Search Results - "Polacco, Benjamin J"

A proximity proteomics pipeline with improved reproducibility and throughput by Zhong, Xiaofang, Li, Qiongyu, Polacco, Benjamin J, Patil, Trupti, Marley, Aaron, Foussard, Helene, Khare, Prachi, Vartak, Rasika, Xu, Jiewei, DiBerto, Jeffrey F, Roth, Bryan L, Eckhardt, Manon, von Zastrow, Mark, Krogan, Nevan J, Hüttenhain, Ruth

“…Proximity labeling (PL) via biotinylation coupled with mass spectrometry (MS) captures spatial proteomes in cells. Large-scale processing requires a workflow…”
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Signaling Modulation Mediated by Ligand Water Interactions with the Sodium Site at μOR by Ople, Rohini S., Ramos-Gonzalez, Nokomis, Li, Qiongyu, Sobecks, Briana L., Aydin, Deniz, Powers, Alexander S., Faouzi, Abdelfattah, Polacco, Benjamin J., Bernhard, Sarah M., Appourchaux, Kevin, Sribhashyam, Sashrik, Eans, Shainnel O., Tsai, Bowen A., Dror, Ron O., Varga, Balazs R., Wang, Haoqing, Hüttenhain, Ruth, McLaughlin, Jay P., Majumdar, Susruta

“…The mu opioid receptor (μOR) is a target for clinically used analgesics. However, adverse effects, such as respiratory depression and physical dependence,…”
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Automated discovery of 3D motifs for protein function annotation by Polacco, Benjamin J., Babbitt, Patricia C.

“…Motivation: Function inference from structure is facilitated by the use of patterns of residues (3D motifs), normally identified by expert knowledge, that…”
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De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking by Chen, Zhen, Shiozaki, Momoko, Haas, Kelsey M, Skinner, Will M, Zhao, Shumei, Guo, Caiying, Polacco, Benjamin J, Yu, Zhiheng, Krogan, Nevan J, Lishko, Polina V, Kaake, Robyn M, Vale, Ronald D, Agard, David A

“…To understand the molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their…”
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Profiling the proximal proteome of the activated μ-opioid receptor by Polacco, Benjamin J., Lobingier, Braden T., Blythe, Emily E., Abreu, Nohely, Khare, Prachi, Howard, Matthew K., Gonzalez-Hernandez, Alberto J., Xu, Jiewei, Li, Qiongyu, Novy, Brandon, Naing, Zun Zar Chi, Shoichet, Brian K., Coyote-Maestas, Willow, Levitz, Joshua, Krogan, Nevan J., Von Zastrow, Mark, Hüttenhain, Ruth

“…The μ-opioid receptor (μOR) represents an important target of therapeutic and abused drugs. So far, most understanding of μOR activity has focused on a subset…”
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Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes by Richards, Alicia L, Chen, Kuei-Ho, Wilburn, Damien B, Stevenson, Erica, Polacco, Benjamin J, Searle, Brian C, Swaney, Danielle L

“…The use of multiple proteases has been shown to increase protein sequence coverage in proteomics experiments; however, due to the additional analysis time…”
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Brahma safeguards canalization of cardiac mesoderm differentiation by Hota, Swetansu K., Rao, Kavitha S., Blair, Andrew P., Khalilimeybodi, Ali, Hu, Kevin M., Thomas, Reuben, So, Kevin, Kameswaran, Vasumathi, Xu, Jiewei, Polacco, Benjamin J., Desai, Ravi V., Chatterjee, Nilanjana, Hsu, Austin, Muncie, Jonathon M., Blotnick, Aaron M., Winchester, Sarah A. B., Weinberger, Leor S., Hüttenhain, Ruth, Kathiriya, Irfan S., Krogan, Nevan J., Saucerman, Jeffrey J., Bruneau, Benoit G.

