Robyn Kaake, PhD
Assistant Professor
Cellular Molecular Pharmacology
School of Medicine

Education & Training

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• Diversity, Equity, and Inclusion Champion Training University of California 03/2022

Grants and Projects

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• Decoding the Chlamydia inclusion membrane protein-host protein interactome, NIH, 2015-2020
• Reactivation of Innate Immune Response Pathways as Treatment for HIV Infection, NIH, 2016-2019

Publications (40)

Top publication keywords:
ProteomeUbiquitin-Protein LigasesMultiprotein ComplexesChromatography, AffinityCore Binding Factor beta SubunitProteasome Endopeptidase ComplexAPOBEC-3G DeaminaseCullin ProteinsProtein Interaction MapsProteomicsTandem Mass Spectrometryvif Gene Products, Human Immunodeficiency VirusProtein Interaction MappingMass SpectrometryCross-Linking Reagents

• Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function.
  Molecular & cellular proteomics : MCP 2024 Jang GM, Annan Sudarsan AK, Shayeganmehr A, Prando Munhoz E, Lao R, Gaba A, Granadillo Rodríguez M, Love RP, Polacco BJ, Zhou Y, Krogan NJ, Kaake RM, Chelico L
• CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells.
  mBio 2024 Rathore U, Haas P, Easwar Kumar V, Hiatt J, Haas KM, Bouhaddou M, Swaney DL, Stevenson E, Zuliani-Alvarez L, McGregor MJ, Turner-Groth A, Ochieng' Olwal C, Bediako Y, Braberg H, Soucheray M, Ott M, …
• Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function.
  bioRxiv : the preprint server for biology 2024 Jang GM, Sudarsan AKA, Shayeganmehr A, Munhoz EP, Lao R, Gaba A, Rodríguez MG, Love RP, Polacco BJ, Zhou Y, Krogan NJ, Kaake RM, Chelico L
• De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking.
  Cell 2023 Chen Z, Shiozaki M, Haas KM, Skinner WM, Zhao S, Guo C, Polacco BJ, Yu Z, Krogan NJ, Lishko PV, Kaake RM, Vale RD, Agard DA
• Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.
  Nature communications 2023 Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, …

