Publications
2023
Paraan, M., Nasef, M., Chou-Zheng, L., Khweis, S.A., Schoeffler, A.J., Hatoum-Aslan, A., Stagg, S.M. and Dunkle, J.A. (2023). The structure of a Type III-A CRISPR-Cas effector complex reveals conserved and idiosyncratic contacts to target RNA and crRNA among Type III-A systems. PLoS One. https://doi.org/10.1371/journal.pone.0287461.
Gogar, R., Carroll, F., Conte, J.V., Nasef, M., Dunkle, J.A. and Frantom, P.A. (2023) The β-latch structural element of the SufS cysteine desulfurase mediates active site accessibility and SufE transpersulfurase positioning. JBC. https://doi.org/10.1016/j.jbc.2023.102966
Gogar, R., Carroll, F., Conte, J.V., Nasef, M., Dunkle, J.A. and Frantom, P.A. (2023) The β-latch structural element of the SufS cysteine desulfurase mediates active site accessibility and SufE transpersulfurase positioning. JBC. https://doi.org/10.1016/j.jbc.2023.102966
2022
Nasef, M., Khweis, S.A. and Dunkle, J.A. (2022). The effect of crRNA–target mismatches on cOA-mediated interference by a type III-A CRISPR-Cas system. RNA Biology 19(1), 1293-1304. https://doi.org/10.1080/15476286.2022.2150812.
Sharkey, R.E., Herbert, J.B., McGaha, D.A., Nguyen, V., Schoeffler, A.J. and Dunkle, J.A. (2022). Three critical regions of the erythromycin resistance methyltransferase, ErmE, are required for function supporting a model for the interaction of Erm family enzymes with substrate rRNA. RNA 28(2), 210-226. Epub 2021/11/20. https://doi.org/10.1261/rna.078946.121.
Sharkey, R.E., Herbert, J.B., McGaha, D.A., Nguyen, V., Schoeffler, A.J. and Dunkle, J.A. (2022). Three critical regions of the erythromycin resistance methyltransferase, ErmE, are required for function supporting a model for the interaction of Erm family enzymes with substrate rRNA. RNA 28(2), 210-226. Epub 2021/11/20. https://doi.org/10.1261/rna.078946.121.
2020
Rowe, S. J., Mecaskey, R.J., Nasef, M., Talton, R.C., Sharkey, R.E., Halliday, J.C. and Dunkle, J.A. (2020). Shared requirements for key residues in the antibiotic resistance enzymes ErmC and ErmE suggest a common mode of RNA recognition. J Biol Chem 295(51) 17476-17485. doi.org/10.1074/jbc.RA120.014280.
Dunkle, J.A., Bruno, M.R. and Frantom, P.A. (2020) Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases. Acta Cryst. D 76, 291-301. https://doi.org/10.1107/S2059798320000790.
Dunkle, J.A., Bruno, M.R. and Frantom, P.A. (2020) Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases. Acta Cryst. D 76, 291-301. https://doi.org/10.1107/S2059798320000790.
2019
Blahut, M., Wise, C. E., Bruno, M. R., Dong, G., Makris, T. M., Frantom, P. A., Dunkle, J. A., and Outten, F. W. (2019) Direct observation of intermediates in the SufS cysteine desulfurase reaction reveals functional roles of conserved active-site residues. J Biol Chem 294(33), 12444-12458. Epub:2019/06/30 https://doi.org/10.1074/jbc.RA119.009471.
Nasef, M., Muffly, M. C., Beckman, A. B., Rowe, S. J., Walker, F. C., Hatoum-Aslan, A., and Dunkle, J. A. (2019) Regulation of cyclic oligoadenylate synthesis by the Staphylococcus epidermidis Cas10-Csm complex. RNA 25, 948-962. Epub 2019/05/12. https://doi.org/10.1261/rna.070417.119.
Dunkle, J.A., Bruno, M.R., Outten, F.W., and Frantom, P.A. (2019). Structural Evidence for Dimer-Interface-Driven Regulation of the Type II Cysteine Desulfurase, SufS. Biochemistry 58, 687-696. Epub 2018/12/21. https://doi.org/10.1021/acs.biochem.8b01122.
Nasef, M., Muffly, M. C., Beckman, A. B., Rowe, S. J., Walker, F. C., Hatoum-Aslan, A., and Dunkle, J. A. (2019) Regulation of cyclic oligoadenylate synthesis by the Staphylococcus epidermidis Cas10-Csm complex. RNA 25, 948-962. Epub 2019/05/12. https://doi.org/10.1261/rna.070417.119.
Dunkle, J.A., Bruno, M.R., Outten, F.W., and Frantom, P.A. (2019). Structural Evidence for Dimer-Interface-Driven Regulation of the Type II Cysteine Desulfurase, SufS. Biochemistry 58, 687-696. Epub 2018/12/21. https://doi.org/10.1021/acs.biochem.8b01122.
