Dunham Lab Publications

2019

Schureck MA, Meisner J, Hoffer ED, Onouha N, Ei Cho S, Lollar P and Dunham CM. (2019) Structural basis of transcriptional regulation by the HigA antitoxin. Molecular Microbiology 111(6):1449-62. PMCID: PMC6561789. [link to PDF] Cover image.

Nguyen HA, Hoffer ED and 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. [link to PDF]

Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscoding. Hoffer ED, Maehigashi T, Fredrick K, Dunham CM. (2019) Nucleic Acids Research  47(3): 1557-63. PMCID: PMC6379664. [link to PDF] Cover image.

2018

Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled Sensors. (2018) Rivera S, Young PG, Hoffer ED, Vansuch GE, Metzler CL, Dunham CM, Weinert EE. Inorganic Chemistry 19:57(22):14386-14395. PMID: 30378421. [link to PDF]

Hong S*, Sunita S*, Maehigashi T, Hoffer ED, Dunkle JA and Dunham CM. (2018) Mechanism of tRNA-mediated +1 ribosomal frameshifting. Proc Natl Acad Sci 115(44):11226-31. PMCID: PMC6217423. *These authors contributed equally. [link to PDF] This paper won the 2018 Cozzarelli Prize from the National Academy of Sciences for the Best Biological Science paper published in PNAS in 2018.

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.

Zhang Y*, Hong S*, Ruangprasert A, Skiniotis G and 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. [link to PDF]

2017

Nguyen HA and Dunham CM. (2017). Genome mining. Digging the tunnel for chemical space. Nature Chemical Biology 13(10): 1061-2. PMID: 289926552. [link to PDF]

Hoffer EA, Miles SJ and 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. [link to PDF] Cover image.

Ruangprasert A, Maehigashi T, Miles SJ and 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. [link to PDF]

2016

Pierson W*, Hoffer ED*, Keedy H, Simms C, Dunham CM# and Zaher H#. (2016). Uniformity of Peotide Release is Maintained by Methylation of Release Factors. Cell Reports 17(1):11-18. PMCID:  PMC5079439. *Co-first and #co-corresponding authors. [link to PDF]

Schureck MA, Repack A, Miles SJ, Marquez J and Dunham CM (2016). Mechanism of endonuclease cleavage by the HigB toxin. Nucleic Acids Research 44(16): 7944-53. PMCID: PMC5027501. [link to PDF].

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. [link to PDF].

2015

Schureck MA, Dunkle JA, Maehigashi T, Miles SJ and Dunham CM. (2015). Defining the mRNA recognition signature of a bacterial protein toxin. Proc Natl Acad Sci 112(45):13862-7. [link to PDF]. Link to LabLand: Emory Health Sciences Research Blog

Maehigashi T*, Ruangprasert A*, Miles SJ and 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. [link to PDF].

Cruz JW, Sharp JD, Hoffer ED, Maehigashi T, Vyedenskaya IO, Konkimalla A, Husson RN, Nickels BE, Dunham CM and Woychik NA (2015). Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase. Nature Communications. 6:7480-7489. PMCID: PMC4620994. [link to PDF].

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. [link to PDF].

2014

Fagan CE, Maehigashi T, Dunkle JA, Miles SJ and Dunham CM (2014). Structural insights into translational recoding by frameshift suppressor tRNASufJ. RNA. 20(12):1944-54.  PMCID: PMC4238358. [link to PDF]

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. [link to PDF]

Maehigashi T*, Dunkle JA*, Miles SJ and 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. [link to PDFLink to LabLand: Emory Health Sciences Research Blog

Ruangprasert A*, Maehigashi T*, Miles SJ, Giridharan N, Liu JX and 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. [link to PDF] *These authors contributed equally.

Schureck MA and Dunham CM (2014). Bacterial warfare again targets the ribosome. 22(5):661-2. Structure. PMID: 24807074. [link to PDF]

Dunkle JA, Vinnal K, Desai PM, Zelinskaya N, Savic M, West DM, Conn GL* and 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 PDF] 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. [link to PDF] *These authors contributed equally.

Schureck MA, Maehigashi T, Miles SJ, Marquez J, Ei Cho S, Erdman R and 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. [link to PDF]

2013

Fagan CE, Dunkle JA, Maehigashi T, Dang MN, Deveraj A, Miles SJ, Qin D, Fredrick K and 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. [link to PDF][link to PDF of commentary]

Jones BL, VanLoozen J, Kim MH, Miles SJ, Dunham CM, Williams LD and 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. [link to PDF]

2012

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. PMCID: PMC3325725. [link to PDF] *These authors contributed equally. #Co-corresponding authors

2009

Leung SW, Apponi LH, Cornejo OE, Kitchen CM, Valentini SR, Pavlath GK, Dunham CM, Corbett AH (2009). Splice variants of the human ZC3H14 gene generate multiple isoforms of a zinc finger polyadenosine RNA binding protein. Gene 439(1-2):71-8. PMCID: PMC2680464. [link to PDF]

Neubauer C*, Gao Y-G*,, Andersen KR*,, Dunham CM, Kelley AC, Hentschel J, Gerdes K Ramakrishnan V, and Brodersen DE (2009). The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE. Cell 139(6): 1084-1095. PMCID: PMC2807027. [link to PDF] *,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. [link to PDF]

2005-2007

Weixlbaumer A, Petry S*, Dunham CM*, Selmer M*, Kelley AC and Ramakrishnan V (2007). Crystal structure of the ribosome recycling factor bound to the ribosome. Nature Structural Molecular Biology 14(8): 733-7. PMID: 17660830. [link to PDF] *These authors contributed equally.

Dunham CM and Conn GL (2007). Recombinant RNA expression. Nature Methods 4(7):547-8. PMID: 17599081. [link to PDF]

Dunham CM*, Selmer M*, Phelps SS, Kelley AC, Suzuki T, Joseph S and 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. [link to PDF] *These authors contributed equally.

Selmer M*, Dunham CM*, Murphy IV FV, Weixlbaumer A, Petry S, Kelley AC, Weir J and Ramakrishnan V (2006). Structure of the 70S Ribosome Complexed with mRNA and tRNA. Science 313(5795):1935-42. PMID: 16959973. [link to PDF]. 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 and 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. [link to PDF]

2002-2003

Dunham CM, Murray JB, and 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. [link to PDF]

Dunham CM*, Dioum EM*, Tuckerman JR, Gonzalez G, Scott WG and 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. [link to PDF] *These authors contributed equally

Murray JB, Dunham CM and 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. [link to PDF]

Burns CS*, Aronoff-Spencer E*, Dunham CM*, Lario P, Avdievich NI, Antholine WE, Olmstead MM, Vrielink A, Gerfen GJ, Peisach J, Scott WG and 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. [link to PDF] *These authors contributed equally. 


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