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Publications

    • Gwangrog Lee, Matthew Bratkowski, Fang Ding
    • , Ailong
    •  Ke, Taekjip Ha*.
     
    Elastic coupling between RNA degradation and unwinding by Rrp44 nuclease. 
    Science. 2012 (Accepted)
     
  • Nam KH, 
  • Kurinov I, 
  • and Ke A*. 
Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca2+-dependent Double-stranded DNA-binding Activity. 
Journal of Biological Chemistry. 2011 Sep 2; 286: 30759-30768 [PubMed] [PDF]
 
Lu C, Smith AM, Ding F, Chowdhury A, Henkin TM, Ke A*. 
Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch. 
Journal of Molecular Biology. 2011 Jun 24;409(5):786-99.  [PubMed] [PDF]
 

 Ding F, Lu C, Zhao W, Rajashankar K, Anderson DL, Jardine PJ, Grimes S, Ke A*. 

Structure and Assembly of the Essential RNA Ring Component of a Viral DNA Packaging Motor. 

Proc Natl Acad Sci U S A. 2011 May 3;108(18):7357-62.  [PubMed] [PDF]

 

Ataide SF, Schmitz N, Shen K, Ke A, Shan SO, Doudna JA*, Ban N*. 
The Crystal Structure of the Signal Recognition Particle in Complex with its Receptor.
Science. 2011 Feb 18;331(6019):881-6.  [PubMed] [PDF]

 

Lu C, Chowdhury A, Ding F, Pradhan V, Tomsic J, Holmes WM, Henkin TM, Ke A*. 
SAM Recognition and Conformational Switching Mechanism in the Bacillus subtilis yitJ SAM-I/S box riboswitch. 
Journal of Molecular Biology. 2010 Dec 17;404(5):803-18.  [PubMed] [PDF]

Perez-Rodriguez R, Huang Q, Wu X, Ding F, Bernardis S, Ke A*, and DeLisa MP*. 
Envelope stress is a trigger of CRISPR-mediated gene silencing in prokaryotes.
Molecular Microbiology. 2011 Feb;79(3):584-99.  [PubMed] [PDF]

Lu C, Ding F, Ke A*.
Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.
PLOS One. 2010 Jan 15;5(1):e8739.  [PubMed] [PDF]

Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ke A*.
Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism.
Nature Structural & Molecular Biology. 2008 May;15:1076-1083. [PubMed] [PDF]

Wang HW*, Wang J, Ding F, Callahan K, Bratkowski MA, Butler JS, Nogales E, Ke A*.
Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing.
Proc Natl Acad Sci U S A. 2007 Oct 23;104:16844-16849. [PubMed] [PDF]

Ke A, Ding F, Batchelor JD, Doudna JA.
Structural roles of monovalent cations in the HDV ribozyme.
Structure. 2007 Mar;15(3):281-7.
[PubMed] [PDF]

Wu S, Ke A, Doudna JA.
A fast and efficient procedure to produce scFvs specific for large macromolecular complexes.
J. Immunol Methods. 2007 Jan 10;318(1-2):95-101. [PubMed] [PDF]

Spanggord RJ, Siu F, Ke A, Doudna JA.
RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle.
Nature Structural & Molecular Biology. 2005 Dec;12(12):1116-22. [PubMed] [PDF]

Ke A, Doudna JA.
Catalytic strategies of self-cleaving ribozymes: Relics of an RNA world?
The RNA World, 3rd Edition. 2005 (Book chapter). The RNA World, 3rd Edition

Ke A, Doudna JA.
Crystallization of RNA and RNA-protein complexes.
Methods. 2004 Nov;34(3):408-14. [PubMed] [PDF]

Ke A, Zhou K, Ding F, Cate JH, Doudna JA.
A conformational switch controls hepatitis delta virus ribozyme catalysis.
Nature. 2004 May 13;429(6988):201-5. [PubMed] [PDF]

Ke A, Wolberger C.
Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera.
Protein Sci. 2003 Feb;12(2):306-12. [PubMed] [PDF]

Ke A, Mathias JR, Vershon AK, Wolberger C.
Structural and thermodynamic characterization of the DNA binding properties of a triple alanine mutant of MATalpha2.
Structure. 2002 Jul;10(7):961-71. [PubMed] [PDF]