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Puglisi Group Research at the SMRL

Joseph D. Puglisi

Professor, Department of Structural Biology
Director, Stanford Magnetic Resonance Laboratory
(650) 498-4397
puglisi@stanford.edu

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Publications:

Lukavsky, PJ; Kim, I; Otto, GA; Puglisi, JD (2003) "Structure of HCV IRES domain II determined by NMR" Nature Struct. Biol., Advance Online Publication PDF PDF

Li, Q; Khosla, C; Puglisi, JD; Liu, CW (2003) "Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrier protein" BIOCHEMISTRY, 42 4648-4657. PDF PDF

Lynch, SR; Gonzalez, RL; Puglisi, JD (2003) "Comparison of x-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex" STRUCTURE, 11 43-53. PDF

Kim, I., Lukavsky, P.J., and Puglisi, J.D. (2002) "NMR Study of 100 kDa HCV IRES RNA Using Segmental Isotope Labeling" J. Am. Chem. Soc., 124, 9338-39. PDF PDF

Lukavsky P.J., Puglisi J.D. (2001) "RNAPack: An integrated NMR approach to RNA structure determination" Methods, 25, 316-332.

Blanchard, S.C., and Puglisi, J.D. (2001) "Solution structure of the A loop of 23S ribosomal RNA. Solution structure of the A loop of 23S ribosomal RNA." PNAS, 98, 3720-21. PDF

Lynch S.R., Puglisi J.D. (2001) "Structural origins of aminoglycoside specificity for prokaryotic ribosomes" J. Mol. Biol., 306, 1037-1058. PDF

Lynch S.R., Puglisi J.D. (2001) "Structure of a eukaryotic decoding region A-site RNA" J. Mol. Biol., 306, 1023-1035. PDF

(Details Below) Lukavsky, P.J., Otto, G.A., Lancaster, A.M., Sarnow P. and Puglisi, J.D. (2000) "Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function" Nature Struct. Biol., 7, 1105-1110. PDF

Lynch, SR; Puglisi, JD (2000) "Application of residual dipolar coupling measurements to identify conformational changes in RNA induced by antibiotics" JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 122 7853-7854. PDF PDF



Details:

Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function

Lukavsky, P.J., Otto, G.A., Lancaster, A.M., Sarnow P. and Puglisi, J.D. (2000) Nature Struct. Biol. 7, 1105-1110. PDF

Abstract: Translation of the hepatitis C virus (HCV) polyprotein is initiated at an internal ribosome entry site (IRES) element in the 5' untranslated region of HCV RNA. The HCV IRES element interacts directly with the 40S subunit, and biochemical experiments have implicated RNA elements near the AUG start codon as required for IRES–40S subunit complex formation. The data we present here show that two RNA stem loops, domains IIId and IIIe, are involved in IRES–40S subunit interaction. The structures of the two RNA domains were solved by NMR spectroscopy and reveal structural features that may explain their role in IRES function.

Figure Caption. Structure of HCV domain IIId stem loop. (Left) Heavy-atom superposition of final 25 structures of HCV IRES domain IIId. Bases are colored in blue and ribose-phosphate backbone in gray. (Right) Single representative structure of the HCV IRES domain IIId, with both S turns high-lighted. Ribose O4' atoms are shown in red, the inverted riboses in blue and the phosphate backbone in yellow.
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