Recent Select Publications
2024
Neha Vithani, Tyson D Todd, Sukrit Singh, Tony Trent, Kendall J Blumer, Gregory R Bowman. G Protein Activation Occurs via a Largely Universal Mechanism. J Phys Chem B. 2024 April 5.
Benjamin C Creekmore, Kathryn Kixmoeller, Ben E Black, Edward B Lee, Yi-Wei Chang. Ultrastructure of human brain tissue vitrified from autopsy revealed by cryo-ET with cryo-plasma FIB milling. Nat Commun. 2024 March 26.
Craig W Gambogi, Gabriel J Birchak, Elie Mer, David M Brown, George Yankson, Kathryn Kixmoeller, Janardan N Gavade, Josh L Espinoza, Prakriti Kashyap, Chris L Dupont, Glennis A Logsdon, Patrick Heun, John I Glass, Ben E Black. Efficient formation of single-copy human artificial chromosomes. Science. 2024 March 21.
Nikaela W Bryan, Aamir Ali, Ewa Niedzialkowska, Leland Mayne, P Todd Stukenberg, Ben E Black. Structural basis for the phase separation of the chromosome passenger complex. Elife. 2024 March 8.
Hayley L Rein, Kara A Bernstein. Variants in the first methionine of RAD51C are homologous recombination proficient due to an alternative start site. DNA Repair. 2024 March 1.
Christopher M Bourne, Cornelius Y Taabazuing. Harnessing Pyroptosis for Cancer Immunotherapy. Cells. 2024 February 16.
Jesse Davila-Calderon, Mei-Ling Li, Srinivasa R Penumutchu, Christina Haddad, Linzy Malcolm, Josephine King, Amanda E Hargrove, Gary Brewer, Blanton S Tolbert. Enterovirus evolution reveals the mechanism of an RNA-targeted antiviral and determinants of viral replication. Sci Adv. 2024 February 16.
Artur Meller, Devin Kelly, Louis G Smith, Gregory R Bowman. Toward physics-based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants. Protein Sci. 2024 February 15.
Nicole R Raniszewski, Jenna N Beyer, Myles I Noel, George M Burslem. Sortase mediated protein ubiquitination with defined chain length and topology. RCS Chem Biol. 2024 February 7.
Katelyn M. Sweeney, Sapanna Chantarawong, Edward M. Barbieri, Greg Cajka, Matthew Liu, Lynn Spruce, Hossein Fazelinia, Bede Portz, Katie Copley, Tomer Lapidot, Lauren Duhamel, Phoebe Greenwald, Naseeb Saida, Reut Shalgi, James Shorter, Ophir Shalem. CRISPR screen for protein inclusion formation uncovers a role for SRRD in the regulation of intermediate filament dynamics and aggresome assembly. PLoS Genet. 2024 February 5.
Hayley L Rein, Kara A Bernstein. Variants in the first methionine of RAD51C are homologous recombination proficient due to an alternative start site. DNA Repair. 2024 February 1.
Dian Ding, Ziyuan Fang, Seohyun Chris Kim, Derek K. O’Flaherty, Xiwen Jia, Talbot B. Stone, Lijun Zhou, Jack W. Szostak. Unusual Base Pair between Two 2‑Thiouridines and Its Implication for Nonenzymatic RNA Copying. J Am Chem Soc. 2024 January 31.
Louis G Smith, Borna Novak, Meghan Osato, David L Mobley, Gregory R Bowman. PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model. J Chem Theory Comput. 2024 January 31.
Kiara N Berríos, Aleksia Barka, Jasleen Gill, Juan C Serrano, Peter F Bailer, Jared B Parker, Niklaus H Evitt, Kiran S Gajula, Junwei Shi, Rahul M Kohli. Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors. Nucleic Acids Res. 2024 January 24.
Daniel C Akuma, Kimberly A Wodzanowski, Ronit Schwartz Wertman, Patrick M Exconde, Víctor R Vázquez Marrero, Chukwuma E Odunze, Daniel Grubaugh, Sunny Shin, Cornelius Taabazuing, Igor E Brodsky. Catalytic activity and autoprocessing of murine caspase-11 mediate noncanonical inflammasome assembly in response to cytosolic LPS. Elife. 2024 January 17.
Nicolas Dos Santos Pacheco, Albert Tell i Puig, Amandine Guérin, Matthew Martinez, Bohumil Maco, Nicolò Tosetti, Estefanía Delgado-Betancourt, Matteo Lunghi, Boris Striepen, Yi-Wei Chang & Dominique Soldati-Favre. Sustained rhoptry docking and discharge requires Toxoplasma gondii intraconoidal microtubule-associated proteins. Nat Commun. 2024 January 9.
Matthew N Gaynes, Trey A Ronnebaum, Kollin Schultz, Jacque L Faylo, Ronen Marmorstein, David W Christianson. Structure of the prenyltransferase in bifunctional copalyl diphosphate synthase from Penicillium fellutanum reveals an open hexamer conformation. J Struct Biol. 2024 January 5.
