PT  - JOURNAL ARTICLE
AU  - Michael Charles Lanz
AU  - Kumar Yugandhar
AU  - Shagun Gupta
AU  - Ethan Sanford
AU  - Vitor Faça
AU  - Stephanie Vega
AU  - Aaron Joiner
AU  - Chris Fromme
AU  - Haiyuan Yu
AU  - Marcus Bustamante Smolka
TI  - In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome
AID  - 10.1101/700070
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 700070
4099  - http://biorxiv.org/content/early/2019/07/13/700070.short
4100  - http://biorxiv.org/content/early/2019/07/13/700070.full
AB  - Phosphorylation is one of the most dynamic and widespread post-translational modifications regulating virtually every aspect of eukaryotic cell biology. Here we present a comprehensive phosphoproteomic dataset for budding yeast, comprised of over 30,000 high confidence phosphorylation sites identified by mass spectrometry. This single dataset nearly doubles the size of the known phosphoproteome in budding yeast and defines a set of cell cycle-regulated phosphorylation events. With the goal of enhancing the identification of functional phosphorylation events, we performed computational positioning of phosphorylation sites on available 3D protein structures and systematically identified events predicted to regulate protein complex architecture. Results reveal a large number of phosphorylation sites mapping to or near protein interaction interfaces, many of which result in steric or electrostatic “clashes” predicted to disrupt the interaction. Phosphorylation site mutants experimentally validate our predictions and support a role for phosphorylation in negatively regulating protein-protein interactions. With the advancement of Cryo-EM and the increasing number of available structures, our approach should help drive the functional and spatial exploration of the phosphoproteome.