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In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome

Michael Charles Lanz, Kumar Yugandhar, Shagun Gupta, Ethan Sanford, Vitor Faça, Stephanie Vega, Aaron Joiner, Chris Fromme, Haiyuan Yu, View ORCID ProfileMarcus Bustamante Smolka
doi: https://doi.org/10.1101/700070
Michael Charles Lanz
Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Kumar Yugandhar
Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Shagun Gupta
Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Ethan Sanford
Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Vitor Faça
Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Stephanie Vega
Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Aaron Joiner
Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Chris Fromme
Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Haiyuan Yu
Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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  • For correspondence: mbs266@cornell.edu haiyuan.yu@cornell.edu
Marcus Bustamante Smolka
Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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  • ORCID record for Marcus Bustamante Smolka
  • For correspondence: mbs266@cornell.edu haiyuan.yu@cornell.edu
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Abstract

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.

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Posted July 13, 2019.
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In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome
Michael Charles Lanz, Kumar Yugandhar, Shagun Gupta, Ethan Sanford, Vitor Faça, Stephanie Vega, Aaron Joiner, Chris Fromme, Haiyuan Yu, Marcus Bustamante Smolka
bioRxiv 700070; doi: https://doi.org/10.1101/700070
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In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome
Michael Charles Lanz, Kumar Yugandhar, Shagun Gupta, Ethan Sanford, Vitor Faça, Stephanie Vega, Aaron Joiner, Chris Fromme, Haiyuan Yu, Marcus Bustamante Smolka
bioRxiv 700070; doi: https://doi.org/10.1101/700070

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