Simpson Joseph

InstitutionUniversity of California San Diego
DepartmentChemistry and Biochemistry
Address9500 Gilman Drive #0314
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    Interaction of Influenza A virus NS1 protein with PABP1 and eIF4G
    NIH/NIAID R03AI123873Dec 1, 2016 - Nov 30, 2018
    Role: Principal Investigator
    Translational Control by the Fragile X Mental Retardation Protein
    NIH/NIGMS R01GM114261Jan 1, 2016 - Nov 30, 2019
    Role: Principal Investigator
    Molecular Mechanism of Translation
    NIH/NIGMS R01GM065265Apr 1, 2002 - May 31, 2013
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Hoernes TP, Faserl K, Juen MA, Kremser J, Gasser C, Fuchs E, Shi X, Siewert A, Lindner H, Kreutz C, Micura R, Joseph S, Höbartner C, Westhof E, Hüttenhofer A, Erlacher MD. Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions. Nat Commun. 2018 Nov 19; 9(1):4865. PMID: 30451861.
      View in: PubMed
    2. Arias-Mireles BH, de Rozieres CM, Ly K, Joseph S. RNA Modulates the Interaction between Influenza A Virus NS1 and Human PABP1. Biochemistry. 2018 May 25. PMID: 29782795.
      View in: PubMed
    3. Shi X, Wu T, M Cole C, K Devaraj N, Joseph S. Optimization of ClpXP activity and protein synthesis in an E. coli extract-based cell-free expression system. Sci Rep. 2018 Feb 22; 8(1):3488. PMID: 29472573.
      View in: PubMed
    4. Hoernes TP, Clementi N, Juen MA, Shi X, Faserl K, Willi J, Gasser C, Kreutz C, Joseph S, Lindner H, Hüttenhofer A, Erlacher MD. Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release. Proc Natl Acad Sci U S A. 2018 Jan 16; 115(3):E382-E389. PMID: 29298914.
      View in: PubMed
    5. Katz FEH, Shi X, Owens CP, Joseph S, Tezcan FA. Determination of nucleoside triphosphatase activities from measurement of true inorganic phosphate in the presence of labile phosphate compounds. Anal Biochem. 2017 03 01; 520:62-67. PMID: 28017740.
      View in: PubMed
    6. Shi X, Joseph S. Mechanism of Translation Termination: RF1 Dissociation Follows Dissociation of RF3 from the Ribosome. Biochemistry. 2016 Nov 15; 55(45):6344-6354. PMID: 27779391.
      View in: PubMed
    7. Shi X, Joseph S. Translocation: lights, camera, and action. Nat Struct Mol Biol. 2016 05 04; 23(5):367-8. PMID: 27142323.
      View in: PubMed
    8. Trappl K, Joseph S. Ribosome Induces a Closed to Open Conformational Change in Release Factor 1. J Mol Biol. 2016 Mar 27; 428(6):1333-1344. PMID: 26827724.
      View in: PubMed
    9. Chen E, Joseph S. Fragile X mental retardation protein: A paradigm for translational control by RNA-binding proteins. Biochimie. 2015 Jul; 114:147-54. PMID: 25701550; PMCID: PMC4458461.
    10. Joseph S. Modification interference analysis of the ribosome. Methods Mol Biol. 2015; 1240:113-23. PMID: 25352140.
      View in: PubMed
    11. Chen E, Sharma MR, Shi X, Agrawal RK, Joseph S. Fragile X mental retardation protein regulates translation by binding directly to the ribosome. Mol Cell. 2014 May 08; 54(3):407-417. PMID: 24746697; PMCID: PMC4019695.
    12. Trappl K, Mathew MA, Joseph S. Thermodynamic and kinetic insights into stop codon recognition by release factor 1. PLoS One. 2014; 9(4):e94058. PMID: 24699820; PMCID: PMC3974865.
    13. Alverdi V, Hetrick B, Joseph S, Komives EA. Direct observation of a transient ternary complex during I?Ba-mediated dissociation of NF-?B from DNA. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):225-30. PMID: 24367071; PMCID: PMC3890772.
    14. Sahu B, Khade PK, Joseph S. Highly conserved base A55 of 16S ribosomal RNA is important for the elongation cycle of protein synthesis. Biochemistry. 2013 Sep 24; 52(38):6695-701. PMID: 24025161.
      View in: PubMed
    15. Khade PK, Shi X, Joseph S. Steric complementarity in the decoding center is important for tRNA selection by the ribosome. J Mol Biol. 2013 Oct 23; 425(20):3778-89. PMID: 23542008; PMCID: PMC3744617.
    16. Sahu B, Khade PK, Joseph S. Functional replacement of two highly conserved tetraloops in the bacterial ribosome. Biochemistry. 2012 Sep 25; 51(38):7618-26. PMID: 22938718; PMCID: PMC3786584.
