Joseph (Jody) Puglisi

Administrative Appointments

• Chair, University Committee on Postdoctoral Affairs, Stanford University , (2008– 2009 )
• Chair, Provost's Advisory Board for Postdoctoral Affairs, Stanford University , (2005– 2008 )
• Chair, Dept of Structural Biology, Stanford University School of Medicine , (2004– present )
• Director, Int'l School of Biological Magnetic Resonance, EMFCSC, Erice, Italy , (2003– present )
• Senior Editor, Structure , (2003– 2007 )
• Member, NIH BBCA Study Section , (2003– 2007 )
• Chair, Postdoctoral Affairs Committee, Stanford University School of Medicine , (2002– 2005 )
• Member, Postdoctoral Affairs Committee, Stanford University School of Medicine , (2001– 2002 )
• Associate Chair, Dept of Structural Biology, Stanford University School of Medicine , (1998– 2004 )
• Director, Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine , (1998– present )

Honors and Awards

• Alfred P. Sloan Research Fellow, Alfred P. Sloan Research Foundation (1997)
• David and Lucille Packard Fellow, David and Lucille Packard Fellowship in Science and Engineering (1994-99)
• Teacher Scholar, Camille and Henry Dreyfus Teacher Scholar Award (1993)

Professional Education

• Ph.D., Univ of California, Berkeley Biophysical Chemistry (1989)
• B.A., The Johns Hopkins University Chemistry (1984)

Postdoctoral Advisees

• Alexey Nikolayevich Petrov, Sotaro Uemura, Tinghe Wu

Graduate & Fellowship Program Affiliations

• Biophysics
• Microbiology and Immunology
• Chemical and Systems Biology
• Structural Biology
• Bioengineering

Community & International Work

• NMR Summer School, Erice-Sicily, Italy More »

Web Site Links

• Puglisi Lab Homepage

Industry Relationships

Stanford is committed to ethical and transparent interactions with our industry partners. It is our policy to disclose payments of $5,000 or more, equity valued at $5,000 or more in a publicly traded company, or any equity in a privately held company, to physicians and scientists employed by Stanford University from companies or other commercial entities with which they interact as part of their professional activities. 

• Consulting: 3V Biosciences, PTC Therapeutics, Pacific Biosciences
• Equity: 3V Biosciences, PTC Therapeutics, Pacific Biosciences

Current Research Interests

The Puglisi group investigates the role of RNA in cellular processes and disease. Our goal is to understand RNA function in terms of molecular structure and dynamics using a variety of biophysical and biological tools. We use nuclear magnetic resonance (NMR) spectroscopy to determine structures of biological molecules, and integrate structural understanding into further mechanistic and functional studies. We investigate dynamics using single-molecule approaches. Our goal is a unified picture of structure, dynamics and function. We are currently focused on the mechanism and regulation of translation, and the role of RNA in viral infections. A long-term goal is to target processes involving RNA with novel therapeutic strategies.

