Joseph (Jody) Puglisi
Publications
- Coordinated conformational and compositional dynamics drive ribosome translocation. Nat Struct Mol Biol. 2013
- The impact of aminoglycosides on the dynamics of translation elongation. Cell Rep. 2013; (2): 497-508
- Digging deep into nucleic acid structure and nucleic acid protein recognition. Curr Opin Struct Biol. 2012; (3): 249-50
- Heterogeneous pathways and timing of factor departure during translation initiation. Nature. 2012; (7407): 390-3
- Initiation factor 2, tRNA, and 50S subunits cooperatively stabilize mRNAs on the ribosome during initiation. Proc Natl Acad Sci U S A. 2012; (13): 4881-5
- Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics. J Am Chem Soc. 2012; (13): 5734-7
- Precursor directed biosynthesis of an orthogonally functional erythromycin analogue: selectivity in the ribosome macrolide binding pocket. J Am Chem Soc. 2012; (29): 12259-65
- Single-molecule analysis of translational dynamics. Cold Spring Harb Perspect Biol. 2012; (9): a011551
- Unraveling the dynamics of ribosome translocation. Curr Opin Struct Biol. 2012; (6): 804-14
- Dynamics of the translational machinery. Curr Opin Struct Biol. 2011; (1): 137-45
- Secondary structure of the HIV reverse transcription initiation complex by NMR. J Mol Biol. 2011; (5): 863-74
- Following the intersubunit conformation of the ribosome during translation in real time. Nat Struct Mol Biol. 2010; (7): 793-800
- Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor. Nature. 2010; (7277): 108-12
- Nucleic acids continue to surprise. Curr Opin Struct Biol. 2010; (3): 259-61
- Real-time tRNA transit on single translating ribosomes at codon resolution. Nature. 2010; (7291): 1012-7
- Single ribosome dynamics and the mechanism of translation. Annu Rev Biophys. 2010: 491-513
- Site-specific labeling of Saccharomyces cerevisiae ribosomes for single-molecule manipulations. Nucleic Acids Res. 2010; (13): e143
- GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Mol Cell. 2009; (1): 37-47
- Improved Dye Stability in Single-molecule Fluorescence Experiments NATO ASI Science Series, Springer. 2009: 83-99
- Resolving the elegant architecture of the ribosome. Mol Cell. 2009; (5): 720-3
- The anti-hepatitis C agent nitazoxanide induces phosphorylation of eukaryotic initiation factor 2alpha via protein kinase activated by double-stranded RNA activation. Gastroenterology. 2009; (5): 1827-35
- Translational insensitivity to potent activation of PKR by HCV IRES RNA. Antiviral Res. 2009; (3): 228-37
- An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys J. 2008; (5): 1826-35
- Irreversible chemical steps control intersubunit dynamics during translation. Proc Natl Acad Sci U S A. 2008; (40): 15364-9
- Nucleic acids and their protein partners. Curr Opin Struct Biol. 2008; (3): 279-81
- Single-molecule imaging of full protein synthesis by immobilized ribosomes. Nucleic Acids Res. 2008; (12): e70
- Translation at the single-molecule level. Annu Rev Biochem. 2008: 177-203
- Biophysical and biochemical investigations of dsRNA-activated kinase PKR. Methods Enzymol. 2007: 373-96
- Fluctuations of transfer RNAs between classical and hybrid states. Biophys J. 2007; (10): 3575-82
- Molecular Insights Into PKR Activation by Viral Double-Stranded RNA NATO Science Series, Springer. 2007: 99-110
- Molecular framework for the activation of RNA-dependent protein kinase. J Biol Chem. 2007; (15): 11474-86
- NMR structural studies of aminoglycoside:RNA interaction Aminoglycoside Antibiotics, Edited by DP Arya, John Wiley & Sons. 2007: 181-207
- PKR: A NMR perspective JPNMRS. 2007; (3): 199-215
- Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome. Nature. 2007; (7134): 454-7
- Probing the conformation of human tRNA(3)(Lys) in solution by NMR. FEBS Lett. 2007; (27): 5307-14
- Purification and characterization of transcribed RNAs using gel filtration chromatography. Nat Protoc. 2007; (12): 3270-7
- Rapid purification of RNAs using fast performance liquid chromatography (FPLC). RNA. 2007; (2): 289-94
- Solution mapping of T cell receptor docking footprints on peptide-MHC. Proc Natl Acad Sci U S A. 2007; (32): 13080-5
- Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase. Protein Sci. 2007; (10): 2093-107
- Structural biology: the dance of domains. Nature. 2007; (7173): 1171-2
- The role of fluctuations in tRNA selection by the ribosome. Proc Natl Acad Sci U S A. 2007; (34): 13661-5
- Thiostrepton inhibition of tRNA delivery to the ribosome. RNA. 2007; (12): 2091-7
- Viral dsRNA inhibitors prevent self-association and autophosphorylation of PKR. J Mol Biol. 2007; (1): 103-13
- Specific recognition of HIV TAR RNA by the dsRNA binding domains (dsRBD1-dsRBD2) of PKR. J Mol Biol. 2006; (2): 430-42
- Uncoupling of RNA binding and PKR kinase activation by viral inhibitor RNAs. J Mol Biol. 2006; (5): 1270-85
- Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis. Biotechnol Bioeng. 2005; (4): 425-35
- Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Res. 2005; (1): 182-9
- Structure determination of large biological RNAs. Methods Enzymol. 2005: 399-416
- Using NMR to Study large RNAs: Case Study of the HCV IRES NATO ASI Science Series, Ios Press. 2005: 75-90
- Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides. RNA. 2004; (5): 889-93
- The pathway of HCV IRES-mediated translation initiation. Cell. 2004; (3): 369-80
- tRNA dynamics on the ribosome during translation. Proc Natl Acad Sci U S A. 2004; (35): 12893-8
- tRNA selection and kinetic proofreading in translation. Nat Struct Mol Biol. 2004; (10): 1008-14
- Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex. Structure. 2003; (1): 43-53
- Design of a cyclic peptide that targets a viral RNA. J Am Chem Soc. 2003; (51): 15704-5
- Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrier protein. Biochemistry. 2003; (16): 4648-57
- Structure of HCV IRES domain II determined by NMR. Nat Struct Biol. 2003; (12): 1033-8
- Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron. Biochemistry. 2003; (48): 14184-96
- NMR study of 100 kDa HCV IRES RNA using segmental isotope labeling. J Am Chem Soc. 2002; (32): 9338-9
- Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction. RNA. 2002; (7): 913-23
- Sequence-specific recognition of the major groove of RNA by deoxystreptamine. Biochemistry. 2002; (20): 6263-70
- Aminoglycoside resistance with homogeneous and heterogeneous populations of antibiotic-resistant ribosomes. Antimicrob Agents Chemother. 2001; (9): 2414-9
- RNAPack: an integrated NMR approach to RNA structure determination. Methods. 2001; (3): 316-32
- Solution structure of the A loop of 23S ribosomal RNA. Proc Natl Acad Sci U S A. 2001; (7): 3720-5
- Structural and functional investigation of the hepatitis C virus IRES. Nucleic Acids Res Suppl. 2001; (1): 263
- Structural origins of aminoglycoside specificity for prokaryotic ribosomes. J Mol Biol. 2001; (5): 1037-58
- Structure of a eukaryotic decoding region A-site RNA. J Mol Biol. 2001; (5): 1023-35
- Application of Residual Dipolar Coupling Measurements to Identify Conformational Changes in RNA Induced by Antibiotics J. Am. Chem. Soc. 2000: 7853-4
- Approaching translation at atomic resolution. Nat Struct Biol. 2000; (10): 855-61
- Biochemical and nuclear magnetic resonance studies of aminoglycoside-RNA complexes. Methods Enzymol. 2000: 240-61
- Interaction of translation initiation factor IF1 with the E. coli ribosomal A site. J Mol Biol. 2000; (1): 1-15
- Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function. Nat Struct Biol. 2000; (12): 1105-10
- mRNA processing: the 3'-end justifies the means. Nat Struct Biol. 2000; (4): 263-4
- Basis for prokaryotic specificity of action of aminoglycoside antibiotics. EMBO J. 1999; (11): 3133-8
- Effect of mutations in the A site of 16 S rRNA on aminoglycoside antibiotic-ribosome interaction. J Mol Biol. 1999; (1): 33-43
- RNA Interaction with Small Ligands and Peptides The RNA World, 2nd Ed.: The Nature of Modern RNA Suggests a Prebiotic RNA World. 1999: 403-425
- Recognition of the codon-anticodon helix by ribosomal RNA. Science. 1999; (5434): 1722-5
- Structural basis for aminoglycoside antibiotic action Ribosomes 1999. 1999: 419-29
- The ribosome revealed. Nat Struct Biol. 1999; (11): 999-1003
- Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNA. J Mol Biol. 1998; (2): 347-62