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• Functional analysis of a common BAG3 allele associated with protection from heart failure.
  Nature Cardiovascular Research 2023 Juan A. Perez-Bermejo, Luke M. Judge, Christina L. Jensen, Kenneth Wu, Hannah L. Watry, Annie Truong, Jaclyn J. Ho, Matthew Carter, Wendy V. Runyon, Robyn M. Kaake, Ernst H. Pulido, Mohammad A. …
• Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
  Nature structural & molecular biology 2023 Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM
• Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
  bioRxiv : the preprint server for biology 2023 Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM
• From systems to structure - using genetic data to model protein structures.
  Nature reviews. Genetics 2022 Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ
• Systems-level effects of allosteric perturbations to a model molecular switch.
  Nature 2021 Perica T, Mathy CJP, Xu J, Jang G?, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T
• Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes.
  Molecular & cellular proteomics : MCP 2021 Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ
• Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Wheat A, Yu C, Wang X, Burke AM, Chemmama IE, Kaake RM, Baker P, Rychnovsky SD, Yang J, Huang L
• Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology.
  Journal of proteome research 2021 Haas P, Muralidharan M, Krogan NJ, Kaake RM, Hüttenhain R
• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
  Science (New York, N.Y.) 2020 Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor…
• Structural basis of CD4 downregulation by HIV-1 Nef.
  Nature structural & molecular biology 2020 Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X
• The Global Phosphorylation Landscape of SARS-CoV-2 Infection.
  Cell 2020 Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray…
• Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection.
  Cell 2020 Ho JSY, Angel M, Ma Y, Sloan E, Wang G, Martinez-Romero C, Alenquer M, Roudko V, Chung L, Zheng S, Chang M, Fstkchyan Y, Clohisey S, Dinan AM, Gibbs J, Gifford R, Shen R, Gu Q, Irigoyen N, Campisi L, …
• A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
  Nature 2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, …
• A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.
  bioRxiv : the preprint server for biology 2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, …
• A systems approach to infectious disease.
  Nature reviews. Genetics 2020 Eckhardt M, Hultquist JF, Kaake RM, Hüttenhain R, Krogan NJ
• Abstract 934: Physical and Genetic Interaction Analyses in Human Pluripotent Stem Cell-Derived Cardiomyocytes to Study Protein Quality Control Disease in the Heart.
  Circulation Research 2019 Juan A Perez-Bermejo, Luke M Judge, Kenneth Wu, Christina L Jensen, Robyn M Kaake, Danielle Swaney, Po-Lin So, Nevan J Krogan, Bruce R Conklin
• Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.
  Cell 2018 Batra J, Hultquist JF, Liu D, Shtanko O, Von Dollen J, Satkamp L, Jang GM, Luthra P, Schwarz TM, Small GI, Arnett E, Anantpadma M, Reyes A, Leung DW, Kaake R, Haas P, Schmidt CB, Schlesinger LS, …
• EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion.
  Scientific reports 2018 Gaber A, Kim SJ, Kaake RM, Bencina M, Krogan N, Šali A, Pavšic M, Lenarcic B
• A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress.
  JCI insight 2017 Judge LM, Perez-Bermejo JA, Truong A, Ribeiro AJ, Yoo JC, Jensen CL, Mandegar MA, Huebsch N, Kaake RM, So PL, Srivastava D, Pruitt BL, Krogan NJ, Conklin BR
• The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity.
  Cell 2017 Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang ZZ, Laffleur B, Kaake RM, McGregor MJ, Haas K, Pefanis E, Albrecht RA, Pache L, Chanda S, Jen J, Ochando J, …
• Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes.
  PLoS genetics 2015 Bilanchone V, Clemens K, Kaake R, Dawson AR, Matheos D, Nagashima K, Sitlani P, Patterson K, Chang I, Huang L, Sandmeyer S
• Synthesis of two new enrichable and MS-cleavable cross-linkers to define protein-protein interactions by mass spectrometry.
  Organic & biomolecular chemistry 2015 Burke AM, Kandur W, Novitsky EJ, Kaake RM, Yu C, Kao A, Vellucci D, Huang L, Rychnovsky SD
• A new in vivo cross-linking mass spectrometry platform to define protein-protein interactions in living cells.
  Molecular & cellular proteomics : MCP 2014 Kaake RM, Wang X, Burke A, Yu C, Kandur W, Yang Y, Novtisky EJ, Second T, Duan J, Kao A, Guan S, Vellucci D, Rychnovsky SD, Huang L
• RNA binding and core complexes constitute the U-insertion/deletion editosome.
  Molecular and cellular biology 2014 Aphasizheva I, Zhang L, Wang X, Kaake RM, Huang L, Monti S, Aphasizhev R
• Characterizing the dynamics of proteasome complexes by proteomics approaches.
  Antioxidants & redox signaling 2014 Kaake RM, Kao A, Yu C, Huang L
• Combining docking site and phosphosite predictions to find new substrates: identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate.
  Cellular signalling 2013 Gordon EA, Whisenant TC, Zeller M, Kaake RM, Gordon WM, Krotee P, Patel V, Huang L, Baldi P, Bardwell L
• Signal-induced disassembly of the SCF ubiquitin ligase complex by Cdc48/p97.
  Molecular cell 2012 Yen JL, Flick K, Papagiannis CV, Mathur R, Tyrrell A, Ouni I, Kaake RM, Huang L, Kaiser P
• Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy.
  Molecular & cellular proteomics : MCP 2012 Fang L, Kaake RM, Patel VR, Yang Y, Baldi P, Huang L
• Oxidative stress-mediated regulation of proteasome complexes.
  Molecular & cellular proteomics : MCP 2011 Aiken CT, Kaake RM, Wang X, Huang L
• Oxidative stress-mediated regulation of proteasome complexes.
  Molecular & Cellular Proteomics 2011 Charity T. Aiken, Robyn M. Kaake, Xiaorong Wang, Lan Huang
• Computational prediction and experimental verification of new MAP kinase docking sites and substrates including Gli transcription factors.
  PLoS computational biology 2010 Whisenant TC, Ho DT, Benz RW, Rogers JS, Kaake RM, Gordon EA, Huang L, Baldi P, Bardwell L
• Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry.
  Molecular & cellular proteomics : MCP 2010 Kaake RM, Wang X, Huang L
• Selective enrichment and identification of azide-tagged cross-linked peptides using chemical ligation and mass spectrometry.
  Journal of the American Society for Mass Spectrometry 2010 Vellucci D, Kao A, Kaake RM, Rychnovsky SD, Huang L
• Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy.
  Journal of proteome research 2010 Kaake RM, Milenkovic T, Przulj N, Kaiser P, Huang L
• Proteomics Analysis of the Drosophila CRAC Channel Complex in the Resting and Active State.
  Biophysical Journal 2010 Aubin Penna, Robyn Kaake, Olga Safrina, Luette Forrest, Andriy V. Yeromin, Peter Kaiser, Lan Huang, Michael D. Cahalan