Leon Palao 3rd, Kenji Murakami, Yi-Wei Chang. Combining per-particle cryo-ET and cryo-EM single particle analysis to elucidate heterogeneous DNA-protein organization. Curr Opin Struct Biol. 2024 January 4.
2023
Sudeshi M Abedeera, Jesse Davila-Calderon, Christina Haddad, Barrington Henry, Josephine King, Srinivasa Penumutchu, Blanton S Tolbert. The Repurposing of Cellular Proteins during Enterovirus A71 Infection. Viruses. 2023 December 31.
Patrick M Exconde, Claudia Hernandez-Chavez, Christopher M Bourne, Rachel M Richards, Mark B Bray, Jan L Lopez, Tamanna Srivastava, Marisa S Egan, Jenna Zhang, William Yoo, Sunny Shin, Bohdana M Discher, Cornelius Y Taabazuing. The tetrapeptide sequence of IL-18 and IL-1β regulates their recruitment and activation by inflammatory caspases. Cell Rep. 2023 December 26.
José J De Jesús-Pérez, Matthew Gabrielle, Sumiyya Raheem, Edwin C Fluck, Tibor Rohacs, Vera Y Moiseenkova-Bell. Structural mechanism of TRPV5 inhibition by econazole. Structure. 2023 December 19.
Andrew C McShan, David Flores-Solis, Yi Sun, Samuel E Garfinkle, Jugmohit S Toor, Michael C Young, Nikolaos G Sgourakis. Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition. Nat Commun. 2023 December 11.
Yi Sun, Tyler J Florio, Sagar Gupta, Michael C Young, Quinlen F Marshall, Samuel E Garfinkle, Georgia F Papadaki, Hau V Truong, Emily Mycek, Peiyao Li, Alvin Farrel, Nicole L Church, Shereen Jabar, Matthew D Beasley, Ben R Kiefel, Mark Yarmarkovich, Leena Mallik, John M Maris, Nikolaos G Sgourakis. Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion. Sci Immunol. 2023 December 1.
Timothé Maujean, Prakash Kannaboina, Adam I Green, George M Burslem. Lead-oriented synthesis of epigenetic relevant scaffolds. Chem Commun. 2023 November 22.
Craig W Gambogi, Nootan Pandey, Jennine M Dawicki-McKenna, Uma P Arora, Mikhail A Liskovykh, Jun Ma, Piero Lamelza, Vladimir Larionov, Michael A Lampson, Glennis A Logsdon, Beth L Dumont, Ben E Black. Centromere innovations within a mouse species. Sci Adv. 2023 November 17.
Iulia Tapescu, Frances Taschuk, Swechha M Pokharel, Oleksandr Zginnyk, Max Ferretti, Peter F Bailer, Kanupryia Whig, Emily A Madden, Mark T Heise, David C Schultz, Sara Cherry. The RNA helicase DDX39A binds a conserved structure in chikungunya virus RNA to control infection. Mol Cell. 2023 November 16.
M Hannah Choi, Liu Hong, Leonardo P Chamorro, Boyd Edwards, Aaron T Timperman. Measuring the electrophoretic mobility and size of single particles using microfluidic transverse AC electrophoresis (TrACE). Lab Chip. 2023 November 8.
Jean M Etersque, Iris K Lee, Nitika Sharma, Kexiang Xu, Andrew Ruff, Justin D Northrup, Swarbhanu Sarkar, Tommy Nguyen, Richard Lauman, George M Burslem, Mark A Sellmyer. Regulation of eDHFR-tagged proteins with trimethoprim PROTACs. Nat Commun. 2023 November 3.
Iulia Tapescu, Frances Taschuk, Swechha M Pokharel, Oleksandr Zginnyk, Max Ferretti, Peter F Bailer, Kanupryia Whig, Emily A Madden, Mark T Heise, David C Schultz, Sara Cherry. 1The RNA helicase DDX39A binds a conserved structure in chikungunya virus RNA to control infection. Mol Cell. 2023 November 2.
Iris K Lee, Nitika Sharma, Estela Noguera-Ortega, Maria Liousia, Miren L Baroja, Jean M Etersque, Jonathan Pham, Swarbhanu Sarkar, Beatriz M Carreno, Gerald P Linette, Ellen Puré, Steven M Albelda, Mark A Sellmyer. A genetically-encoded protein tag for control and quantitative imaging of CAR T cell therapy. Mol Ther. 2023 November 1.
Sagar Gupta, Santrupti Nerli, Sreeja Kutti Kandy, Glenn L Mersky, Nikolaos G Sgourakis. HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes. Nat Commun. 2023 October 10.
Jennifer Ramirez, Samantha X Pancoe, Elizabeth Rhoades, E James Petersson. The Effects of Lipids on α-Synuclein Aggregation In Vitro. Biomolecules. 2023 October 2.
Raghavendar R Sanganna Gari, Grigory Tagiltsev, Ruth A Pumroy, Yining Jiang, Martin Blackledge, Vera Y Moiseenkova-Bell, Simon Scheuring. Intrinsically disordered regions in TRPV2 mediate protein-protein interactions. Commun Biol. 2023 September 22.