- HIV-1 A-rich RNA loop mimics the tRNA anticodon structure. Nat Struct Biol. 1998; (12): 1033-6
- NMR structure determination of an antibiotic-RNA complex NATO ASI Series. 1998: 173-82
- Nuclear magnetic resonance spectroscopy of RNA CSHL Press (In RNA Structure and Function, (Symons, R. W., and Grunberg-Manago, M., eds).. 1998: 117-46
- Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. J Mol Biol. 1998; (2): 333-45
- Structural origins of gentamicin antibiotic action. EMBO J. 1998; (22): 6437-48
- rRNA chemical groups required for aminoglycoside binding. Biochemistry. 1998; (21): 7716-24
- Structural basis for aminoglycoside antibiotic action Many Faces of RNA. 1997: 97-111
- Structure of a conserved RNA component of the peptidyl transferase centre. Nat Struct Biol. 1997; (10): 775-8
- RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide. J Mol Biol. 1996; (4): 421-36
- Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science. 1996; (5291): 1367-71
- Biochemical and NMR studies of RNA conformation with an emphasis on RNA pseudoknots. Methods Enzymol. 1995: 323-50
- Investigating the structure and function of translation initiation factor 1 in Escherichia coli. Nucleic Acids Symp Ser. 1995; (33): 170-1
- Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science. 1995; (5239): 1200-3
- Welcome guests to the RNA World: Proteins that interact with RNA Chemistry and Biology. 1995: 581
- NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end. Proc Natl Acad Sci U S A. 1994; (24): 11467-71
- Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA. EMBO J. 1993; (7): 2949-57
- Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase. Nucleic Acids Res. 1993; (1): 41-9
- Role of RNA structure in arginine recognition of TAR RNA. Proc Natl Acad Sci U S A. 1993; (8): 3680-4
- tRNA structure and aminoacylation efficiency. Prog Nucleic Acid Res Mol Biol. 1993: 129-206
- Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science. 1992; (5066): 76-80
- Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase. Proc Natl Acad Sci U S A. 1992; (13): 5882-6
- Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities. J Mol Biol. 1992; (2): 323-33
- Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. Nucleic Acids Res. 1992; (17): 4515-23
- Structure and Function of HIV TAR RNA Advances in Life Sciences, (In Structural Tools for the Analysis of Protein-Nucleic Acid Complexes, D Lilley, H Heumann, D Suck, ed.).. 1992: 269-85
- Identity elements for specific aminoacylation of yeast tRNA(Asp) by cognate aspartyl-tRNA synthetase. Science. 1991; (5013): 1696-9
- RNA Pseudoknots Accts Chem. Res. 1991; (24): 152-8
- Synthesis and purification of large amounts of RNA oligonucleotides. Biotechniques. 1991; (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). Biochimie. 1990 Jun-Jul; (6-7): 453-61
- Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides. Biochimie. 1990; (10): 735-43
- Conformation of an RNA pseudoknot. J Mol Biol. 1990; (2): 437-53
- RNA pseudoknots. Stability and loop size requirements. J Mol Biol. 1990; (2): 455-70
- Solution conformation of an RNA hairpin loop. Biochemistry. 1990; (17): 4215-26
- Absorbance melting curves of RNA. Methods Enzymol. 1989: 304-25
- Nucleic Acids from A to Z Blackwell Scientific Publications, Oxford (In Frontiers of Macromolecular Science, (T Saegusa, T Higashimura and A Abe, eds.).. 1989: 519-24
- RNA folding: pseudoknots, loops and bulges. Bioessays. 1989; (4): 100-6
- A pseudoknotted RNA oligonucleotide. Nature. 1988; (6153): 283-6
- Pseudoknotted RNA Oligonucleotides UCLA Symposia Series, Alan R Liss Inc, New York, NY (In Molecular Biology of RNA, T. Cech, ed.). 1988: 25-32
- RNA structure from A to Z. Cold Spring Harb Symp Quant Biol. 1987: 135-46
- Raman spectroscopic study of left-handed Z-RNA. Biochemistry. 1987; (26): 8624-30
- Stabilization of Z-RNA by chemical bromination and its recognition by anti-Z-DNA antibodies. Biochemistry. 1987; (16): 5191-9
- The Left-Handed Z-Form of Double-Stranded RNA Adenine Press, New York (In Biomolecular Stereodynamics, IV). 1986: 179-200
- Z-RNA: A Left-Handed Double Helix Plenum Press (In Structure and Dynamics of RNA). 1986: 55-68
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