Recent Publications
Bhola M, Abe K, Orozco P, Rahnamoun H, Avila-Lopez P, Taylor E, Muhammad N, Liu B, Patel P, Marko JF, Starner AC, He C, Van Nostrand EL, Mondragón A, Lauberth SM. RNA interacts with topoisomerase I to adjust DNA topology. Mol Cell. 2024 Sep 5;84(17):3192-3208.e11. doi: 10.1016/j.molcel.2024.07.032. Epub 2024 Aug 21. PMID: 39173639; PMCID: PMC11380577.
Casler JC, Harper CS, White AJ, Anderson HL, Lackner LL. Mitochondria-ER-PM contacts regulate mitochondrial division and PI(4)P distribution. J Cell Biol. 2024 Sep 2;223(9):e202308144. doi: 10.1083/jcb.202308144. Epub 2024 May 23. PMID: 38781029; PMCID: PMC11116812.
Nijhawan AK, Leshchev D, Hsu DJ, Chan AM, Rimmerman D, Hong J, Kosheleva I, Henning R, Kohlstedt KL, Chen LX. Unlocking the unfolded structure of ubiquitin: Combining time-resolved x-ray solution scattering and molecular dynamics to generate unfolded ensembles. J Chem Phys. 2024 Jul 21;161(3):035101. doi: 10.1063/5.0217013. PMID: 39007394; PMCID: PMC11257700.
Manley OM, Shriver TJ, Xu T, Melendrez IA, Palacios P, Robson SA, Guo Y, Kelleher NL, Ziarek JJ, Rosenzweig AC. A multi-iron enzyme installs copper-binding oxazolone/thioamide pairs on a nontypeable Haemophilus influenzae virulence factor. Proc Natl Acad Sci U S A. 2024 Jul 9;121(28):e2408092121. doi: 10.1073/pnas.2408092121. Epub 2024 Jul 5. PMID: 38968106; PMCID: PMC11252979.
Larmore M, Palomero OE, Kamat NP, DeCaen PG. A synthetic method to assay polycystin channel biophysics. bioRxiv [Preprint]. 2024 May 6:2024.05.06.592666. doi: 10.1101/2024.05.06.592666. PMID: 38766162; PMCID: PMC11100589.
Bushhouse DZ, Fu J, Lucks JB. RNA folding kinetics control riboswitch sensitivity in vivo. bioRxiv [Preprint]. 2024 Mar 29:2024.03.29.587317. doi: 10.1101/2024.03.29.587317. PMID: 38585885; PMCID: PMC10996619.
Wytock TP, Motter AE. Cell reprogramming design by transfer learning of functional transcriptional networks. ArXiv [Preprint]. 2024 Mar 7:arXiv:2403.04837v1. Update in: Proc Natl Acad Sci U S A. 2024 Mar 12;121(11):e2312942121. doi: 10.1073/pnas.2312942121. PMID: 38495570; PMCID: PMC10942484.
Yang H, Ho MB, Lundahl MN, Mosquera MA, Broderick WE, Broderick JB, Hoffman BM. ENDOR Spectroscopy Reveals the "Free" 5'-Deoxyadenosyl Radical in a Radical SAM Enzyme Active Site Actually is Chaperoned by Close Interaction with the Methionine-Bound [4Fe-4S]2+ Cluster. J Am Chem Soc. 2024 Feb 14;146(6):3710-3720. doi: 10.1021/jacs.3c09428. Epub 2024 Feb 3. PMID: 38308759.
Rivera KG, Tanaka KJ, Buechel ER, Origel O Jr, Harrison A, Mason KM, Pinkett HW. Antimicrobial Peptide Recognition Motif of the Substrate Binding Protein SapA from Nontypeable Haemophilus influenzae. Biochemistry. 2024 Feb 6;63(3):294-311. doi: 10.1021/acs.biochem.3c00562. Epub 2024 Jan 8. PMID: 38189237; PMCID: PMC10851439.
