Search Results - "Paulo, Joao A."

The PINK1-PARKIN Mitochondrial Ubiquitylation Pathway Drives a Program of OPTN/NDP52 Recruitment and TBK1 Activation to Promote Mitophagy by Heo, Jin-Mi, Ordureau, Alban, Paulo, Joao A., Rinehart, Jesse, Harper, J. Wade

“…Damaged mitochondria are detrimental to cellular homeostasis. One mechanism for removal of damaged mitochondria involves the PINK1-PARKIN pathway, which…”
Get full text

Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry by Schweppe, Devin K, Prasad, Satendra, Belford, Michael W, Navarrete-Perea, José, Bailey, Derek J, Huguet, Romain, Jedrychowski, Mark P, Rad, Ramin, McAlister, Graeme, Abbatiello, Susan E, Woulters, Eloy R, Zabrouskov, Vlad, Dunyach, Jean-Jacques, Paulo, João A, Gygi, Steven P

“…Multiplexed, isobaric tagging methods are powerful techniques to increase throughput, precision, and accuracy in quantitative proteomics. The dynamic range and…”
Get full text

Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3 by Navarrete-Perea, José, Yu, Qing, Gygi, Steven P, Paulo, Joao A

“…Mass spectrometry (MS) coupled toisobaric labeling has developed rapidly into a powerful strategy for high-throughput protein quantification. Sample…”
Get full text

Detection and Quantitation of Circulating Human Irisin by Tandem Mass Spectrometry by Jedrychowski, Mark P., Wrann, Christiane D., Paulo, Joao A., Gerber, Kaitlyn K., Szpyt, John, Robinson, Matthew M., Nair, K. Sreekumaran, Gygi, Steven P., Spiegelman, Bruce M.

“…Exercise provides many health benefits, including improved metabolism, cardiovascular health, and cognition. We have shown previously that FNDC5, a type I…”
Get full text

Systematic quantitative analysis of ribosome inventory during nutrient stress by An, Heeseon, Ordureau, Alban, Körner, Maria, Paulo, Joao A., Harper, J. Wade

“…Mammalian cells reorganize their proteomes in response to nutrient stress through translational suppression and degradative mechanisms using the proteasome and…”
Get full text

Global Landscape and Dynamics of Parkin and USP30-Dependent Ubiquitylomes in iNeurons during Mitophagic Signaling by Ordureau, Alban, Paulo, Joao A., Zhang, Jiuchun, An, Heeseon, Swatek, Kirby N., Cannon, Joe R., Wan, Qiaoqiao, Komander, David, Harper, J. Wade

“…The ubiquitin ligase Parkin, protein kinase PINK1, USP30 deubiquitylase, and p97 segregase function together to regulate turnover of damaged mitochondria via…”
Get full text

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome by Huttlin, Edward L., Bruckner, Raphael J., Navarrete-Perea, Jose, Cannon, Joe R., Baltier, Kurt, Gebreab, Fana, Gygi, Melanie P., Thornock, Alexandra, Zarraga, Gabriela, Tam, Stanley, Szpyt, John, Gassaway, Brandon M., Panov, Alexandra, Parzen, Hannah, Fu, Sipei, Golbazi, Arvene, Maenpaa, Eila, Stricker, Keegan, Guha Thakurta, Sanjukta, Zhang, Tian, Rad, Ramin, Pan, Joshua, Nusinow, David P., Paulo, Joao A., Schweppe, Devin K., Vaites, Laura Pontano, Harper, J. Wade, Gygi, Steven P.

“…Thousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome. Through…”
Get full text

Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics by Schweppe, Devin K, Eng, Jimmy K, Yu, Qing, Bailey, Derek, Rad, Ramin, Navarrete-Perea, Jose, Huttlin, Edward L, Erickson, Brian K, Paulo, Joao A, Gygi, Steven P

“…Multiplexed quantitative analyses of complex proteomes enable deep biological insight. While a multitude of workflows have been developed for multiplexed…”
Get full text

Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling by Paek, Jaeho, Kalocsay, Marian, Staus, Dean P., Wingler, Laura, Pascolutti, Roberta, Paulo, Joao A., Gygi, Steven P., Kruse, Andrew C.

“…G-protein-coupled receptors (GPCRs) play critical roles in regulating physiological processes ranging from neurotransmission to cardiovascular function…”
Get full text

TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples by Li, Jiaming, Van Vranken, Jonathan G., Pontano Vaites, Laura, Schweppe, Devin K., Huttlin, Edward L., Etienne, Chris, Nandhikonda, Premchendar, Viner, Rosa, Robitaille, Aaron M., Thompson, Andrew H., Kuhn, Karsten, Pike, Ian, Bomgarden, Ryan D., Rogers, John C., Gygi, Steven P., Paulo, Joao A.

“…Isobaric labeling empowers proteome-wide expression measurements simultaneously across multiple samples. Here an expanded set of 16 isobaric reagents based on…”
Get full text

Proteome-wide mapping of short-lived proteins in human cells by Li, Jiaming, Cai, Zhenying, Vaites, Laura Pontano, Shen, Ning, Mitchell, Dylan C., Huttlin, Edward L., Paulo, Joao A., Harry, Brian L., Gygi, Steven P.

