2024
Mattingly JM, Nguyen HA, Roy B, Fredrick K, Dunham CM (2024) Structural basis of noncanonical initiation complexes, Journal of Biological Chemistry, Aug 31:107743. doi: 10.1016/j.jbc.2024. 107743. PMID: 39222680
Monroe J, Eyler DE, Mitchell L, Deb I, Bojanowski A, Srinivas P, Dunham CM, Roy B, Frank AT, Koutmou KS (2024) N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation. Nature Communications 5(1):8119. PMID: 39284850
2023
Marathe N*, Nguyen HA*, Alumasa JN, Kuzmishin Nagy AB, VazquezM, Dunham CM#, Keiler KC# (2023) Antibiotic that inhibits trans-translation blocks binding of EF-Tu to tmRNA but not to tRNA. mBio. e0146123. doi: 10.1128/mbio.01461-23. bioRxiv: doi: 10.1101/2023.06.09.544387. *co-first authors, #co-corresponding authors
Srinivas P, Nosrati M, Zelinskaya N, Dey D, Comstock LR, Dunham CM#, Conn GL# (2023) 30S subunit recognition and G1405 modification by the aminoglycoside-resistance 16S ribosomal RNA methyltransferase RmtC. Proc Natl Acad Sci. 120(25):e2304128120. PMID: 37307464. #co-corresponding author
bioRxiv. doi: 10.1101/2023.03.13. 532395. PMID: 36993224.
Nguyen HA, Hoffer ED, Maehigashi T, Fagan CE, Dunham CM (2023) Structural basis for reduced ribosomal A-site fidelity in response to P-site codon-anticodon mismatches. Journal of Biological Chemistry, 299(4):104608. PMCID: PMC10140155.
bioRxiv. doi: 10.1101/2023.01.28.526049. PMID: 36747737
Hassan A, Byju S, Freitas FC, Roc C, Pender N, Nguyen K, Kimbrough EM, Mattingly J, Gonzalez Jr. RL, Oliveira RJ, Dunham CM, Whitford PC (2023) Ratchet, swivel, tilt and roll: A complete description of subunit rotation in the ribosome. Nucleic Acids Research. 51(2):919-934. PMCID: PMC9881166.
2022
Srinivas P, Keiler K, Dunham CM (2022) Druggable differences: Targeting mechanistic differences between trans-translation and translation for selection antibiotic action. BioEssays. 44(8):e2200046, PMCID: PMC9308750.
Laughlin ZT, Dey D, Zelinskaya N, Witek MA, Srinivas P, Nguyen HA, Kuiper EG, Comstock LR, Dunham CM, Conn GL (2022) 50S subunit recognition and modification by the Mycobacterium tuberculosis ribosomal RNA methyltransferase TlyA. Proc Natl Acad Sci. 119(14):e2120352119. PMCID: PMC9168844.
2021
Dai W, Darst SA, Dunham CM, Landick R, Petsko G, Weixlbaumer A (2021) Seeing gene expression in cells: the future of structural biology. Faculty Reviews. 10:(79). (commentary)
Mattingly JM and Dunham CM (2021) ESKAPE Velocity: Total Synthesis Platforms Promise to Increase the Pace and Diversity of Antibiotic Development. Nature Structure & Molecular Biology. Epub doi: 10.1038/s41594-021-00708-0. PMID: 34961787. (preview)
Aron ZD*, Mehrani A*, Hoffer ED*, Connolly KL, Torhan MC, Alumasa JN, Srinivas P, Cabrera M, Hosangadi D, Barbor JS, Cardinale S, Kwasny S, Butler M, Opperman T, Bowlin T, Jerse A, Stagg SM, Dunham CM#, Keiler KC# (2021) Ribosome rescue inhibitors clear Neisseria gonorrhoeae in vivo using a new mechanism. Nature Communications. 12(1):1799. PMCID: PMC7979765. *co-first authors, #co-corresponding authors.