Daffern N, Radhakrishnan I. Per-ARNT-Sim (PAS) Domains in Basic Helix-Loop-Helix (bHLH)-PAS Transcription Factors and Coactivators: Structures and Mechanisms. J Mol Biol. 2024 Feb 1;436(3):168370. doi: 10.1016/j.jmb.2023.168370. Epub 2023 Nov 20. PMID: 37992889; PMCID: PMC10922228.
Tucci FJ, Jodts RJ, Hoffman BM, Rosenzweig AC. Product analog binding identifies the copper active site of particulate methane monooxygenase. Nat Catal. 2023 Dec;6(12):1194-1204. doi: 10.1038/s41929-023-01051-x. Epub 2023 Nov 6. PMID: 38187819; PMCID: PMC10766429.
Vogt A, He Y. Structure and mechanism in non-homologous end joining. DNA Repair (Amst). 2023 Oct;130:103547. doi: 10.1016/j.dnarep.2023.103547. Epub 2023 Jul 29. PMID: 37556875; PMCID: PMC10528545.
Talyzina A, Han Y, Banerjee C, Fishbain S, Reyes A, Vafabakhsh R, He Y. Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation. Mol Cell. 2023 Aug 3;83(15):2641-2652.e7. doi: 10.1016/j.molcel.2023.06.015. Epub 2023 Jul 3. PMID: 37402369; PMCID: PMC10528418.
Daffern N, Kelley K, Villegas JA, Radhakrishnan I. Prostaglandins as Candidate Ligands for a Per-ARNT-Sim (PAS) Domain of Steroid Receptor Coactivator 1 (SRC1). bioRxiv [Preprint]. 2023 Jul 13:2023.07.13.548854. doi: 10.1101/2023.07.13.548854. PMID: 37502902; PMCID: PMC10369948.
Ng LC, Harris BJ, Larmore M, Ta MC, Vien TN, Tokars VL, Yarov-Yarovoy V, DeCaen PG. Energetic landscape of polycystin channel gating. EMBO Rep. 2023 Jul 5;24(7):e56783. doi: 10.15252/embr.202356783. Epub 2023 May 9. PMID: 37158562; PMCID: PMC10328073.
Jodts RJ, Wittkop M, Ho MB, Broderick WE, Broderick JB, Hoffman BM, Mosquera MA. Computational Description of Alkylated Iron-Sulfur Organometallic Clusters. J Am Chem Soc. 2023 Jun 28;145(25):13879-13887. doi: 10.1021/jacs.3c03062. Epub 2023 Jun 12. PMID: 37307050; PMCID: PMC10573082.
Chen S, Vogt A, Lee L, Naila T, McKeown R, Tomkinson AE, Lees-Miller SP, He Y. Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ. Sci Adv. 2023 Jun 2;9(22):eadg2838. doi: 10.1126/sciadv.adg2838. Epub 2023 May 31. PMID: 37256947; PMCID: PMC10413680.
Bushhouse DZ, Lucks JB. Tuning strand displacement kinetics enables programmable ZTP riboswitch dynamic range in vivo. Nucleic Acids Res. 2023 Apr 11;51(6):2891-2903. doi: 10.1093/nar/gkad110. PMID: 36864761; PMCID: PMC10085676.
Esarte Palomero O, Larmore M, DeCaen PG. Polycystin Channel Complexes. Annu Rev Physiol. 2023 Feb 10;85:425-448. doi: 10.1146/annurev-physiol-031522-084334. PMID: 36763973; PMCID: PMC10029091.
Chan AM, Nijhawan AK, Hsu DJ, Leshchev D, Rimmerman D, Kosheleva I, Kohlstedt KL, Chen LX. The Role of Transient Intermediate Structures in the Unfolding of the Trp-Cage Fast-Folding Protein: Generating Ensembles from Time-Resolved X-ray Solution Scattering with Genetic Algorithms. J Phys Chem Lett. 2023 Feb 9;14(5):1133-1139. doi: 10.1021/acs.jpclett.2c03680. Epub 2023 Jan 27. PMID: 36705525; PMCID: PMC10167713.