“…Rapid protein degradation enables cells to quickly modulate protein abundance. Dysregulation of short-lived proteins plays essential roles in disease…”
Get full text

Architecture of the human interactome defines protein communities and disease networks by Huttlin, Edward L., Bruckner, Raphael J., Paulo, Joao A., Cannon, Joe R., Ting, Lily, Baltier, Kurt, Colby, Greg, Gebreab, Fana, Gygi, Melanie P., Parzen, Hannah, Szpyt, John, Tam, Stanley, Zarraga, Gabriela, Pontano-Vaites, Laura, Swarup, Sharan, White, Anne E., Schweppe, Devin K., Rad, Ramin, Erickson, Brian K., Obar, Robert A., Guruharsha, K. G., Li, Kejie, Artavanis-Tsakonas, Spyros, Gygi, Steven P., Harper, J. Wade

“…Affinity purification–mass spectrometry elucidates protein interaction networks and co-complexes to build, to our knowledge, the largest experimentally derived…”
Get full text

Defining roles of PARKIN and ubiquitin phosphorylation by PINK1 in mitochondrial quality control using a ubiquitin replacement strategy by Ordureau, Alban, Heo, Jin-Mi, Duda, David M., Paulo, Joao A., Olszewski, Jennifer L., Yanishevski, David, Rinehart, Jesse, Schulman, Brenda A., Harper, J. Wade

“…Significance PINK1 protein kinase and PARKIN UB ligase are mutated in inherited forms of Parkinson’s disease and several cancers. Thus, it is of great…”
Get full text

Systematic Analysis of Human Cells Lacking ATG8 Proteins Uncovers Roles for GABARAPs and the CCZ1/MON1 Regulator C18orf8/RMC1 in Macroautophagic and Selective Autophagic Flux by Vaites, Laura Pontano, Paulo, Joao A., Huttlin, Edward L., Harper, J. Wade

“…Selective autophagy and macroautophagy sequester specific organelles/substrates or bulk cytoplasm, respectively, inside autophagosomes as cargo for delivery to…”
Get full text

A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments by Paulo, Joao A., O’Connell, Jeremy D., Gygi, Steven P.

“…Isobaric labeling is a powerful strategy for quantitative mass spectrometry-based proteomic investigations. A complication of such analyses has been the…”
Get full text

Compensatory metabolic networks in pancreatic cancers upon perturbation of glutamine metabolism by Biancur, Douglas E., Paulo, Joao A., Małachowska, Beata, Quiles Del Rey, Maria, Sousa, Cristovão M., Wang, Xiaoxu, Sohn, Albert S. W., Chu, Gerald C., Gygi, Steven P., Harper, J. Wade, Fendler, Wojciech, Mancias, Joseph D., Kimmelman, Alec C.

“…Pancreatic ductal adenocarcinoma is a notoriously difficult-to-treat cancer and patients are in need of novel therapies. We have shown previously that these…”
Get full text

pH-Gated Succinate Secretion Regulates Muscle Remodeling in Response to Exercise by Reddy, Anita, Bozi, Luiz H.M., Yaghi, Omar K., Mills, Evanna L., Xiao, Haopeng, Nicholson, Hilary E., Paschini, Margherita, Paulo, Joao A., Garrity, Ryan, Laznik-Bogoslavski, Dina, Ferreira, Julio C.B., Carl, Christian S., Sjøberg, Kim A., Wojtaszewski, Jørgen F.P., Jeppesen, Jacob F., Kiens, Bente, Gygi, Steven P., Richter, Erik A., Mathis, Diane, Chouchani, Edward T.

“…In response to skeletal muscle contraction during exercise, paracrine factors coordinate tissue remodeling, which underlies this healthy adaptation. Here we…”
Get full text

The BioPlex Network: A Systematic Exploration of the Human Interactome by Huttlin, Edward L., Ting, Lily, Bruckner, Raphael J., Gebreab, Fana, Gygi, Melanie P., Szpyt, John, Tam, Stanley, Zarraga, Gabriela, Colby, Greg, Baltier, Kurt, Dong, Rui, Guarani, Virginia, Vaites, Laura Pontano, Ordureau, Alban, Rad, Ramin, Erickson, Brian K., Wühr, Martin, Chick, Joel, Zhai, Bo, Kolippakkam, Deepak, Mintseris, Julian, Obar, Robert A., Harris, Tim, Artavanis-Tsakonas, Spyros, Sowa, Mathew E., De Camilli, Pietro, Paulo, Joao A., Harper, J. Wade, Gygi, Steven P.

“…Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput…”
Get full text

Autophagy is required for proper cysteine homeostasis in pancreatic cancer through regulation of SLC7A11 by Mukhopadhyay, Subhadip, Biancur, Douglas E., Parker, Seth J., Yamamoto, Keisuke, Banh, Robert S., Paulo, Joao A., Mancias, Joseph D., Kimmelman, Alec C.

“…Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer and is highly refractory to current therapies. We had previously shown that…”
Get full text

Epstein-Barr-Virus-Induced One-Carbon Metabolism Drives B Cell Transformation by Wang, Liang Wei, Shen, Hongying, Nobre, Luis, Ersing, Ina, Paulo, Joao A., Trudeau, Stephen, Wang, Zhonghao, Smith, Nicholas A., Ma, Yijie, Reinstadler, Bryn, Nomburg, Jason, Sommermann, Thomas, Cahir-McFarland, Ellen, Gygi, Steven P., Mootha, Vamsi K., Weekes, Michael P., Gewurz, Benjamin E.

“…Epstein-Barr virus (EBV) causes Burkitt, Hodgkin, and post-transplant B cell lymphomas. How EBV remodels metabolic pathways to support rapid B cell outgrowth…”
Get full text