Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones

Gabrielle Stetz, Amanda Tse, Gennady M. Verkhivker
2018 Scientific Reports  
Dissecting structure-encoded determinants of allosteric cross-talk between post-translational modification sites in the Hsp90 chaperones. Sci Rep 8, 6899, https://doi. Post-translational modifications (PTMs) represent an important regulatory instrument that modulates structure, dynamics and function of proteins. The large number of PTM sites in the Hsp90 proteins that are scattered throughout different domains indicated that synchronization of multiple PTMs through a combinatorial code can be
more » ... voked as an important mechanism to orchestrate diverse chaperone functions and recognize multiple client proteins. In this study, we have combined structural and coevolutionary analysis with molecular simulations and perturbation response scanning analysis of the Hsp90 structures to characterize functional role of PTM sites in allosteric regulation. The results reveal a small group of conserved PTMs that act as global mediators of collective dynamics and allosteric communications in the Hsp90 structures, while the majority of flexible PTM sites serve as sensors and carriers of the allosteric structural changes. This study provides a comprehensive structural, dynamic and network analysis of PTM sites across Hsp90 proteins, identifying specific role of regulatory PTM hotspots in the allosteric mechanism of the Hsp90 cycle. We argue that plasticity of a combinatorial PTM code in the Hsp90 may be enacted through allosteric coupling between effector and sensor PTM residues, which would allow for timely response to structural requirements of multiple modified enzymes. Significant biological insights in the functional roles of diverse PTM types in regulation of protein families and signaling networks have been obtained in recent years by utilizing systems-level quantitative analyses, including high-resolution mass spectrometry (MS) and systems biology approaches 1-6 . According to these large-scale investigations, PTMs can regulate protein activity through diverse mechanisms, including modifications of binding sites and protein-protein interactions, protein localization, degradation, cleavage, and allosteric regulation of enzyme activity. Systematic functional analysis of 200,000 phosphorylation, acetylation, and ubiquitination sites from 11 eukaryotic species prioritized the functional relevance of PTMs in cross-regulatory events and protein-protein interactions by considering evolutionary conservation patterns of PTMs within domain families 5 . Diversity and sensitivity of PTM-mediated regulation is enabled not only by individual PTM sites and specific PTM types, but often through cooperative action and mutual interdependencies between multiple PTMs, which is often referred as functional PTM cross-talk 6-8 . Multiple PTMs can be linked through evolutionary and functional couplings that can be used to distinguish PTM-mediated regulatory hotspots and molecular switches of protein functions and allosteric interactions 6 . A comparative analysis of multiple PTM types in different eukaryotic species revealed correlated evolution of PTM pairs in proteins, showing that coevolving PTM pairs are not necessarily close in sequence space but can often enjoy structural proximity and physical interactions, forming regulatory centers in protein structures 7 . A proteome-wide survey of co-occurring phosphorylation pairs that tend to be modified together showed that these PTMs can be often functionally associated 8 . Using large experimental data
doi:10.1038/s41598-018-25329-4 pmid:29720613 pmcid:PMC5932063 fatcat:myzd2ceo4vdtxdfi62iua7zili