Adams LM, DeHart CJ, Drown BS, Anderson LC, Bocik W, Boja ES, Hiltke TM, Hendrickson CL, Rodriguez H, Caldwell M, Vafabakhsh R, Kelleher NL. Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling. J Biol Chem. 2023 Jan;299(1):102768. doi: 10.1016/j.jbc.2022.102768. Epub 2022 Dec 5. PMID: 36470426; PMCID: PMC9808003.
Koo CW, Hershewe JM, Jewett MC, Rosenzweig AC. Cell-Free Protein Synthesis of Particulate Methane Monooxygenase into Nanodiscs. ACS Synth Biol. 2022 Dec 16;11(12):4009-4017. doi: 10.1021/acssynbio.2c00366. Epub 2022 Nov 23. PMID: 36417751; PMCID: PMC9910172.
Cavin-Meza G, Mullen TJ, Czajkowski ER, Wolff ID, Divekar NS, Finkle JD, Wignall SM. ZYG-9ch-TOG promotes the stability of acentrosomal poles via regulation of spindle microtubules in C. elegans oocyte meiosis. PLoS Genet. 2022 Nov 30;18(11):e1010489. doi: 10.1371/journal.pgen.1010489. PMID: 36449516; PMCID: PMC9757581.
Cheng L, White EN, Brandt NL, Yu AM, Chen AA, Lucks JB. Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch. Nucleic Acids Res. 2022 Nov 28;50(21):12001-12018. doi: 10.1093/nar/gkac102. PMID: 35348734; PMCID: PMC9756952.
Steinkühler J, Jacobs ML, Boyd MA, Villaseñor CG, Loverde SM, Kamat NP. PEO-b-PBD Diblock Copolymers Induce Packing Defects in Lipid/Hybrid Membranes and Improve Insertion Rates of Natively Folded Peptides. Biomacromolecules. 2022 Nov 14;23(11):4756-4765. doi: 10.1021/acs.biomac.2c00936. Epub 2022 Nov 1. PMID: 36318160; PMCID: PMC9667879.
Dimitrova VS, Song S, Karagiaridi A, Marand A, Pinkett HW. Detergent Alternatives: Membrane Protein Purification Using Synthetic Nanodisc Polymers. Methods Mol Biol. 2022;2507:375-387. doi: 10.1007/978-1-0716-2368-8_20. PMID: 35773593; PMCID: PMC9361707.
White AJ, Harper CS, Rosario EM, Dietz JV, Addis HG, Fox JL, Khalimonchuk O, Lackner LL. Loss of Num1-mediated cortical dynein anchoring negatively impacts respiratory growth. J Cell Sci. 2022 Nov 1;135(21):jcs259980. doi: 10.1242/jcs.259980. Epub 2022 Oct 31. PMID: 36185004; PMCID: PMC9687553.
Zhu Y, Koo CW, Cassidy CK, Spink MC, Ni T, Zanetti-Domingues LC, Bateman B, Martin-Fernandez ML, Shen J, Sheng Y, Song Y, Yang Z, Rosenzweig AC, Zhang P. Structure and activity of particulate methane monooxygenase arrays in methanotrophs. Nat Commun. 2022 Sep 5;13(1):5221. doi: 10.1038/s41467-022-32752-9. PMID: 36064719; PMCID: PMC9445010.
McCollum MM, Larmore M, Ishihara S, Ng LCT, Kimura LF, Guadarrama E, Ta MC, Vien TN, Frost GB, Scheidt KA, Miller RE, DeCaen PG. Targeting the tamoxifen receptor within sodium channels to block osteoarthritic pain. Cell Rep. 2022 Aug 23;40(8):111248. doi: 10.1016/j.celrep.2022.111248. PMID: 36001977; PMCID: PMC9523973.
Daffern N, Radhakrishnan I. A Novel Mechanism of Coactivator Recruitment by the Nurr1 Nuclear Receptor. J Mol Biol. 2022 Aug 30;434(16):167718. doi: 10.1016/j.jmb.2022.167718. Epub 2022 Jul 8. PMID: 35810793; PMCID: PMC9922031.
