acetylation more frequently contributes to binding in a locally stabilizing fashion, while the opposite is true for phosphorylations (Figs 2 and S4). These effects might be the consequence of the local changes introduced by the respective modifications: while phosphorylation brings about a negative charge that must be compensated by neighboring positively charged residues, PLOS COMPUTATIONAL BIOLOGY acetylation diminishes the charge from the lysine side chain.…”

Mass Spectrometry-Based Characterization of the Virion Proteome, Phosphoproteome, and Associated Kinase Activity of Human Cytomegalovirus

“…It was notably shown to decorate three-quarters of the detected proteins in human cells to various degrees [73]. A major role played by phosphorylation is intervening in the stabilization or destabilization of protein-protein interactions [74][75][76][77][78][79]. Therefore, the knowledge on the phosphorylation status of HCMV virion proteins may help in understanding how this particular PTM influences the assembly and stability of this multiprotein system.…”

The functional landscape of the human phosphoproteome

“…Therefore, prioritization strategies are crucial to facilitate the discovery of highly relevant phosphosites 10 . Different methodologies have been proposed, including identifying phosphosites that are highly conserved 11,12 , located at interface positions [13][14][15] , showing strong regulation, or combinations of such features 10,16 . Mutational studies have also been used to characterize relevant phosphorylations 17 , but cannot yet be applied to human phosphorylation at scale.…”