Melissa Birol, Isabella Ioana Douzoglou Muñoz, Elizabeth Rhoades. The C-terminus of α-Synuclein regulates its dynamic cellular internalization by Neurexin 1β. Mol Biol Cell. 2023 September 20.
Mirna El Khatib, Azar O Motlagh, Jenna N Beyer, Thomas Troxler, Srinivasa Rao Allu, Qi Sun, George M Burslem, Sergei A Vinogradov. Direct Measurements of FLASH-Induced Changes in Intracellular Oxygenation. Int J Radiat Oncol Biol Phys. 2023 September 18.
Korrie L. Mack, Hanna Kim, Edward M. Barbieri, JiaBei Lin, Sylvanne Braganza, Meredith E. Jackrel, Jamie E. DeNizio, Xiaohui Yan, Edward Chuang, Amber Tariq, Ryan R. Cupo, Laura M. Castellano, Kim A. Caldwell, Guy A. Caldwell, James Shorter. Tuning Hsp104 specificity to selectively detoxify α-synuclein. Mol Cell. 2023 August 24.
Matthew Martinez, Shrawan Kumar Mageswaran, Amandine Guérin, William David Chen, Cameron Parker Thompson, Sabine Chavin, Dominique Soldati-Favre, Boris Striepen, Yi-Wei Chang. Origin and arrangement of actin filaments for gliding motility in apicomplexan parasites revealed by cryo-electron tomography. Nat Commun. 2023 August 9.
Arunika Das, Katelyn G Boese, Kikue Tachibana, Sung Hee Baek, Michael A Lampson, Ben E Black. Centromere-specifying nucleosomes persist in aging mouse oocytes in the absence of nascent assembly. Curr Biol. 2023 August 4.
Georgia F Papadaki, Claire H Woodward, Michael C Young, Trenton J Winters, George M Burslem, Nikolaos G Sgourakis. A Chicken Tapasin ortholog can chaperone empty HLA-B*37:01 molecules independent of other peptide-loading components. J Biol Chem. 2023 August 3.
Tong Wang, Johanna M Fowler, Laura Liu, Christian E Loo, Meiqi Luo, Emily K Schutsky, Kiara N Berríos, Jamie E DeNizio, Ashley Dvorak, Nick Downey, Saira Montermoso, Bianca Y Pingul, MacLean Nasrallah, Walraj S Gosal, Hao Wu, Rahul M Kohli. Direct enzymatic sequencing of 5-methylcytosine at single-base resolution. Nat Chem Biol. 2023 June 15.
Buyan Pan, Sarah M Gardner, Kollin Schultz, Ryann M Perez, Sunbin Deng, Marie Shimogawa, Kohei Sato, Elizabeth Rhoades, Ronen Marmorstein, E James Petersson. Semi-Synthetic CoA-α-Synuclein Constructs Trap N-Terminal Acetyltransferase NatB for Binding Mechanism Studies. J Am Chem Soc. 2023 June 15.
Yi Sun, Michael C. Young, Claire H. Woodward, Julia N. Danon, Hau V. Truong, Sagar Gupta, Trenton J. Winters, Joan Font-Burgada, George M. Burslem, Nikolaos G. Sgourakis. Universal open MHC-I molecules for rapid peptide loading and enhanced complex stability across HLA allotypes. PNAS. 2023 June 13.
Xuepeng Wei, Kollin Schultz, Hannah L Pepper, Emily Megill, Austin Vogt, Nathaniel W Snyder, Ronen Marmorstein. Allosteric role of the citrate synthase homology domain of ATP citrate lyase. Nat Commun. 2023 April 19.
Xiangrui Zeng, Anson Kahng, Liang Xue, Julia Mahamid, Yi-Wei Chang, Min Xu. High-throughput cryo-ET structural pattern mining by unsupervised deep iterative subtomogram clustering. Proc Natl Acad Sci U S A. 2023 April 7.
Yulia Gonskikh, Julian Stoute, Hui Shen, Krista Budinich, Bianca Pingul, Kollin Schultz, Heidi Elashal, Ronen Marmorstein, Junwei Shi, Kathy Fange Liu. Noncatalytic regulation of 18 S rRNA methyltransferase DIMT1 in acute myeloid leukemia. Genes Dev. 2023 April 6.
Hannah Hyun-Sook Kim, Mostofa Rafid Uddin, Min Xu, Yi-Wei Chang. Computational methods toward unbiased pattern mining and structure determination in cryo-electron tomography data. J Mol Biol. 2023 March 30.
Michael B Cory, Chloe M Jones, Kyle D Shaffer, Yarra Venkatesh, Sam Giannakoulias, Ryann M Perez, Marshall G Lougee, Eshe Hummingbird, Vinayak V Pagar, Christina M Hurley, Allen Li, Robert H Mach, Rahul M Kohli, E James Petersson. FRETing About the Details: Case studies in the use of a genetically encoded fluorescent amino acid for distance-dependent energy transfer. Protein Sci. 2023 March 28.
Artur Meller, Soumendranath Bhakat, Shahlo Solieva, Gregory R Bowman. Accelerating Cryptic Pocket Discovery Using AlphaFold. J Chem Theory Comput. 2023 March 22.