Wolff ID, Hollis JA, Wignall SM. Acentrosomal spindle assembly and maintenance in Caenorhabditis elegans oocytes requires a kinesin-12 nonmotor microtubule interaction domain. Mol Biol Cell. 2022 Jul 1;33(8):ar71. doi: 10.1091/mbc.E22-05-0153. Epub 2022 May 20. PMID: 35594182; PMCID: PMC9635285.
Bushhouse DZ, Choi EK, Hertz LM, Lucks JB. How does RNA fold dynamically? J Mol Biol. 2022 Sep 30;434(18):167665. doi: 10.1016/j.jmb.2022.167665. Epub 2022 Jun 1. PMID: 35659535; PMCID: PMC9474645.
Herrera A, Kim Y, Chen J, Jedrzejczak R, Shukla S, Maltseva N, Joachimiak G, Welk L, Wiersum G, Jaroszewski L, Godzik A, Joachimiak A, Satchell KJF. A Genomic Island of Vibrio cholerae Encodes a Three-Component Cytotoxin with Monomer and Protomer Forms Structurally Similar to Alpha-Pore-Forming Toxins. J Bacteriol. 2022 May 17;204(5):e0055521. doi: 10.1128/jb.00555-21. Epub 2022 Apr 18. PMID: 35435721; PMCID: PMC9112891.
Schamber MR, Vafabakhsh R. Mechanism of sensitivity modulation in the calcium-sensing receptor via electrostatic tuning. Nat Commun. 2022 Apr 22;13(1):2194. doi: 10.1038/s41467-022-29897-y. PMID: 35459864; PMCID: PMC9033857.
Nijhawan AK, Chan AM, Hsu DJ, Chen LX, Kohlstedt KL. Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures. J Phys Chem B. 2021 Nov 18;125(45):12401-12412. doi: 10.1021/acs.jpcb.1c05820. Epub 2021 Nov 8. PMID: 34748336; PMCID: PMC9096987.
Thavarajah W, Hertz LM, Bushhouse DZ, Archuleta CM, Lucks JB. RNA Engineering for Public Health: Innovations in RNA-Based Diagnostics and Therapeutics. Annu Rev Chem Biomol Eng. 2021 Jun 7;12:263-286. doi: 10.1146/annurev-chembioeng-101420-014055. Epub 2021 Apr 26. PMID: 33900805; PMCID: PMC9714562.
Verosloff MS, Corcoran WK, Dolberg TB, Bushhouse DZ, Leonard JN, Lucks JB. RNA Sequence and Structure Determinants of Pol III Transcriptional Termination in Human Cells. J Mol Biol. 2021 Jun 25;433(13):166978. doi: 10.1016/j.jmb.2021.166978. Epub 2021 Apr 1. PMID: 33811918; PMCID: PMC8169631.
Sula A, Hollingworth D, Ng LCT, Larmore M, DeCaen PG, Wallace BA. A tamoxifen receptor within a voltage-gated sodium channel. Mol Cell. 2021 Mar 18;81(6):1160-1169.e5. doi: 10.1016/j.molcel.2020.12.048. Epub 2021 Jan 26. PMID: 33503406; PMCID: PMC7980221.
Agrawal, D.K., Tang, X., Westbrook, A., Marshall, R., Maxwell, C.S., Lucks, J., Noireaux, V., Beisel, C.L., Dunlop, M.J., and Franco, E. (2018). Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression. ACS Synth Biol.
Chan, C.W., Kiesel, B.R., and Mondragon, A. (2018). Crystal Structure of Human Rpp20/Rpp25 Reveals Quaternary Level Adaptation of the Alba Scaffold as Structural Basis for Single-stranded RNA Binding. J Mol Biol.
Daffern, N., Chen, Z., Zhang, Y., Pick, L., and Radhakrishnan, I. (2018). Solution Nuclear Magnetic Resonance Studies of the Ligand-Binding Domain of an Orphan Nuclear Receptor Reveal a Dynamic Helix in the Ligand-Binding Pocket. Biochemistry 57, 1977-1986.
de Paz, A.M., Cybulski, T.R., Marblestone, A.H., Zamft, B.M., Church, G.M., Boyden, E.S., Kording, K.P., and Tyo, K.E.J. (2018). High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing. Nucleic Acids Res.