Srinivas P, Steiner RE, Pavelich IJ, Guerrero-Ferreira R, Juneja P, Ibba M, Dunham CM (2021) Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy. Nucleic Acids Research. 49(20):11800-11809. PMCID: PMC8599791.
2020
Hoffer ED, Hong S, Sunita S, Whitford P, Gonzalez RL Jr, Dunham CM (2020) Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing. eLife. 9:e51898. doi: 10.7554/eLife.51898. PMCID: PMC7577736.
Nguyen HA, Sunita S, Dunham CM (2020) Disruption of evolutionarily conserved tRNA elements impairs accurate decoding. Proc Natl Acad Sci. 117(28):16333–38. PMCID: PMC7368331.
2019
Nosrati M, Dey D, Mehrani A, Strassler SE, Zelinskaya N, Hoffer ED, Stagg SM, Dunham CM, Conn GL (2019) Functionally critical residues in the aminoglycoside resistance-associated methyltransferase RmtC play distinct roles in 30S substrate recognition. Journal of Biological Chemistry 294(46):17642-53. PMCID: PMC6873201.
Pavelich IJ, Maehigashi T, Ruangprasert A, Hoffer ED, Miles SJ, Dunham CM (2019) Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability. Nucleic Acids Research 47(19):10400-13. PMCID: PMC6821326.
Schureck MA, Meisner J, Hoffer ED, Onouha N, Ei Cho S, Lollar P, Dunham CM (2019) Structural basis of transcriptional regulation by the HigA antitoxin. Molecular Microbiology 111(6):1449-62. PMCID: PMC6561789. Cover image.
Nguyen HA, Hoffer ED, Dunham CM (2019) Importance of tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNAProCGG for decoding. Journal of Biological Chemistry 294(14):5281-91. PMCID: PMC6462517. Selected as the Editor’s Pick, an honor bestowed on the top 2% of papers published in JBC.
Hoffer ED, Maehigashi T, Fredrick K, Dunham CM (2019) Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscoding. Nucleic Acids Research 47(3):1557-63. PMCID: PMC6379664. Cover image.
2018
Hong S*, Sunita S*, Maehigashi T, Hoffer ED, Dunkle JA, Dunham CM (2018) Mechanism of tRNA-mediated +1 ribosomal frameshifting. Proc Natl Acad Sci 115(44):11226-31. PMCID: PMC6217423. *These authors contributed equally.
Commentary by JF Atkins. Culmination of a half-century quest reveals insight into mutant tRNA-mediated frameshifting after tRNA departure from the decoding center. Proc Natl Acad Sci 115(44):11221-23. PMCID: PMC6217412.
Winner of the 2018 Cozzarelli Prize from the National Academy of Sciences for the Best Biological Science paper published in PNAS
Rivera S, Young PG, Hoffer ED, Vansuch GE, Metzler CL, Dunham CM, Weinert EE. (2018) Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled Sensors. Inorganic Chemistry 19:57(22):14386-14395. PMID: 30378421.
Zhang Y*, Hong S*, Ruangprasert A, Skiniotis G, Dunham CM. (2018) Alternative modes of E-site tRNA binding in the presence of structured mRNAs at the mRNA entrance channel. Structure. 26(3):437-445. PMCID: PMC5842130.
2017
Nguyen HA, Dunham CM (2017) Genome mining. Digging the tunnel for chemical space. Nature Chemical Biology 13(10): 1061-2. PMID: 289926552.
Hoffer EA, Miles SJ, Dunham CM (2017) The structure and function of Mycobacterium tuberculosis MazF-mt6 provides insights into conserved features of MazF endonucleases. Journal of Biological Chemistry 292(19):7718-26. PMCID: PMC5427253. Cover image.
Ruangprasert A, Maehigashi T, Miles SJ, Dunham CM (2017) Importance of the E. coli DinJ antitoxin carboxy terminus for toxin suppression and regulated proteolysis. Molecular Microbiology 104(1):65-77. PMID: 28164393.