Publications

• Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor. Bokoch MP,  Zou Y, Rasmussen SG, Liu CW, Nygaard R, Rosenbaum DM, Fung JJ, Choi HJ, Thian FS, Kobilka TS, Puglisi JD, Weis WI, Pardo L, Prosser RS, Mueller L, Kobilka BK.  Nature.  2010; 463 (7277): 108-12
• Resolving the elegant architecture of the ribosome. Puglisi JD,  Mol Cell.  2009; 36 (5): 720-3
• Translational insensitivity to potent activation of PKR by HCV IRES RNA. Shimoike T,  McKenna SA, Lindhout DA, Puglisi JD.  Antiviral Res.  2009; 83 (3): 228-37
• GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Marshall RA,  Aitken CE, Puglisi JD.  Mol Cell.  2009; 35 (1): 37-47
• The anti-hepatitis C agent nitazoxanide induces phosphorylation of eukaryotic initiation factor 2alpha via protein kinase activated by double-stranded RNA activation. Elazar M,  Liu M, McKenna SA, Liu P, Gehrig EA, Puglisi JD, Rossignol JF, Glenn JS.  Gastroenterology.  2009; 137 (5): 1827-35
• Irreversible chemical steps control intersubunit dynamics during translation. Marshall RA,  Dorywalska M, Puglisi JD.  Proc Natl Acad Sci U S A.  2008; 105 (40): 15364-9
• An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Aitken CE,  Marshall RA, Puglisi JD.  Biophys J.  2008; 94 (5): 1826-35
• Nucleic acids and their protein partners. Puglisi JD,  Doudna JA.  Curr Opin Struct Biol.  2008; 18 (3): 279-81
• Single-molecule imaging of full protein synthesis by immobilized ribosomes. Uemura S,  Iizuka R, Ueno T, Shimizu Y, Taguchi H, Ueda T, Puglisi JD, Funatsu T.  Nucleic Acids Res.  2008; 36 (12): e70
• Translation at the single-molecule level. Marshall RA,  Aitken CE, Dorywalska M, Puglisi JD.  Annu Rev Biochem.  2008; 77 177-203
• Fluctuations of transfer RNAs between classical and hybrid states. Kim HD,  Puglisi JD, Chu S.  Biophys J.  2007; 93 (10): 3575-82
• Structural biology: the dance of domains. Puglisi JD,  Nature.  2007; 450 (7173): 1171-2
• Biophysical and biochemical investigations of dsRNA-activated kinase PKR. McKenna SA,  Lindhout DA, Shimoike T, Puglisi JD.  Methods Enzymol.  2007; 430 373-96
• Purification and characterization of transcribed RNAs using gel filtration chromatography. McKenna SA,  Kim I, Puglisi EV, Lindhout DA, Aitken CE, Marshall RA, Puglisi JD.  Nat Protoc.  2007; 2 (12): 3270-7
• Probing the conformation of human tRNA(3)(Lys) in solution by NMR. Puglisi EV,  Puglisi JD.  FEBS Lett.  2007; 581 (27): 5307-14
• Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase. Alekseyev VY,  Liu CW, Cane DE, Puglisi JD, Khosla C.  Protein Sci.  2007; 16 (10): 2093-107
• The role of fluctuations in tRNA selection by the ribosome. Lee TH,  Blanchard SC, Kim HD, Puglisi JD, Chu S.  Proc Natl Acad Sci U S A.  2007; 104 (34): 13661-5
• Solution mapping of T cell receptor docking footprints on peptide-MHC. Varani L,  Bankovich AJ, Liu CW, Colf LA, Jones LL, Kranz DM, Puglisi JD, Garcia KC.  Proc Natl Acad Sci U S A.  2007; 104 (32): 13080-5
• Viral dsRNA inhibitors prevent self-association and autophosphorylation of PKR. McKenna SA,  Lindhout DA, Shimoike T, Aitken CE, Puglisi JD.  J Mol Biol.  2007; 372 (1): 103-13
• Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome. Uemura S,  Dorywalska M, Lee TH, Kim HD, Puglisi JD, Chu S.  Nature.  2007; 446 (7134): 454-7