Erbas, A., de la Cruz, M.O., and Marko, J.F. (2018). Effects of electrostatic interactions on ligand dissociation kinetics. Phys Rev E 97, 022405.
Jackobel, A.J., Han, Y., He, Y., and Knutson, B.A. (2018). Breaking the mold: structures of the RNA polymerase I transcription complex reveal a new path for initiation. Transcription.
Jayakanthan, S., Braiterman, L.T., Hasan, N.M., Unger, V.M., and Lutsenko, S. (2017). Human copper transporter ATP7B (Wilson disease protein) forms stable dimers in vitro and in cells. J Biol Chem 292, 18760-18774.
Kang, M.K., and Tullman-Ercek, D. (2018). Engineering expression and function of membrane proteins. Methods.
Kenney, G.E., Dassama, L.M.K., Pandelia, M.E., Gizzi, A.S., Martinie, R.J., Gao, P., DeHart, C.J., Schachner, L.F., Skinner, O.S., Ro, S.Y., Zhu, X., Sadek, M., Thomas, P.M., Almo, S.C., Bollinger, J.M., Jr., Krebs, C., Kelleher, N.L., and Rosenzweig, A.C. (2018). The biosynthesis of methanobactin. Science 359, 1411-1416.
Kightlinger, W., Lin, L., Rosztoczy, M., Li, W., DeLisa, M.P., Mrksich, M., and Jewett, M.C. (2018). Design of glycosylation sites by rapid synthesis and analysis of glycosyltransferases. Nat Chem Biol.
Klosowiak, J.L., Park, S., Smith, K.P., French, M.E., Focia, P.J., Freymann, D.M., and Rice, S.E. (2016). Structural insights into Parkin substrate lysine targeting from minimal Miro substrates. Sci Rep 6, 33019.
Kraft, L.M., and Lackner, L.L. (2018). Mitochondrial anchors: Positioning mitochondria and more. Biochem Biophys Res Commun 500, 2-8.
Labbadia, J., Brielmann, R.M., Neto, M.F., Lin, Y.F., Haynes, C.M., and Morimoto, R.I. (2017). Mitochondrial Stress Restores the Heat Shock Response and Prevents Proteostasis Collapse during Aging. Cell Rep 21, 1481-1494.
Levitz, J., Habrian, C., Bharill, S., Fu, Z., Vafabakhsh, R., and Isacoff, E.Y. (2016). Mechanism of Assembly and Cooperativity of Homomeric and Heteromeric Metabotropic Glutamate Receptors. Neuron 92, 143-159.
Li, K., Rodosthenous, R.S., Kashanchi, F., Gingeras, T., Gould, S.J., Kuo, L.S., Kurre, P., Lee, H., Leonard, J.N., Liu, H., Lombo, T.B., Momma, S., Nolan, J.P., Ochocinska, M.J., Pegtel, D.M., Sadovsky, Y., Sanchez-Madrid, F., Valdes, K.M., Vickers, K.C., Weaver, A.M., Witwer, K.W., Zeng, Y., Das, S., Raffai, R.L., and Howcroft, T.K. (2018). Advances, challenges, and opportunities in extracellular RNA biology: insights from the NIH exRNA Strategic Workshop. JCI Insight 3.
Liu, X., Vien, T., Duan, J., Sheu, S.H., DeCaen, P.G., and Clapham, D.E. (2018). Polycystin-2 is an essential ion channel subunit in the primary cilium of the renal collecting duct epithelium. Elife 7.
Morgan, M.A.J., Rickels, R.A., Collings, C.K., He, X., Cao, K., Herz, H.M., Cozzolino, K.A., Abshiru, N.A., Marshall, S.A., Rendleman, E.J., Sze, C.C., Piunti, A., Kelleher, N.L., Savas, J.N., and Shilatifard, A. (2017). A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation. Genes Dev 31, 2003-2014.
Mullen, T.J., and Wignall, S.M. (2017). Interplay between microtubule bundling and sorting factors ensures acentriolar spindle stability during C. elegans oocyte meiosis. PLoS Genet 13, e1006986.