Laura M Agosto, Michael J Mallory, Max B Ferretti, Davia Blake, Keegan S Krick, Matthew R Gazzara, Benjamin A Garcia, Kristen W Lynch. Alternative splicing of HDAC7 regulates its interaction with 14-3-3 proteins to alter histone marks and target gene expression. Cell Rep. 2023 March 17.
Grant Eilers, Kushol Gupta, Audrey Allen, Saira Montermoso, Hemma Murali, Robert Sharp, Young Hwang, Frederic D. Bushman, Gregory Van Duyne. Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization. PLoS Pathog. 2023 March 3.
Artur Meller, Michael Ward, Jonathan Borowsky, Meghana Kshirsagar, Jeffrey M Lotthammer, Felipe Oviedo, Juan Lavista Ferres, Gregory R Bowman. Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network. Nat Commun. 2023 March 1.
Longsheng Lai, Yee-Wai Cheung, Matthew Martinez, Kathryn Kixmoeller, Leon Palao III, Stefan Steimle, Meng-Chiao Ho, Ben E. Black, Erh-Min Lai & Yi-Wei Chang. In Situ Structure Determination of Bacterial Surface Nanomachines Using Cryo-Electron Tomography. Methods Mol Biol. 2023 February 27.
Charlotte M Fare, Kevin Rhine, Andrew Lam, Sua Myong, James Shorter. A minimal construct of nuclear-import receptor Karyopherin-β2 defines the regions critical for chaperone and disaggregation activity. J Biol Chem. 2023 February 27.
Yi Sun, Georgia F Papadaki , Christine A Devlin, Julia N Danon, Michael C Young, Trenton J Winters, George M Burslem, Erik Procko, Nikolaos G Sgourakis. Xeno interactions between MHC-I proteins and molecular chaperones enable ligand exchange on a broad repertoire of HLA allotypes. Sci Adv. 2023 Feburary 24.
Nancy Schek, Jia-Ying Lee, George M Burslem, Eric Witze. Chemical probe mediated visualization of protein S-palmitoylation in patient tissue samples. Front Physiol. 2023 February 21.
Kofi K. Acheampong, Dylan L. Schaff, Benjamin L. Emert, Jonathan Lake, Sam Reffsin, Emily K. Shea, Courtney E. Comar, Leslie A. Litzky, Nigar A. Khurram, Rebecca L. Linn, Michael Feldman, Susan R. Weiss, Kathleen T. Montone, Sara Cherry, Sydney M. Shaffer. Subcellular Detection of SARS-CoV-2 RNA in Human Tissue Reveals Distinct Localization in Alveolar Type 2 Pneumocytes and Alveolar Macrophages. mBio. 2023 February 8.
Jose J Gorbea Colón, Leon Palao 3rd, Shin-Fu Chen, Hee Jong Kim, Laura Snyder, Yi-Wei Chang, Kuang-Lei Tsai, Kenji Murakami. Structural basis of a transcription pre-initiation complex on a divergent promoter. Mol Cell. 2023 January 26.
Artur Meller, Jeffrey M Lotthammer, Louis G Smith, Borna Novak, Lindsey A Lee, Catherine C Kuhn, Lina Greenberg, Leslie A Leinwand, Michael J Greenberg, Gregory R Bowman. Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains. Elife. 2023 January 27.
Georgia F. Papadaki, Omar Ani, Tyler J. Florio, Michael C. Young, Julia N. Danon, Yi Sun, Devin Dersh, and Nikolaos G. Sgourakis. Decoupling peptide binding from T cell receptor recognition with engineered chimeric MHC-I molecules. Front. Immunol. 2023 January 25.
2022
Sunbin Deng, Sarah M Gardner, Leah Gottlieb, Buyan Pan, E James Petersson, and Ronen Marmorstein. Molecular role of NAA38 in thermostability and catalytic activity of the human NatC N-terminal acetyltransferase. Structure. 2022 December 30.
Juan C. Serrano, Dora von Trentini, Kiara N. Berríos, Aleksia Barka, Ivan J. Dmochowski, and Rahul M. Kohli. Structure-Guided Design of a Potent and Specific Inhibitor against the Genomic Mutator APOBEC3A. ACS Chem. Biol. 2022 December 8.
Michael B. Cory, Allen Li, Christina M. Hurley, Zachary M. Hostetler, Yarra Venkatesh, Chloe M. Jones, E. James Petersson, and Rahul M. Kohli. Engineered RecA Constructs Reveal the Minimal SOS Activation Complex. Biochemistry. 2022 December 6.
Alisa Cario, Sanjula P Wickramasinghe, Elizabeth Rhoades, Christopher L Berger. The N-terminal disease-associated R5L Tau mutation increases microtubule shrinkage rate due to disruption of microtubule-bound Tau patches. J Biol Chem. 2022 November 29.
Sang Hoon Chong, Yi Hong Ong, Mirna El Khatib, Srinivasa Rao Allu, Ashwin B Parthasarathy, Joel H Greenberg, Arjun G Yodh, Sergei A Vinogradov. Real-time tracking of brain oxygen gradients and blood flow during functional activation. Neurophotonics. 2022 November 28.