• Molecular framework for the activation of RNA-dependent protein kinase. McKenna SA,  Lindhout DA, Kim I, Liu CW, Gelev VM, Wagner G, Puglisi JD.  J Biol Chem.  2007; 282 (15): 11474-86
• Rapid purification of RNAs using fast performance liquid chromatography (FPLC). Kim I,  McKenna SA, Viani Puglisi E, Puglisi JD.  RNA.  2007; 13 (2): 289-94
• Thiostrepton inhibition of tRNA delivery to the ribosome. Gonzalez RL,  Chu S, Puglisi JD.  RNA.  2007; 13 (12): 2091-7
• Specific recognition of HIV TAR RNA by the dsRNA binding domains (dsRBD1-dsRBD2) of PKR. Kim I,  Liu CW, Puglisi JD.  J Mol Biol.  2006; 358 (2): 430-42
• Uncoupling of RNA binding and PKR kinase activation by viral inhibitor RNAs. McKenna SA,  Kim I, Liu CW, Puglisi JD.  J Mol Biol.  2006; 358 (5): 1270-85
• Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis. Underwood KA,  Swartz JR, Puglisi JD.  Biotechnol Bioeng.  2005; 91 (4): 425-35
• Site-specific labeling of the ribosome for single-molecule spectroscopy. Dorywalska M,  Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD.  Nucleic Acids Res.  2005; 33 (1): 182-9
• Structure determination of large biological RNAs. Lukavsky PJ,  Puglisi JD.  Methods Enzymol.  2005; 394 399-416
• tRNA dynamics on the ribosome during translation. Blanchard SC,  Kim HD, Gonzalez RL, Puglisi JD, Chu S.  Proc Natl Acad Sci U S A.  2004; 101 (35): 12893-8
• Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides. Lukavsky PJ,  Puglisi JD.  RNA.  2004; 10 (5): 889-93
• tRNA selection and kinetic proofreading in translation. Blanchard SC,  Gonzalez RL, Kim HD, Chu S, Puglisi JD.  Nat Struct Mol Biol.  2004; 11 (10): 1008-14
• The pathway of HCV IRES-mediated translation initiation. Otto GA,  Puglisi JD.  Cell.  2004; 119 (3): 369-80
• Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex. Lynch SR,  Gonzalez RL, Puglisi JD.  Structure.  2003; 11 (1): 43-53
• Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron. Schroeder SJ,  Fountain MA, Kennedy SD, Lukavsky PJ, Puglisi JD, Krugh TR, Turner DH.  Biochemistry.  2003; 42 (48): 14184-96
• Design of a cyclic peptide that targets a viral RNA. Runyon ST,  Puglisi JD.  J Am Chem Soc.  2003; 125 (51): 15704-5
• Structure of HCV IRES domain II determined by NMR. Lukavsky PJ,  Kim I, Otto GA, Puglisi JD.  Nat Struct Biol.  2003; 10 (12): 1033-8
• Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrier protein. Li Q,  Khosla C, Puglisi JD, Liu CW.  Biochemistry.  2003; 42 (16): 4648-57
• NMR study of 100 kDa HCV IRES RNA using segmental isotope labeling. Kim I,  Lukavsky PJ, Puglisi JD.  J Am Chem Soc.  2002; 124 (32): 9338-9
• Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction. Otto GA,  Lukavsky PJ, Lancaster AM, Sarnow P, Puglisi JD.  RNA.  2002; 8 (7): 913-23
• Sequence-specific recognition of the major groove of RNA by deoxystreptamine. Yoshizawa S,  Fourmy D, Eason RG, Puglisi JD.  Biochemistry.  2002; 41 (20): 6263-70
• Structure of a eukaryotic decoding region A-site RNA. Lynch SR,  Puglisi JD.  J Mol Biol.  2001; 306 (5): 1023-35
• Structural and functional investigation of the hepatitis C virus IRES. Puglisi JD,  Kim I, Lukavsky P, Otto G, Lancaster A, Sarnow P.  Nucleic Acids Res Suppl.  2001; (1): 263
• Solution structure of the A loop of 23S ribosomal RNA. Blanchard SC,  Puglisi JD.  Proc Natl Acad Sci U S A.  2001; 98 (7): 3720-5
