BMB students produce substantial bodies of work that lead to high quality, peer-reviewed publications. The menus below highlight the first-author papers our students have published in recent years.
Structure and evolution of neuronal wiring receptors and ligands. Elena Cortes, Joseph Pak, Engin Ozkan. Dev Dyn. 2023 Jan;252(1):27-60. doi: 10.1002/dvdy.512. Epub 2022 Jul 6.
Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder. Szymon P Kordon, Przemyslaw Dutka, Justyna M Adamska, Sumit J Bandekar, Katherine Leon, Satchal K Erramilli, Brock Adams, Jingxian Li, Anthony Kossiakoff, Demet Arac. Nat Commun. 2023 Feb 6;14(1):635. doi: 10.1038/s41467-023-36312-7.
Folding of Prestin’s Anion-Binding Site and the Mechanism of Outer Hair Cell Electromotility. Lin, X., Haller, P., Bavi, N., Faruk, N., Perozo, E., Sosnick, T. R. BioRxiv. doi:10.1101/2023.02.27.530320 (2023)
Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations. Noah Pena, Wen Zhang, Christopher Watkins, Mateusz Halucha, Hala Alshammary, Matthew M Hernandez, Wen-Chun Liu, Randy A Albrecht, Adolfo Garcia-Sastre, Viviana Simon, Christopher Katanski, Tao Pan. Front Cell Dev Biol. 2022 Feb 3;10:768356. doi: 10.3389/fcell.2022.768356. eCollection 2022.
Deaza-modification of MR1 ligands modulates recognition by MR1-restricted T cells. Haihong Jin, Nicole Ladd, Andrew M Peev, Gwendolyn M Swarbrick, Meghan Cansler, Megan Null, Christopher T Boughter, Curtis McMurtrey, Aaron Nilsen, Karen M Dobos, William H Hildebrand, Deborah A Lewinsohn, Erin J Adams, David M Lewinsohn, Melanie J Harriff. Sci Rep. 2022 Dec 29;12(1):22539. doi: 10.1038/s41598-022-26259-y.
Substrate-driven assembly of a translocon for multipass membrane proteins.Arunkumar Sundaram, Melvin Yamsek, Frank Zhong, Yogesh Hooda, Ramanujan S Hegde, Robert Keenan. Nature. 2022 Nov;611(7934):167-172. doi: 10.1038/s41586-022-05330-8. Epub 2022 Oct 19.
tRNA abundance, modification and fragmentation in nasopharyngeal swabs as biomarkers for COVID-19 severity. Christopher D Katanski, Hala Alshammary, Christopher P Watkins, Sihao Huang, Ana Gonzales-Reiche, Emilia Mia Sordillo, Harm Van Bakel, Mount Sinai PSP study group, Karen Lolans, Viviana Simon, Tao Pan. Front Cell Dev Biol. 2022 Nov 1;10:999351. doi: 10.3389/fcell.2022.999351. eCollection 2022.
Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing. Christopher D Katanski, Christopher P Watkins, Wen Zhang, Matthew Reyer, Samuel Miller, Tao Pan. Nucleic Acids Res. 2022 Sep 23;50(17):e99. doi: 10.1093/nar/gkac517.
A New Reaction for Improved Calibration of EPR Rapid-Freeze Quench Times: Kinetics of Ethylene Diamine Tetraacetate (EDTA) Transfer from Calcium(II) to Copper(II). Abigail L Schroeter, Hao Yang, Christopher D James, Brian M Hoffman, Peter E Doan. Appl Magn Reson. 2022 Sep;53(7-9):1195-1210. doi: 10.1007/s00723-021-01448-6. Epub 2021 Nov 20.
Engineering of a synthetic antibody fragment for structural and functional studies of K+ channels. Ahmed Rohaim, Tomasz Slezak, Young Hoon Koh, Lydia Blachowicz, Anthony Kossiakoff, Benoit roux. J Gen Physiol. 2022 Apr 4;154(4):e202112965. doi: 10.1085/jgp.202112965. Epub 2022 Mar 2.
Development of in vivo HDX-MS with applications to a TonB-dependent transporter and other proteins. Lin, X., Zmyslowski, A. M., Gagnon, I. A., Nakamoto, R. K. & Sosnick, T. R. Protein Science. 31, e4402 (2022).