2016
Pierson W*, Hoffer ED*, Keedy H, Simms C, Dunham CM#, Zaher H#. (2016) Uniformity of Peptide Release is Maintained by Methylation of Release Factors. Cell Reports 17(1):11-18. PMCID: PMC5079439. *Co-first and #co-corresponding authors.
Schureck MA, Repack A, Miles SJ, Marquez J, Dunham CM (2016) Mechanism of endonuclease cleavage by the HigB toxin. Nucleic Acids Research 44(16): 7944-53. PMCID: PMC5027501.
Schureck MA, Maehigashi T, Miles SJ, Marquez J and Dunham CM (2016) mRNA bound to the 30S subunit is a HigB endonuclease substrate. RNA 22(8):1261-70. PMCID: PMC4931118.
2015
Schureck MA, Dunkle JA, Maehigashi T, Miles SJ, Dunham CM (2015) Defining the mRNA recognition signature of a bacterial protein toxin. Proc Natl Acad Sci 112(45):13862-7. Link to LabLand: Emory Health Sciences Research Blog
Maehigashi T*, Ruangprasert A*, Miles SJ, Dunham CM (2015) Molecular basis of ribosome regulation and mRNA hydrolysis by the E. coli YafQ toxin. Nucleic Acids Research 43(16):8002-12. PMID: 26261214. *These authors contributed equally.
Cruz JW, Sharp JD, Hoffer ED, Maehigashi T, Vyedenskaya IO, Konkimalla A, Husson RN, Nickels BE, Dunham CM, Woychik NA (2015) Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase. Nature Communications. 6:7480-7489. PMCID: PMC4620994.
Dunkle JA, Dunham CM (2015) Mechanisms of mRNA frame maintenance and its subversion during translation of the genetic code. Biochimie 114:90-6. PMCID: PMC4458409.
2014
Fagan CE, Maehigashi T, Dunkle JA, Miles SJ, Dunham CM (2014) Structural insights into translational recoding by frameshift suppressor tRNASufJ. RNA. 20(12):1944-54. PMCID: PMC4238358.
Washington AZ, Benicewicz DB, Canzoneri JC, Fagan CE, Mwakwari SC, Maehigashi T, Dunham CM*, Oyelere AK* (2014) Macrolide-peptide conjugates as probes of the path of travel of the nascent peptides through the ribosome. ACS Chemical Biology 9(11):2621-31. PMCID: PMC4245169. *These authors contributed equally.
Maehigashi T*, Dunkle JA*, Miles SJ, Dunham CM (2014) Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem-loops. Proc Natl Acad Sci, 111(35):12740-5. PMCID: PMC4156745. *These authors contributed equally.
Featured in LabLand: Emory Health Sciences Research
Ruangprasert A*, Maehigashi T*, Miles SJ, Giridharan N, Liu JX, Dunham CM (2014) Mechanisms of toxin inhibition and transcriptional repression by E. coli DinJ-YafQ. Journal of Biological Chemistry, 289(30):20559-69. PMCID: PMC4110269. *These authors contributed equally.
Schureck MA, Dunham CM (2014) Bacterial warfare again targets the ribosome. 22(5):661-2. Structure. PMID: 24807074.
Dunkle JA, Vinnal K, Desai PM, Zelinskaya N, Savic M, West DM, Conn GL*, Dunham CM* (2014) Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA. Proc Natl Acad Sci, 111(17):6275-80. PMCID: PMC4035980. Link to LabLand: Emory Health Sciences Research Blog *Co-corresponding authors.
Cruz JW*, Rothenbacher FP*, Maehigashi T, Lane WS, Dunham CM, Woychik NA (2014) Doc toxin is a kinase that inactivates elongation factor Tu. Journal of Biological Chemistry 289(11):7788-98. PMCID: PMC3953291. *These authors contributed equally.
Schureck MA, Maehigashi T, Miles SJ, Marquez J, Ei Cho S, Erdman R, Dunham CM (2014) Structure of the P. vulgaris HigB-(HigA)2-HigB toxin-antitoxin complex. Journal of Biological Chemistry, 289(2):1060-70. PMCID: PMC3887174.