Dayi Chen and Aaron T. Timperman. Analyte Enrichment via Ion Concentration Polarization with Hydrogel Plugs Polymerized in PDMS Microchannels by a Facile and Comprehensive Method for Improved Polymerization. Anal. Chem. 2022 November 1.
M Daniel Ricketts, Ryan P Emptage, Gerd A Blobel, Ronen Marmorstein. The heme-regulated inhibitor kinase requires dimerization for heme-sensing activity. J Biol Chem. 2022 October 29.
Davia Blake, Caleb M Radens, Max B Ferretti, Matthew R Gazzara, Kristen W Lynch. Alternative splicing of apoptosis genes promotes human T cell survival. Elife. 2022 October 20.
Natoya J Peart, Jae Yeon Hwang, Mathieu Quesnel-Vallières, Matthew J Sears, Yuequin Yang, Peter Stoilov, Yoseph Barash, Juw Won Park, Kristen W Lynch, Russ P Carstens. The global Protein-RNA interaction map of ESRP1 defines a post-transcriptional program that is essential for epithelial cell function. iScience. 2022 October 21.
Daniela Sparvoli, Jason Delabre, Diana Marcela Penarete-Vargas, Shrawan Kumar Mageswaran, Lev M Tsypin, Justine Heckendorn, Liam Theveny, Marjorie Maynadier, Marta Mendonça Cova, Laurence Berry-Sterkers, Amandine Guérin, Jean-François Dubremetz, Serge Urbach, Boris Striepen, Aaron P Turkewitz, Yi-Wei Chang, Maryse Lebrun. An apical membrane complex for triggering rhoptry exocytosis and invasion in Toxoplasma. EMBO J. 2022 October 17.
Fares Saïdi, Utkarsha Mahanta, Adyasha Panda, Ahmad A Kezzo, Nicolas Y Jolivet, Razieh Bitazar, Gavin John, Matthew Martinez, Abdelkader Mellouk, Charles Calmettes, Yi-Wei Chang, Gaurav Sharma, Salim T Islam. Bacterial Outer Membrane Polysaccharide Export (OPX) Proteins Occupy Three Structural Classes with Selective β-Barrel Porin Requirements for Polymer Secretion. Microbiol Spectr. 2022 October 6.
Ryan R. Cupo, Alexandrea N. Rizo, Gabriel A. Braun, Kushol Gupta, Daniel R. Southworth, James Shorter. Unique structural features govern the activity of a human mitochondrial AAA+ disaggregase, Skd3. Cell Reports. 2022 September 27.
DOI: https://www.cell.com/cell-reports/fulltext/S2211-1247(22)01249-9
Tatjana Weil, Abbna Kirupakaran, My-Hue Le, Philipp Rebmann, Joel Mieres-Perez, Leila Issmail, Carina Conzelmann, Janis A. Müller, Lena Rauch, Andrea Gilg, Lukas Wettstein, Rüdiger Groß, Clarissa Read, Tim Bergner, Sandra Axberg Pålsson, Nadja Uhlig, Valentina Eberlein, Heike Wöll, Frank-Gerrit Klärner, Steffen Stenger, Beate M. Kümmerer, Hendrik Streeck, Giorgio Fois, Manfred Frick, Peter Braubach, Anna-Lena Spetz, Thomas Grunwald, James Shorter, Elsa Sanchez-Garcia, Thomas Schrader, and Jan Münch. Advanced Molecular Tweezers with Lipid Anchors against SARS-CoV-2 and Other Respiratory Viruses. JACS Au. 2022 September 6.
Thong T Luong, Zheqi Li, Nolan Priedigkeit, Phoebe S Parker, Stefanie Böhm, Kyle Rapchak, Adrian V Lee, Kara A Bernstein. Hrq1/RECQL4 regulation is critical for preventing aberrant recombination during DNA intrastrand crosslink repair and is upregulated in breast cancer. PLos Genet. 2022 September 20.
Alexandra E. Perlegos, Emily J. Shields, Hui Shen, Kathy Fange Liu, Nancy M. Bonini. Mettl3-dependent m6A modification attenuates the brain stress response in Drosophila. Nat Commun. 2022 September 14.
Shoumei Bai, Sarah E Taylor, Mohd Azrin Jamalruddin, Stacy McGonigal, Edward Grimley, Dongli Yang, Kara A Bernstein, Ronald J Buckanovich. Targeting Therapeutic Resistance and Multinucleate Giant Cells in CCNE1-Amplified HR-Proficient Ovarian Cancer. Mol. Cancer Ther. 2022 September 6.
Yang Mei, Troy E Messick, Jayaraju Dheekollu, Hee Jong Kim, Sudheer Molugu, Leonardo Josué Castro Muñoz, Vera Moiskeenkova-Bell, Kenji Murakami, Paul M Lieberman. Cryo-EM Structure and Functional Studies of EBNA1 Binding to the Family of Repeats and Dyad Symmetry Elements of Epstein-Barr Virus oriP. J. Virol. 2022 August 29.