Molecular and structural basis of olfactory sensory neuron axon coalescence by Kirrel receptors. Jing Wang, Neelima Vaddadi, Joseph S Pak, Yeonwoo Park, Sabrina Quilez, Christina Roman, Emilie Dumontier, Joseph W Thornton, Jean Francois Cloutier, Engin Ozkan. Cell Rep. 2021 Nov 2;37(5):109940. doi: 10.1016/j.celrep.2021.109940.
Programmable technologies to manipulate gene expression at the RNA level. Huachun Liu, Simone Rauch, Bryan C Dickinson. Curr Opin Chem Biol. 2021 Oct;64:27-37. doi: 10.1016/j.cbpa.2021.03.004. Epub 2021 Apr 27.
Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule disassembly. Gea Cereghetti, Caroline Wilson-Zbinden, Vera M Kissling, Maren Diether, Alexandra Arm, Haneul Yoo, Ilaria Piazza, Shady Saad, Paola Picotti, D Allan Drummond, Uwe Sauer, Reinhard Dechant, Matthias Peter. Nat Cell Biol. 2021 Oct;23(10):1085-1094. doi: 10.1038/s41556-021-00760-4. Epub 2021 Oct 6.
Engineered Ultra-High Affinity Synthetic Antibodies for SARS-CoV-2 Neutralization and Detection. Tomasz Slezak, Anthony Kossiakoff. J Mol Biol. 2021 May 14;433(10):166956. doi: 10.1016/j.jmb.2021.166956. Epub 2021 Mar 26.
β-amyloid model core peptides: Effects of hydrophobes and disulfides. Laura M L Hawk, Jay M Pittman, Patrick C Moore, Atul K Srivastava, Jonanthan Zerweck, Joshua TB Williams, Andrew J Hawk, Joseph R Sachleben, Stephen Meredith. Protein Sci. 2020 Feb;29(2):527-541. doi: 10.1002/pro.3778. Epub 2019 Nov 25.
Alternative splicing controls teneurin-latrophilin interaction and synapse specificity by a shape-shifting mechanism. Jingxian Li, Yuan Xie, Shaleeka Cornelius, Xian Jiang, Richard Sando, Szymon P Kordon, Man Pan, Katherine Leon, Thomas C Sudhof, Minglei Zhao, Demet Arac. Nat Commun. 2020 May 1;11(1):2140. doi: 10.1038/s41467-020-16029-7.
Production of MR1 Tetramers Loaded with Microbial Ligands. Nicole A Ladd, Cara A Froyd, Erin J Adams. Methods Mol Biol. 2020;2098:191-207. doi: 10.1007/978-1-0716-0207-2_13.
β-Amyloid aggregation and heterogeneous nucleation. Atul K Srivastava, Jay M Pittman, Jonathan Zerweck, Bharat S Venkata, Patrick C Moore, Joseph R Sachleben, Stephen Meredith. Protein Sci. 2019 Sep;28(9):1567-1581. doi: 10.1002/pro.3674. Epub 2019 Aug 6.
Nanodroplet Oligomers (NanDOs) of Aβ40. Jay M Pittman, Atul K Srivastava, Christopher t Boughter, Bharat Somireddy Venkata, Jonathan Zerweck, Patrick C Moore, Izabela Smok, Marco Tonelli, Joseph R Sachleben, Stephen Meredith. Biochemistry.2021 Sep 14;60(36):2691-2703. doi: 10.1021/acs.biochem.1c00147. Epub 2021 May 24.
Programmable RNA-Guided RNA Effector Proteins Built from Human Parts. Simone Rauch, Emily He, Michael Srienc, Huiging Zhou, Zijie Zhang, Bryan C Dickinson. Cell. 2019 Jun 27;178(1):122-134.e12. doi: 10.1016/j.cell.2019.05.049. Epub 2019 Jun 20.
A Phage-Assisted Continuous Selection Approach for Deep Mutational Scanning of Protein-Protein Interactions. Julia Zinkus-Boltz, Craig DeValk, Bryan C Dickinson. ACS Chem Biol. 2019 Dec 20;14(12):2757-2767. doi: 10.1021/acschembio.9b00669. Epub 2019 Dec 6.