2012-2013
Fagan CE, Dunkle JA, Maehigashi T, Dang MN, Deveraj A, Miles SJ, Qin D, Fredrick K, Dunham CM (2013) Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state. Proc Natl Acad Sci 110(24):9716-21. PMCID: PMC3683721.
Jones BL, VanLoozen J, Kim MH, Miles SJ, Dunham CM, Williams LD, Snell TW (2013) Stress granules form in Brachionus manjavacas (Rotifera) in response to a variety of stressors. Comp Biochem Physiol A Mol Integr Physiol. 166(2):375-84. PMID: 23856158.
Meisner J*, Maehigashi T*, André I, Dunham CM#, Moran CP Jr#. (2012). Structure of the basal components of a bacterial transporter. Proc Natl Acad Sci 109(14):5446-51.*These authors contributed equally. #Co-corresponding authors
Postdoctoral Work
Neubauer C*, Gao Y-G*,, Andersen KR*,, Dunham CM, Kelley AC, Hentschel J, Gerdes K Ramakrishnan V, Brodersen DE (2009) The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE. Cell 139(6): 1084-1095. PMCID: PMC2807027. *These authors contributed equally.
Gao Y-G, Selmer M, Dunham CM, Weixlbaumer A, Kelley AC, Ramakrishnan V (2009) The Structure of the Ribosome with Elongation Factor G Trapped in the Posttranslocational State. Science 326(5953): 694-99. PMCID: PMC3763468.
Weixlbaumer A, Petry S*, Dunham CM*, Selmer M*, Kelley AC, Ramakrishnan V (2007) Crystal structure of the ribosome recycling factor bound to the ribosome. Nature Structural Molecular Biology 14(8): 733-7. PMID: 17660830. *These authors contributed equally.
Dunham CM and Conn GL (2007) Recombinant RNA expression. Nature Methods 4(7):547-8. PMID: 17599081.
Dunham CM*, Selmer M*, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V (2007) Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit. RNA 13(6):817-23. PMCID: PMC1869038. *These authors contributed equally.
Selmer M*, Dunham CM*, Murphy IV FV, Weixlbaumer A, Petry S, Kelley AC, Weir J, Ramakrishnan V (2006) Structure of the 70S Ribosome Complexed with mRNA and tRNA. Science 313(5795):1935-42. PMID: 16959973.
Highlighted in the ‘News and Views’ section, Nature Structural & Molecular Biology, 13:864. *These authors contributed equally.
Petry S, Broderson DE, Murphy IV FV, Dunham CM, Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V (2005) Crystal structures of release factors RF1 and RF2 bound to a programmed ribosome with a cognate stop codon. Cell 123(7):1255-66. PMID: 16377566.
PhD Research
Dunham CM, Murray JB, Scott WG (2003) A Helical Twist-Induced Conformational Switch Activates Cleavage in the Hammerhead Ribozyme. Journal of Molecular Biology, 332(2):327-36. PMID: 12948485.
Dunham CM*, Dioum EM*, Tuckerman JR, Gonzalez G, Scott WG, Gilles-Gonzalez M-A (2003) A distal arginine in oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure. Biochemistry, 42(25):7701-7708. PMID:12820879. *These authors contributed equally
Murray JB, Dunham CM, Scott WG (2002) A pH-Dependent Conformational Change, Rather than the Chemical Step, Appears to be Rate-Limiting in the Hammerhead Ribozyme Cleavage Reaction. Journal of Molecular Biology, 315(2):121-130. PMID: 11779233.
Burns CS*, Aronoff-Spencer E*, Dunham CM*, Lario P, Avdievich NI, Antholine WE, Olmstead MM, Vrielink A, Gerfen GJ, Peisach J, Scott WG, Millhauser GL (2002) Molecular Features of the Copper Binding Sites in the Octarepeat Domain of the Prion Protein. Biochemistry, 41(12):3991-4001. PMID: 11900542. *These authors contributed equally.