Mirna El Khatib, Andrei V. Cheprakov, and Sergei A. Vinogradov. Unusual Reactivity and Metal Affinity of Water-Soluble Dipyrrins. Inorg Chem. 2022 August 2.
Papita Mandal, Karthik Eswara, Zhadyra Yerkesh, Vladlena Kharchenko, Levani Zandarashvili, Kacper Szczepski, Dalila Bensaddek, Łukasz Jaremko, Ben E Black, Wolfgang Fischle. Molecular basis of hUHRF1 allosteric activation for synergistic histone modification binding by PI5P. Sci Adv. 2022 August 26.
Alexander J. Polino, Justin J. Miller, Soumendranath Bhakat, Suhas Bobba, Gregory R. Bowman, Daniel E. Goldberg. The nepenthesin insert in the Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme function. J Biol Chem. 2022 August 8
PMID: 35972732
Iris K Lee, Estela Noguera-Ortega, Zebin Xiao, Leslie Todd, John Scholler, Decheng Song, Maria Liousia, Katheryn Lohith, Kexiang Xu, Kimberly J Edwards, Michael D Farwell, Carl H June, Steven M Albelda, Ellen Pure, Mark A Sellmyer. Monitoring Therapeutic Response to Anti-Fibroblast Activation Protein (FAP) CAR T Cells using [18F]AlF-FAPI-74. Clin Cancer Res. 2022 August 16
PMID: 35972732
Kimberly J Edwards, Bryan Chang, Hasan Babazada, Katheryn Lohith, Daniel H Park, Michael D Farwell, Mark A Sellmyer. Using CD69 PET Imaging to Monitor Immunotherapy-Induced Immune Activation. Cancer Immunol Res. 2022 July 21
PMID: 35862229
Xuepeng Wei, Kathryn Kixmoeller, Elana Baltrusaitis, Xiaolu Yang, Ronen Marmorstein. Allosteric role of a structural NADP + molecule in glucose-6-phosphate dehydrogenase activity. Proc Natl Acad Sci U S A. 2022 July 19
PMID: 35858355
Andrew C. McShan, Christine A. Devlin, Georgia F. Papadaki, Yi Sun, Adam I. Green, Giora I. Morozov, George M. Burslem, Erik Procko, Nikolaos G. Sgourakis. TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules. Nat Chem Biol. 2022 June 20
PMID: 35725941
Eva Erlebach, Luca Ravotto, Matthias T Wyss, Jacqueline Condrau, Thomas Troxler, Sergei A Vinogradov, Bruno Weber. Measurement of cerebral oxygen pressure in living mice by two-photon phosphorescence lifetime microscopy. STAR Protoc. 2022 June 17
Mirna El Khatib, Alexander L. Van Slyke, Anastasia Velalopoulou, Michele M. Kim, Khayrullo Shoniyozov, Srinivasa Rao Allu, Eric E. Diffenderfer, Theresa M. Busch, Rodney D. Wiersma, Cameron J. Koch, Sergei A. Vinogradov. Ultrafast Tracking of Oxygen Dynamics during Proton FLASH. Int J Radiat Oncol Biol Phys. 2022 Mar 18
PMID: 35314293
David C. Schultz, Robert M. Johnson, Kasirajan Ayyanathan, Jesse Miller, Kanupriya Whig, Brinda Kamalia, Mark Dittmar, Stuart Weston, Holly L. Hammond, Carly Dillen, Jeremy Ardanuy, Louis Taylor, Jae Seung Lee, Minghua Li, Emily Lee, Clarissa Shoffler, Christopher Petucci, Samuel Constant, Marc Ferrer, Christoph A. Thaiss, Matthew B. Frieman, Sara Cherry. Pyrimidine inhibitors synergize with nucleoside analogues to block SARS-CoV-2. Nature. 2022 Feb 7
PMID: 35130559
Chun Yang, Rina Fujiwara, Hee Jong Kim, Pratik Basnet, Yunye Zhu, Jose J Gorbea Colón, Stefan Steimle, Benjamin A Garcia, Craig D Kaplan, Kenji Murakami. Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Mol Cell. 2022 Jan 11;S1097-2765(21)01082-0
PMID: 35051353
2021
Elisha Segrist, Mark Dittmar, Beth Gold, Sara Cherry. Orally acquired cyclic dinucleotides drive dSTING-dependent antiviral immunity in enterocytes. Cell Rep. 2021 Dec 28;37(13):110150
PMID: 34965418
Marie-France Langelier, Ramya Billur, Aleksandr Sverzhinsky, Ben E. Black, John M. Pascal. HPF1 dynamically controls the PARP1/2 balance between initiating and elongating ADP-ribose modifications. Nat Commun. 2021 Nov 18;12(1):6675
PMID: 34795260
Catalina Salinas-Luypaert, Praveen Kumar Allu, Glennis A Logsdon, Jennine M. Dawicki-McKenna, Craig W. Gambogi, Daniele Fachinetti, Ben E. Black. Gene replacement strategies validate the use of functional tags on centromeric chromatin and invalidate an essential role for CENP-A K124ub . Cell Rep. 2021 Nov 2;37(5):109924
PMID: 34731637
Leah Gottlieb, Lin Guo, James Shorter, Ronen Marmorstein. N-alpha-acetylation of Huntingtin protein increases its propensity to aggregate. J Biol Chem. 2021 Oct 31;101363
PMID: 34732320
Michael Grasso, Gavin J. Bond, Ye-Jin Kim, Stefanie Boyd, Maria Matson Dzebo, Sebastian Valenzuela, Tiffany Tsang, Natalie A. Schibrowsky, Katherine B. Alwan, Ninian J. Blackburn, George M. Burslem, Pernilla Wittung-Stafshede, Duane D. Winkler, Ronen Marmorstein, Donita C. Brady. The copper chaperone CCS facilitates copper binding to MEK1/2 to promote kinase activation. J Biol Chem. 2021 Oct 26;101314.