Cellular sensing by phase separation: Using the process, not just the products. Haneul Yoo, Catherine Triandafillou, D Allan Drummond. J Biol Chem. 2019 May 3;294(18):7151-7159. doi: 10.1074/jbc.TM118.001191.
Butyrophilin3A proteins and Vγ9Vδ2 T cell activation. Gu S, Borowska MT, Boughter CT, Adams EJ. Semin Cell Dev Biol. 2018 Mar 9. pii: S1084-9521(16)30436-0. doi: 10.1016/j.semcdb.2018.02.007. Review. PMID: 2947103
Kudryashova E, Heisler DB, Williams B, Harker AJ, Shafer K, Quinlan ME, Kovar DR, Vavylonis D, Kudryashov DS. 2018. Actin Cross-Linking Toxin Is a Universal Inhibitor of Tandem-Organized and Oligomeric G-Actin Binding Proteins. Curr Biol 28:1536-1547.e9. doi:10.1016/j.cub.2018.03.065. PMCID:PMC5964048.
Programmable RNA Binding Proteins for Imaging and Therapeutics. Simone Rauch, Bryan C Dickinson. Biochemistry. 2018 Jan 30;57(4):363-364. doi: 10.1021/acs.biochem.7b01101. Epub 2017 Nov 17.
Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on Vγ9Vδ2 T cell activation. Gu S, Sachleben JR, Boughter CT, Nawrocka WI, Borowska MT, Tarrasch JT, Skiniotis G, Roux B, Adams EJ. Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7311-E7320. doi: 10.1073/pnas.1707547114. Epub 2017 Aug 14. PMID: 28807997 [see notes above]
Burke TA, Harker AJ, Dominguez R, Kovar DR. 2017. The bacterial virulence factors VopL and VopF nucleate actin from the pointed end. J Cell Biol. doi:10.1083/jcb.201608104. PMCID:PMC5412564.
Leonard, J.D., Gilmore, D.C., Dileepan, T., Nawrocka, W.I., Chao, J.L., Schoenbach, M.H., Jenkins, M.K., Adams, E.J., and Savage, P.A. (2017). Identification of Natural Regulatory T Cell Epitopes Reveals Convergence on a Dominant Autoantigen. Immunity, 47(1):107-117.
Wohlever, M., Mateja, A., McGilvray, P. T., Day, K.J., Keenan, R.J. (2017). Msp1 Is a Membrane Protein Dislocase for Tail-Anchored Proteins. Molecular Cell, 67(2): 1-9.
Riback, J.A., Katanski, C.D., Kear-Scott, J.L., Pilipenko, E.V., Rojek, A.E., Sosnick, T.R., and Drummond, D.A. (2017). Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response.Cell, 168(6 ): 1028-1040.
Anghel, S.A., McGilvray, P. T., Hegde, M.S., Keenan, R.J. (2017). Identification of Oxa1 Homologs Operating in the Eukaryotic Endoplasmic Reticulum. Cell Reports, 21: 1-9.
Dominik PK, Borowska MT, Dalmas O, Kim SS, Perozo E, Keenan RJ, Kossiakoff AA. Conformational chaperones for structural studies of membrane proteins using antibody phage display with nanodiscs. Structure. 2016 Feb 2;24(2):300-9. Epub 2015 Dec 31. doi: 10.1016/j.str.2015.11.014. PMID: 26749445 [ this is from UChicago biosciences https://biosciences.uchicago.edu/current-students/2016-student-publications]
Winkelman JD, Suarez C, Hocky GM, Harker AJ, Morganthaler AN, Christensen JR, Voth GA, Bartles JR, Kovar DR. 2016. Fascin- and α-Actinin-Bundled Networks Contain Intrinsic Structural Features that Drive Protein Sorting. Current Biology 26:2697-2706. doi:10.1016/j.cub.2016.07.080. PMCID:PMC5119644.
A YidC-like Protein in the Archaeal Plasma Membrane. Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ. Structure. 2015 Sep 1;23(9):1715-1724. doi: 10.1016/j.str.2015.06.025. Epub 2015 Aug 6. PMID: 26256539