O'Flaherty, D.K., Kamat, N.P., Mirza, F.N., Li, L., Prywes, N., and Szostak, J.W. (2018). Copying of Mixed-Sequence RNA Templates inside Model Protocells. J Am Chem Soc 140, 5171-5178.
Parisien, J.P., Lenoir, J.J., Mandhana, R., Rodriguez, K.R., Qian, K., Bruns, A.M., and Horvath, C.M. (2018). RNA sensor LGP2 inhibits TRAF ubiquitin ligase to negatively regulate innate immune signaling. EMBO Rep.
Purohit, R., Ross, M.O., Batelu, S., Kusowski, A., Stemmler, T.L., Hoffman, B.M., and Rosenzweig, A.C. (2018). Cu(+)-specific CopB transporter: Revising P1B-type ATPase classification. Proc Natl Acad Sci U S A 115, 2108-2113.
Rima, B., Collins, P., Easton, A., Fouchier, R., Kurath, G., Lamb, R.A., Lee, B., Maisner, A., Rota, P., and Wang, L.F. (2018). Problems of classification in the family Paramyxoviridae. Arch Virol 163, 1395-1404.
Sanders, S.J., Campbell, A.J., Cottrell, J.R., Moller, R.S., Wagner, F.F., Auldridge, A.L., Bernier, R.A., Catterall, W.A., Chung, W.K., Empfield, J.R., George, A.L., Jr., Hipp, J.F., Khwaja, O., Kiskinis, E., Lal, D., Malhotra, D., Millichap, J.J., Otis, T.S., Petrou, S., Pitt, G., Schust, L.F., Taylor, C.M., Tjernagel, J., Spiro, J.E., and Bender, K.J. (2018). Progress in Understanding and Treating SCN2A-Mediated Disorders. Trends Neurosci.
Smith, L.M., and Kelleher, N.L. (2018). Proteoforms as the next proteomics currency. Science 359, 1106-1107.
Sump, B., and Brickner, J.H. (2017). Nup98 regulation of histone methylation promotes normal gene expression and may drive leukemogenesis. Genes Dev 31, 2201-2203.
Tanaka, K.J., Song, S., Mason, K., and Pinkett, H.W. (2018). Selective substrate uptake: The role of ATP-binding cassette (ABC) importers in pathogenesis. Biochim Biophys Acta 1860, 868-877.
Vaeth, M., Yang, J., Yamashita, M., Zee, I., Eckstein, M., Knosp, C., Kaufmann, U., Karoly Jani, P., Lacruz, R.S., Flockerzi, V., Kacskovics, I., Prakriya, M., and Feske, S. (2017). ORAI2 modulates store-operated calcium entry and T cell-mediated immunity. Nat Commun 8, 14714.
Velasco, E., Wang, S., Sanet, M., Fernandez-Vazquez, J., Jove, D., Glaria, E., Valledor, A.F., O'Halloran, T.V., and Balsalobre, C. (2018). A new role for Zinc limitation in bacterial pathogenicity: modulation of alpha-hemolysin from uropathogenic Escherichia coli. Sci Rep 8, 6535.
Verma, K.D., Massing, J.O., Kamper, S.G., Carney, C.E., MacRenaris, K.W., Basilion, J.P., and Meade, T.J. (2017). Synthesis and evaluation of MR probes for targeted-reporter imaging. Chem Sci 8, 5764-5768.
Wytock, T.P., Fiebig, A., Willett, J.W., Herrou, J., Fergin, A., Motter, A.E., and Crosson, S. (2018). Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate. PLoS Genet 14, e1007284.
Zheng, J., Chen, L., Skinner, O.S., Ysselstein, D., Remis, J., Lansbury, P., Skerlj, R., Mrosek, M., Heunisch, U., Krapp, S., Charrow, J., Schwake, M., Kelleher, N.L., Silverman, R.B., and Krainc, D. (2018). beta-Glucocerebrosidase Modulators Promote Dimerization of beta-Glucocerebrosidase and Reveal an Allosteric Binding Site. J Am Chem Soc.