PMID: 34715128
Kiara N Berríos, Niklaus H. Evitt, Rachel A. DeWeerd, Diqiu Ren, Meiqi Luo, Aleksia Barka, Tong Wang, Caroline R. Bartman, Yemin Lan, Abby M. Green, Junwei Shi, Rahul M Kohli. Controllable genome editing with split-engineered base editors. Nat Chem Biol. 2021 Oct 18
PMID: 34663942
Chloe M. Jones, D. Miklos Robkis, Robert J. Blizzard, Mika Munari, Yarra Venkatesh, Tiberiu S. Mihaila, Alex J. Eddins, Ryan A. Mehl, William N. Zagotta, Sharona E. Gordon and E. James Petersson. Genetic encoding of a highly photostable, long lifetime fluorescent amino acid for imaging in mammalian cells. Chem. Sci., 2021, 12, 11955-11964
PMID to come
Hui Shen, Yulia Gonskikh, Julian Stoute, Kathy Fange Liu. Human DIMT1 generates N 26,6 A-dimethylation-containing small RNAs. J Biol Chem. 2021 Aug 30.
PMID: 34473991
Hana M. Odeh, Charlotte M. Fare, James Shorter. Nuclear-import receptors counter deleterious phase transitions in neurodegenerative disease. J Mol Biol. 2021 Aug 28.
PMID: 34464655
Adam I. Green and George M. Burslem. Photochemical synthesis of an epigenetic focused tetrahydroquinoline library. RSC Med Chem. 2021 Aug 25;12(10):1780-1786
PMID: 34778779
Tofayel Ahmed, Collin R. Nisler, Edwin C. Fluck 3rd, Sanket Walujkar, Marcos Sotomayor, Vera Y. Moiseenkova-Bell. Structure of the ancient TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium. Structure. 2021 Aug 24.
PMID: 34453887
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2020
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2019
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Esipova TV, Barrett MJP, Erleback E, Masunov AE, Weber B, Vinogradov SA. Oxyphor 2P: A High-Performance Probe for Deep-Tissue Longitudinal Oxygen Imaging. Cell Metab. 2019 Mar 5;29(3):736-744.
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2018
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Hughes TET, Pumroy RA, Yazici AT, Kasimova MA, Fluck EC, Huynh KW, Samanta A, Molugu SK, Zhou ZH, Carnevale V, Rohacs T, Moiseenkova-Bell VY. Structural insights on TRPV5 gating by endogenous modulators. Nat Commun. 2018 Oct 10;9(1):4198.
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Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM. Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using DNA deaminase. Nat Biotechnol. 2018 Oct 8.
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Guo L, Kim HJ, Wang H, Monaghan J, Freyermuth F, Sung JC, O'Donovan K, Fare CM, Diaz Z, Singh N, Zhang ZC, Coughlin M, Sweeny EA, DeSantis ME, Jackrel ME, Rodell CB, Burdick JA, King OD, Gitler AD, Lagier-Tourenne C, Pandey UB, Chook YM, Taylor JP, Shorter J. Nuclear-Import Receptors Reverse Aberrant Phase Transitions of RNA-Binding Proteins with Prion-like Domains. Cell. 2018 Apr 19;173(3):677-692.
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Friedman ES, Bittinger K, Esipova TV, Hou L, Chau L, Jiang J, Mesaros C, Lund PJ, Liang X, FitzGerald GA, Goulian M, Lee D, Garcia BA, Blair IA, Vinogradov SA, Wu GD. Microbes vs. chemistry in the origin of the anaerobic gut lumen. Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4170-4175.
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2017
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Doliba NM, Liu Q, Li C, Chen P, Liu C, Naji A, Matschinsky FM. Inhibition of cholinergic potentiation of insulin secretion from pancreatic islets by chronic elevation of glucose and fatty acids: Protection by casein kinase 2 inhibitor. Mol Metab. 2017 Oct;6(10):1240-1253.
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Iwata-Otsubo A, Dawicki-McKenna JM, Akera T, Falk SJ, Chmátal L, Yang K, Sullivan BA, Schultz RM, Lampson MA, Black BE. Expanded Satellite Repeats Amplify a Discrete CENP-A Nucleosome Assembly Site on Chromosomes that Drive in Female Meiosis. Curr Biol. 2017 Aug 7;27(15):2365-2373.