“…Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization 1 , 2 . Canalization is essential for…”
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Protein Interaction Map of APOBEC3 Enzyme Family Reveals Deamination-Independent Role in Cellular Function by Jang, Gwendolyn M., Annan Sudarsan, Arun Kumar, Shayeganmehr, Arzhang, Prando Munhoz, Erika, Lao, Reanna, Gaba, Amit, Granadillo Rodríguez, Milaid, Love, Robin P., Polacco, Benjamin J., Zhou, Yuan, Krogan, Nevan J., Kaake, Robyn M., Chelico, Linda

“…Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and…”
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Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis by Kehrer, Thomas, Cupic, Anastasija, Ye, Chengjin, Yildiz, Soner, Bouhaddou, Mehdi, Crossland, Nicholas A., Barrall, Erika A., Cohen, Phillip, Tseng, Anna, Çağatay, Tolga, Rathnasinghe, Raveen, Flores, Daniel, Jangra, Sonia, Alam, Fahmida, Mena, Ignacio, Aslam, Sadaf, Saqi, Anjali, Rutkowska, Magdalena, Ummadi, Manisha R., Pisanelli, Giuseppe, Richardson, R. Blake, Veit, Ethan C., Fabius, Jacqueline M., Soucheray, Margaret, Polacco, Benjamin J., Ak, Baran, Marin, Arturo, Evans, Matthew J., Swaney, Danielle L., Gonzalez-Reiche, Ana S., Sordillo, Emilia M., van Bakel, Harm, Simon, Viviana, Zuliani-Alvarez, Lorena, Fontoura, Beatriz M.A., Rosenberg, Brad R., Krogan, Nevan J., Martinez-Sobrido, Luis, García-Sastre, Adolfo, Miorin, Lisa

“…Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes several proteins that inhibit host interferon responses. Among these, ORF6 antagonizes…”
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A global view of structure–function relationships in the tautomerase superfamily by Davidson, Rebecca, Baas, Bert-Jan, Akiva, Eyal, Holliday, Gemma L., Polacco, Benjamin J., LeVieux, Jake A., Pullara, Collin R., Zhang, Yan Jessie, Whitman, Christian P., Babbitt, Patricia C.

“…The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted…”
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Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP by Cakir, Zeynep, Lord, Samuel J., Zhou, Yuan, Jang, Gwendolyn M., Polacco, Benjamin J., Eckhardt, Manon, Jimenez-Morales, David, Newton, Billy W., Orr, Adam L., Johnson, Jeffrey R., da Cruz, Alexandre, Mullins, R. Dyche, Krogan, Nevan J., Mahley, Robert W., Swaney, Danielle L.

“…Apolipoprotein (apo) E4 is the major genetic risk factor for Alzheimer’s disease. While neurons generally produce a minority of the apoE in the central nervous…”
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A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function by Holliday, Gemma L, Brown, Shoshana D, Mischel, David, Polacco, Benjamin J, Babbitt, Patricia C

“…Abstract Determining the molecular function of enzymes discovered by genome sequencing represents a primary foundation for understanding many aspects of…”
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Organic and inorganic mercurials have distinct effects on cellular thiols, metal homeostasis, and Fe-binding proteins in Escherichia coli by LaVoie, Stephen P., Mapolelo, Daphne T., Cowart, Darin M., Polacco, Benjamin J., Johnson, Michael K., Scott, Robert A., Miller, Susan M., Summers, Anne O.

“…The protean chemical properties of the toxic metal mercury (Hg) have made it attractive in diverse applications since antiquity. However, growing public…”
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Discovering Mercury Protein Modifications in Whole Proteomes Using Natural Isotope Distributions Observed in Liquid Chromatography-Tandem Mass Spectrometry by Polacco, Benjamin J., Purvine, Samuel O., Zink, Erika M., LaVoie, Stephen P., Lipton, Mary S., Summers, Anne O., Miller, Susan M.

“…The identification of peptides that result from post-translational modifications is critical for understanding normal pathways of cellular regulation as well…”
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Superfamily active site templates by Meng, Elaine C., Polacco, Benjamin J., Babbitt, Patricia C.