2018
Hong, S., Sunita, S., Maehigashi, T., Hoffer, E.D., Dunkle, J.A. and Dunham, C.M. (2018) Mechanism of tRNA-mediated +1 ribosomal frameshifting. Proc Natl Acad Sci U S A. 115(44):11226-11231. Epub 2018/09/29. https://doi.org/10.1073/pnas.1809319115.
2017
Walker, F.C., Chou-Zheng, L., Dunkle, J.A., and Hatoum-Aslan, A. (2017). Molecular determinants for CRISPR RNA maturation in the Cas10-Csm complex and roles for non-Cas nucleases. Nucleic Acids Res 45(4), 2112-2123. Epub 2017/02/17. https://doi.org/10.1093/nar/gkw891.
2015
Schureck, M.A., Dunkle, J.A., Maehigashi, T., Miles, S.J., and Dunham, C.M. (2015). Defining the mRNA recognition signature of a bacterial toxin protein. Proc Natl Acad Sci U S A 112, 13862-13867.
Dunkle, J.A., and Dunham, C.M. (2015). Mechanisms of mRNA frame maintenance and its subversion during translation of the genetic code. Biochimie 114, 90-96.
Dunkle, J.A., and Dunham, C.M. (2015). Mechanisms of mRNA frame maintenance and its subversion during translation of the genetic code. Biochimie 114, 90-96.
2014
Maehigashi, T., Dunkle, J.A., Miles, S.J., and Dunham, C.M. (2014). Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops. Proc Natl Acad Sci U S A 111, 12740-12745. Pubmed link
Fagan, C.E., Maehigashi, T., Dunkle, J.A., Miles, S.J., and Dunham, C.M. (2014). Structural insights into translational recoding by frameshift suppressor tRNASufJ. RNA 20, 1944-1954.
Dunkle, J.A., Vinal, K., Desai, P.M., Zelinskaya, N., Savic, M., West, D.M., Conn, G.L., and Dunham, C.M. (2014). Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA. Proc Natl Acad Sci U S A 111, 6275-6280.
Fagan, C.E., Maehigashi, T., Dunkle, J.A., Miles, S.J., and Dunham, C.M. (2014). Structural insights into translational recoding by frameshift suppressor tRNASufJ. RNA 20, 1944-1954.
Dunkle, J.A., Vinal, K., Desai, P.M., Zelinskaya, N., Savic, M., West, D.M., Conn, G.L., and Dunham, C.M. (2014). Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA. Proc Natl Acad Sci U S A 111, 6275-6280.
2013
Fagan, C.E., Dunkle, J.A., Maehigashi, T., Dang, M.N., Devaraj, A., Miles, S.J., Qin, D., Fredrick, K., and Dunham, C.M. (2013). Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state. Proc Natl Acad Sci U S A 110, 9716-9721.
Dunkle, J.A., and Cate, J.H. (2013). An Introduction to the Structure and Function of the Ribosome. EcoSal Plus 5.
Dunkle, J.A., and Cate, J.H. (2013). An Introduction to the Structure and Function of the Ribosome. EcoSal Plus 5.
2012
McGinnis, J.L., Dunkle, J.A., Cate, J.H., and Weeks, K.M. (2012). The mechanisms of RNA SHAPE chemistry. J Am Chem Soc 134, 6617-6624.
2011
Dunkle, J.A., Wang, L., Feldman, M.B., Pulk, A., Chen, V.B., Kapral, G.J., Noeske, J., Richardson, J.S., Blanchard, S.C., and Cate, J.H. (2011). Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science 332, 981-984.
2010
Llano-Sotelo, B., Dunkle, J., Klepacki, D., Zhang, W., Fernandes, P., Cate, J.H., and Mankin, A.S. (2010). Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis. Antimicrob Agents Chemother 54, 4961-4970.
Dunkle, J.A., Xiong, L., Mankin, A.S., and Cate, J.H. (2010). Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action. Proc Natl Acad Sci U S A 107, 17152-17157.
Dunkle, J.A., and Cate, J.H. (2010). Ribosome structure and dynamics during translocation and termination. Annu Rev Biophys 39, 227-244.
Dunkle, J.A., Xiong, L., Mankin, A.S., and Cate, J.H. (2010). Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action. Proc Natl Acad Sci U S A 107, 17152-17157.
Dunkle, J.A., and Cate, J.H. (2010). Ribosome structure and dynamics during translocation and termination. Annu Rev Biophys 39, 227-244.
2009
Zhang, W., Dunkle, J.A., and Cate, J.H. (2009). Structures of the ribosome in intermediate states of ratcheting. Science 325, 1014-1017.