PMID: 28756949
Gazzara MR, Mallory MJ, Roytenberg R, Lindberg JP, Jha A, Lynch KW, Barash Y. Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes. Genome Res. 2017 Aug;27(8):1360-1370.
PMID: 28512194
Gates SN, Yokom AL, Lin J, Jackrel ME, Rizo AN, Kendsersky NM, Buell CE, Sweeny EA, Mack KL, Chuang E, Torrente MP, Su M, Shorter J, Southworth DR. Ratchet-like polypeptide translocation mechanism of the AAA+ disaggregase Hsp104. Science. 2017 Jul 21;357(6348):273-279.
PMID: 28619716
Gupta K, Sharp R, Yuan JB, Li H, Van Duyne GD. Coiled-coil interactions mediate serine integrase directionality. Nucleic Acids Res. 2017 Jul 7;45(12):7339-7353.
PMID: 28549184
Caro JA, Harpole KW, Kasinath V, Lim J, Granja J, Valentine KG, Sharp KA, Wand AJ. Entropy in molecular recognition by proteins. Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6563-6568.
PMID: 28584100
Guo LY, Allu PK, Zandarashvili L, McKinley KL, Sekulic N, Dawicki-McKenna JM, Fachinetti D, Logsdon GA, Jamiolkowski RM, Cleveland DW, Cheeseman IM, Black BE. Centromeres are maintained by fastening CENP-A to DNA and directing an arginine anchor-dependent nucleosome transition. Nat Commun. 2017 Jun 9;8:15775.
PMID: 28598437
Wilson DF, Cember ATJ, Matschinsky FM. The thermodynamic basis of glucose-stimulated insulin release: a model of the core mechanism. Physiol Rep. 2017 Jun;5(12).
PMID: 28655753
Liu MY, Torabifard H, Crawford DJ, DeNizio JE, Cao XJ, Garcia BA, Cisneros GA, Kohli RM. Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Nat Chem Biol. 2017 Feb;13(2):181-187.
PMID: 27918559
Fachinetti D, Logsdon GA, Abdullah A, Selzer EB, Cleveland DW, Black BE. CENP-A Modifications on Ser68 and Lys124 Are Dispensable for Establishment, Maintenance, and Long-Term Function of Human Centromeres. Dev Cell. 2017 Jan 9;40(1):104-113.
PMID: 28073008
Kodali G, Mancini JA, Solomon LA, Episova TV, Roach N, Hobbs CJ, Wagner P, Mass OA, Aravindu K, Barnsley JE, Gordon KC, Officer DL, Dutton PL, Moser CC. Design and engineering of water-soluble light-harvesting protein maquettes. Chem Sci. 2017 Jan 1;8(1):316-324.
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2016
Grasso M, Estrada MA, Ventocilla C, Samanta M, Maksimoska J, Villanueva J, Winkler JD, Marmorstein R. Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAF(V600E) Conformation. ACS Chem Biol. 2016 Oct 21;11(10):2876-2888.
PMID: 27571413
He C, Sidoli S, Warneford-Thomson R, Tatomer DC, Wilusz JE, Garcia BA, Bonasio R. High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. Mol Cell. 2016 Oct 20;64(2):416-430.
PMID: 27768875
Yokom AL, Gates SN, Jackrel ME, Mack KL, Su M, Shorter J, Southworth DR. Spiral architecture of the Hsp104 disaggregase reveals the basis for polypeptide translocation. Nat Struct Mol Biol. 2016 Sep;23(9):830-7.
PMID: 27478928
Molleston JM, Sabin LR, Moy RH, Menghani SV, Rausch K, Gordesky-Gold B, Hopkins KC, Zhou R, Jensen TH, Wilusz JE, Cherry S. A conserved virus-induced cytoplasmic TRAMP-like complex recruits the exosome to target viral RNA for degradation. Genes Dev. 2016 Jul 15;30(14):1658-70.
PMID: 27474443
Lin S, Yuan ZF, Han Y, Marchione DM, Garcia BA. Preferential Phosphorylation on Old Histones during Early Mitosis in Human Cells. J Biol Chem. 2016 Jul 15;291(29):15342-57.
PMID: 27226594
Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA. A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics. Mol Cell Proteomics. 2016 Jul;15(7):2462-75.
PMID: 27114449
Ajith S, Gazzara MR, Cole BS, Shankarling G, Martinez NM, Mallory MJ, Lynch KW. Position-dependent activity of CELF2 in the regulation of splicing and implications for signal-responsive regulation in T cells. RNA Biol. 2016 Jun 2;13(6):569-81.
PMID: 27096301
Laxmikanthan G, Xu C, Brilot AF, Warren D, Steele L, Seah N, Tong W, Grigorieff N, Landy A, Van Duyne GD. Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction. Elife. 2016 May 25;5.
PMID: 27223329
Smoak EM, Stein P, Schultz RM, Lampson MA, Black BE. Long-Term Retention of CENP-A Nucleosomes in Mammalian Oocytes Underpins Transgenerational Inheritance of Centromere Identity. Curr Biol. 2016 Apr 25;26(8):1110-6.
PMID: 27040782