“…We show that three‐dimensional signatures consisting of only a few functionally important residues can be diagnostic of membership in superfamilies of enzymes…”
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The Global Phosphorylation Landscape of SARS-CoV-2 Infection by Bouhaddou, Mehdi, Memon, Danish, Meyer, Bjoern, White, Kris M., Rezelj, Veronica V., Correa Marrero, Miguel, Polacco, Benjamin J., Melnyk, James E., Ulferts, Svenja, Kaake, Robyn M., Batra, Jyoti, Richards, Alicia L., Stevenson, Erica, Gordon, David E., Rojc, Ajda, Obernier, Kirsten, Fabius, Jacqueline M., Soucheray, Margaret, Miorin, Lisa, Moreno, Elena, Koh, Cassandra, Tran, Quang Dinh, Hardy, Alexandra, Robinot, Rémy, Vallet, Thomas, Nilsson-Payant, Benjamin E., Hernandez-Armenta, Claudia, Dunham, Alistair, Weigang, Sebastian, Knerr, Julian, Modak, Maya, Quintero, Diego, Zhou, Yuan, Dugourd, Aurelien, Valdeolivas, Alberto, Patil, Trupti, Li, Qiongyu, Hüttenhain, Ruth, Cakir, Merve, Muralidharan, Monita, Kim, Minkyu, Jang, Gwendolyn, Tutuncuoglu, Beril, Hiatt, Joseph, Guo, Jeffrey Z., Xu, Jiewei, Bouhaddou, Sophia, Mathy, Christopher J.P., Gaulton, Anna, Manners, Emma J., Félix, Eloy, Shi, Ying, Goff, Marisa, Lim, Jean K., McBride, Timothy, O’Neal, Michael C., Cai, Yiming, Chang, Jason C.J., Broadhurst, David J., Klippsten, Saker, De wit, Emmie, Leach, Andrew R., Kortemme, Tanja, Shoichet, Brian, Ott, Melanie, Saez-Rodriguez, Julio, tenOever, Benjamin R., Mullins, R. Dyche, Fischer, Elizabeth R., Kochs, Georg, Grosse, Robert, García-Sastre, Adolfo, Vignuzzi, Marco, Johnson, Jeffery R., Shokat, Kevan M., Swaney, Danielle L., Beltrao, Pedro, Krogan, Nevan J.

“…The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions…”
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A SARS-CoV-2 protein interaction map reveals targets for drug repurposing by Gordon, David E, Jang, Gwendolyn M, Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, White, Kris M, O'Meara, Matthew J, Rezelj, Veronica V, Guo, Jeffrey Z, Swaney, Danielle L, Tummino, Tia A, Hüttenhain, Ruth, Kaake, Robyn M, Richards, Alicia L, Tutuncuoglu, Beril, Foussard, Helene, Batra, Jyoti, Haas, Kelsey, Modak, Maya, Kim, Minkyu, Haas, Paige, Polacco, Benjamin J, Braberg, Hannes, Fabius, Jacqueline M, Eckhardt, Manon, Soucheray, Margaret, Bennett, Melanie J, Cakir, Merve, McGregor, Michael J, Li, Qiongyu, Meyer, Bjoern, Roesch, Ferdinand, Vallet, Thomas, Mac Kain, Alice, Miorin, Lisa, Moreno, Elena, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Shi, Ying, Zhang, Ziyang, Shen, Wenqi, Kirby, Ilsa T, Melnyk, James E, Chorba, John S, Lou, Kevin, Dai, Shizhong A, Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Lyu, Jiankun, Mathy, Christopher J P, Perica, Tina, Pilla, Kala Bharath, Ganesan, Sai J, Saltzberg, Daniel J, Rakesh, Ramachandran, Liu, Xi, Rosenthal, Sara B, Calviello, Lorenzo, Venkataramanan, Srivats, Liboy-Lugo, Jose, Lin, Yizhu, Huang, Xi-Ping, Liu, YongFeng, Wankowicz, Stephanie A, Bohn, Markus, Safari, Maliheh, Ugur, Fatima S, Koh, Cassandra, Savar, Nastaran Sadat, Tran, Quang Dinh, Shengjuler, Djoshkun, Fletcher, Sabrina J, O'Neal, Michael C, Cai, Yiming, Chang, Jason C J, Broadhurst, David J, Klippsten, Saker, Sharp, Phillip P, Wenzell, Nicole A, Kuzuoglu-Ozturk, Duygu, Wang, Hao-Yuan, Trenker, Raphael, Young, Janet M, Cavero, Devin A, Hiatt, Joseph, Roth, Theodore L, Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Stroud, Robert M, Frankel, Alan D, Rosenberg, Oren S, Verba, Kliment A, Agard, David A, Ott, Melanie, Emerman, Michael, Jura, Natalia