• Aminoglycoside resistance with homogeneous and heterogeneous populations of antibiotic-resistant ribosomes. Recht MI,  Puglisi JD.  Antimicrob Agents Chemother.  2001; 45 (9): 2414-9
• RNAPack: an integrated NMR approach to RNA structure determination. Lukavsky PJ,  Puglisi JD.  Methods.  2001; 25 (3): 316-32
• Structural origins of aminoglycoside specificity for prokaryotic ribosomes. Lynch SR,  Puglisi JD.  J Mol Biol.  2001; 306 (5): 1037-58
• Biochemical and nuclear magnetic resonance studies of aminoglycoside-RNA complexes. Lynch SR,  Recht MI, Puglisi JD.  Methods Enzymol.  2000; 317 240-61
• mRNA processing: the 3'-end justifies the means. Puglisi JD,  Nat Struct Biol.  2000; 7 (4): 263-4
• Interaction of translation initiation factor IF1 with the E. coli ribosomal A site. Dahlquist KD,  Puglisi JD.  J Mol Biol.  2000; 299 (1): 1-15
• Approaching translation at atomic resolution. Puglisi JD,  Blanchard SC, Green R.  Nat Struct Biol.  2000; 7 (10): 855-61
• Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function. Lukavsky PJ,  Otto GA, Lancaster AM, Sarnow P, Puglisi JD.  Nat Struct Biol.  2000; 7 (12): 1105-10
• The ribosome revealed. Green R,  Puglisi JD.  Nat Struct Biol.  1999; 6 (11): 999-1003
• Effect of mutations in the A site of 16 S rRNA on aminoglycoside antibiotic-ribosome interaction. Recht MI,  Douthwaite S, Dahlquist KD, Puglisi JD.  J Mol Biol.  1999; 286 (1): 33-43
• Recognition of the codon-anticodon helix by ribosomal RNA. Yoshizawa S,  Fourmy D, Puglisi JD.  Science.  1999; 285 (5434): 1722-5
• Basis for prokaryotic specificity of action of aminoglycoside antibiotics. Recht MI,  Douthwaite S, Puglisi JD.  EMBO J.  1999; 18 (11): 3133-8
• Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNA. Fourmy D,  Recht MI, Puglisi JD.  J Mol Biol.  1998; 277 (2): 347-62
• rRNA chemical groups required for aminoglycoside binding. Blanchard SC,  Fourmy D, Eason RG, Puglisi JD.  Biochemistry.  1998; 37 (21): 7716-24
• Structural origins of gentamicin antibiotic action. Yoshizawa S,  Fourmy D, Puglisi JD.  EMBO J.  1998; 17 (22): 6437-48
• HIV-1 A-rich RNA loop mimics the tRNA anticodon structure. Puglisi EV,  Puglisi JD.  Nat Struct Biol.  1998; 5 (12): 1033-6
• Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. Fourmy D,  Yoshizawa S, Puglisi JD.  J Mol Biol.  1998; 277 (2): 333-45
• Structure of a conserved RNA component of the peptidyl transferase centre. Puglisi EV,  Green R, Noller HF, Puglisi JD.  Nat Struct Biol.  1997; 4 (10): 775-8
• Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Fourmy D,  Recht MI, Blanchard SC, Puglisi JD.  Science.  1996; 274 (5291): 1367-71
• RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide. Recht MI,  Fourmy D, Blanchard SC, Dahlquist KD, Puglisi JD.  J Mol Biol.  1996; 262 (4): 421-36
• Investigating the structure and function of translation initiation factor 1 in Escherichia coli. Dahlquist K,  Puglisi JD.  Nucleic Acids Symp Ser.  1995; (33): 170-1
• Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Puglisi JD,  Chen L, Blanchard S, Frankel AD.  Science.  1995; 270 (5239): 1200-3
• Biochemical and NMR studies of RNA conformation with an emphasis on RNA pseudoknots. Puglisi JD,  Wyatt JR.  Methods Enzymol.  1995; 261 323-50
• NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end. Puglisi EV,  Puglisi JD, Williamson JR, RajBhandary UL.  Proc Natl Acad Sci U S A.  1994; 91 (24): 11467-71
• Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA. Pütz J,  Puglisi JD, Florentz C, Giegé R.  EMBO J.  1993; 12 (7): 2949-57
• Role of RNA structure in arginine recognition of TAR RNA. Puglisi JD,  Chen L, Frankel AD, Williamson JR.  Proc Natl Acad Sci U S A.  1993; 90 (8): 3680-4
• Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase. Puglisi JD,  Pütz J, Florentz C, Giegé R.  Nucleic Acids Res.  1993; 21 (1): 41-9
• tRNA structure and aminoacylation efficiency. Giegé R,  Puglisi JD, Florentz C.  Prog Nucleic Acid Res Mol Biol.  1993; 45 129-206
• Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities. Perret V,  Florentz C, Puglisi JD, Giegé R.  J Mol Biol.  1992; 226 (2): 323-33
• Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. Batey RT,  Inada M, Kujawinski E, Puglisi JD, Williamson JR.  Nucleic Acids Res.  1992; 20 (17): 4515-23
• Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Puglisi JD,  Tan R, Calnan BJ, Frankel AD, Williamson JR.  Science.  1992; 257 (5066): 76-80
• Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase. Rudinger J,  Puglisi JD, Pütz J, Schatz D, Eckstein F, Florentz C, Giegé R.  Proc Natl Acad Sci U S A.  1992; 89 (13): 5882-6
• Identity elements for specific aminoacylation of yeast tRNA(Asp) by cognate aspartyl-tRNA synthetase. Pütz J,  Puglisi JD, Florentz C, Giegé R.  Science.  1991; 252 (5013): 1696-9
• Synthesis and purification of large amounts of RNA oligonucleotides. Wyatt JR,  Chastain M, Puglisi JD.  Biotechniques.  1991; 11 (6): 764-9
• Exploring the aminoacylation function of transfer RNA by macromolecular engineering approaches. Involvement of conformational features in the charging process of yeast tRNA(Asp). Giegé R,  Florentz C, Garcia A, Grosjean H, Perret V, Puglisi J, Théobald-Dietrich A, Ebel JP.  Biochimie.  1990 Jun-Jul; 72 (6-7): 453-61
• Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides. Perret V,  Garcia A, Puglisi J, Grosjean H, Ebel JP, Florentz C, Giegé R.  Biochimie.  1990; 72 (10): 735-43
• RNA pseudoknots. Stability and loop size requirements. Wyatt JR,  Puglisi JD, Tinoco I.  J Mol Biol.  1990; 214 (2): 455-70
• Conformation of an RNA pseudoknot. Puglisi JD,  Wyatt JR, Tinoco I.  J Mol Biol.  1990; 214 (2): 437-53
• Solution conformation of an RNA hairpin loop. Puglisi JD,  Wyatt JR, Tinoco I.  Biochemistry.  1990; 29 (17): 4215-26
• RNA folding: pseudoknots, loops and bulges. Wyatt JR,  Puglisi JD, Tinoco I.  Bioessays.  1989; 11 (4): 100-6
• Absorbance melting curves of RNA. Puglisi JD,  Tinoco I.  Methods Enzymol.  1989; 180 304-25
• A pseudoknotted RNA oligonucleotide. Puglisi JD,  Wyatt JR, Tinoco I.  Nature.  1988; 331 (6153): 283-6
• Stabilization of Z-RNA by chemical bromination and its recognition by anti-Z-DNA antibodies. Hardin CC,  Zarling DA, Puglisi JD, Trulson MO, Davis PW, Tinoco I.  Biochemistry.  1987; 26 (16): 5191-9
• RNA structure from A to Z. Tinoco I,  Davis PW, Hardin CC, Puglisi JD, Walker GT, Wyatt J.  Cold Spring Harb Symp Quant Biol.  1987; 52 135-46
• Raman spectroscopic study of left-handed Z-RNA. Trulson MO,  Cruz P, Puglisi JD, Tinoco I, Mathies RA.  Biochemistry.  1987; 26 (26): 8624-30