“…A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019…”
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SARS-CoV-2 variants evolve convergent strategies to remodel the host response by Bouhaddou, Mehdi, Reuschl, Ann-Kathrin, Polacco, Benjamin J., Thorne, Lucy G., Ummadi, Manisha R., Ye, Chengjin, Rosales, Romel, Pelin, Adrian, Batra, Jyoti, Jang, Gwendolyn M., Xu, Jiewei, Moen, Jack M., Richards, Alicia L., Zhou, Yuan, Harjai, Bhavya, Stevenson, Erica, Rojc, Ajda, Ragazzini, Roberta, Whelan, Matthew V.X., Furnon, Wilhelm, De Lorenzo, Giuditta, Cowton, Vanessa, Syed, Abdullah M., Ciling, Alison, Deutsch, Noa, Pirak, Daniel, Dowgier, Giulia, Mesner, Dejan, Turner, Jane L., McGovern, Briana L., Rodriguez, M. Luis, Leiva-Rebollo, Rocio, Dunham, Alistair S., Zhong, Xiaofang, Eckhardt, Manon, Fossati, Andrea, Liotta, Nicholas F., Kehrer, Thomas, Cupic, Anastasija, Rutkowska, Magdalena, Mena, Ignacio, Aslam, Sadaf, Hoffert, Alyssa, Foussard, Helene, Olwal, Charles Ochieng’, Huang, Weiqing, Zwaka, Thomas, Pham, John, Lyons, Molly, Donohue, Laura, Griffin, Aliesha, Nugent, Rebecca, Holden, Kevin, Deans, Robert, Aviles, Pablo, Lopez-Martin, Jose A., Jimeno, Jose M., Obernier, Kirsten, Fabius, Jacqueline M., Soucheray, Margaret, Hüttenhain, Ruth, Jungreis, Irwin, Kellis, Manolis, Echeverria, Ignacia, Verba, Kliment, Bonfanti, Paola, Beltrao, Pedro, Sharan, Roded, Doudna, Jennifer A., Martinez-Sobrido, Luis, Patel, Arvind H., Palmarini, Massimo, Miorin, Lisa, White, Kris, Swaney, Danielle L., Garcia-Sastre, Adolfo, Jolly, Clare, Zuliani-Alvarez, Lorena, Towers, Greg J., Krogan, Nevan J.

“…SARS-CoV-2 variants of concern (VOCs) emerged during the COVID-19 pandemic. Here, we used unbiased systems approaches to study the host-selective forces…”
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De novo protein identification in mammalian sperm using in situ cryo-electron tomography and AlphaFold2 docking by Chen, Zhen, Shiozaki, Momoko, Haas, Kelsey M., Skinner, Will M., Zhao, Shumei, Guo, Caiying, Polacco, Benjamin J., Yu, Zhiheng, Krogan, Nevan J., Lishko, Polina V., Kaake, Robyn M., Vale, Ronald D., Agard, David A.

“…To understand molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their…”
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Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets by Haas, Kelsey M., McGregor, Michael J., Bouhaddou, Mehdi, Polacco, Benjamin J., Kim, Eun-Young, Nguyen, Thong T., Newton, Billy W., Urbanowski, Matthew, Kim, Heejin, Williams, Michael A. P., Rezelj, Veronica V., Hardy, Alexandra, Fossati, Andrea, Stevenson, Erica J., Sukerman, Ellie, Kim, Tiffany, Penugonda, Sudhir, Moreno, Elena, Braberg, Hannes, Zhou, Yuan, Metreveli, Giorgi, Harjai, Bhavya, Tummino, Tia A., Melnyk, James E., Soucheray, Margaret, Batra, Jyoti, Pache, Lars, Martin-Sancho, Laura, Carlson-Stevermer, Jared, Jureka, Alexander S., Basler, Christopher F., Shokat, Kevan M., Shoichet, Brian K., Shriver, Leah P., Johnson, Jeffrey R., Shaw, Megan L., Chanda, Sumit K., Roden, Dan M., Carter, Tonia C., Kottyan, Leah C., Chisholm, Rex L., Pacheco, Jennifer A., Smith, Maureen E., Schrodi, Steven J., Albrecht, Randy A., Vignuzzi, Marco, Zuliani-Alvarez, Lorena, Swaney, Danielle L., Eckhardt, Manon, Wolinsky, Steven M., White, Kris M., Hultquist, Judd F., Kaake, Robyn M., García-Sastre, Adolfo, Krogan, Nevan J.

“…Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV…”
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