    17. Shi X, Khade PK, Sanbonmatsu KY, Joseph S. Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis. J Mol Biol. 2012 Jun 08; 419(3-4):125-38. PMID: 22459262; PMCID: PMC3348345.
    18. Khade PK, Joseph S. Messenger RNA interactions in the decoding center control the rate of translocation. Nat Struct Mol Biol. 2011 Oct 23; 18(11):1300-2. PMID: 22020300.
      View in: PubMed
    19. Field A, Hetrick B, Mathew M, Joseph S. Histidine 197 in release factor 1 is essential for a site binding and peptide release. Biochemistry. 2010 Nov 02; 49(43):9385-90. PMID: 20873815; PMCID: PMC2967428.
    20. Hetrick B, Khade PK, Lee K, Stephen J, Thomas A, Joseph S. Polyamines accelerate codon recognition by transfer RNAs on the ribosome. Biochemistry. 2010 Aug 24; 49(33):7179-89. PMID: 20666453; PMCID: PMC2952548.
    21. García-Ortega L, Alvarez-García E, Gavilanes JG, Martínez-del-Pozo A, Joseph S. Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding. Nucleic Acids Res. 2010 Jul; 38(12):4108-19. PMID: 20215430; PMCID: PMC2896532.
    22. Khade P, Joseph S. Functional interactions by transfer RNAs in the ribosome. FEBS Lett. 2010 Jan 21; 584(2):420-6. PMID: 19914248; PMCID: PMC2795042.
    23. Hetrick B, Lee K, Joseph S. Kinetics of stop codon recognition by release factor 1. Biochemistry. 2009 Dec 01; 48(47):11178-84. PMID: 19874047; PMCID: PMC2789991.
    24. Shi X, Chiu K, Ghosh S, Joseph S. Bases in 16S rRNA important for subunit association, tRNA binding, and translocation. Biochemistry. 2009 Jul 28; 48(29):6772-82. PMID: 19545171; PMCID: PMC2782751.
    25. Garcia-Ortega L, Stephen J, Joseph S. Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation. Mol Cell. 2008 Oct 24; 32(2):292-9. PMID: 18951096.
      View in: PubMed
    26. Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V. Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit. RNA. 2007 Jun; 13(6):817-23. PMID: 17416634; PMCID: PMC1869038.
    27. Studer SM, Joseph S. Binding of mRNA to the bacterial translation initiation complex. Methods Enzymol. 2007; 430:31-44. PMID: 17913633.
      View in: PubMed
    28. Feinberg JS, Joseph S. A conserved base-pair between tRNA and 23 S rRNA in the peptidyl transferase center is important for peptide release. J Mol Biol. 2006 Dec 15; 364(5):1010-20. PMID: 17045291.
      View in: PubMed
    29. Ali IK, Lancaster L, Feinberg J, Joseph S, Noller HF. Deletion of a conserved, central ribosomal intersubunit RNA bridge. Mol Cell. 2006 Sep 15; 23(6):865-74. PMID: 16973438.
      View in: PubMed
    30. Komoda T, Sato NS, Phelps SS, Namba N, Joseph S, Suzuki T. The A-site finger in 23 S rRNA acts as a functional attenuator for translocation. J Biol Chem. 2006 Oct 27; 281(43):32303-9. PMID: 16950778.
      View in: PubMed
    31. Phelps SS, Gaudin C, Yoshizawa S, Benitez C, Fourmy D, Joseph S. Translocation of a tRNA with an extended anticodon through the ribosome. J Mol Biol. 2006 Jul 14; 360(3):610-22. PMID: 16787653.
      View in: PubMed
    32. Studer SM, Joseph S. Unfolding of mRNA secondary structure by the bacterial translation initiation complex. Mol Cell. 2006 Apr 07; 22(1):105-15. PMID: 16600874.
      View in: PubMed
    33. Feinberg JS, Joseph S. Ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of P-site tRNA are not essential for EF-G catalyzed translocation. RNA. 2006 Apr; 12(4):580-8. PMID: 16489185; PMCID: PMC1421097.
    34. Sanbonmatsu KY, Joseph S, Tung CS. Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A. 2005 Nov 01; 102(44):15854-9. PMID: 16249344; PMCID: PMC1266076.
    35. Phelps SS, Joseph S. Non-bridging phosphate oxygen atoms within the tRNA anticodon stem-loop are essential for ribosomal A site binding and translocation. J Mol Biol. 2005 Jun 03; 349(2):288-301. PMID: 15890196.
      View in: PubMed
    36. Ghosh S, Joseph S. Nonbridging phosphate oxygens in 16S rRNA important for 30S subunit assembly and association with the 50S ribosomal subunit. RNA. 2005 May; 11(5):657-67. PMID: 15811917; PMCID: PMC1370752.
    37. Phelps SS, Malkiewicz A, Agris PF, Joseph S. Modified nucleotides in tRNA(Lys) and tRNA(Val) are important for translocation. J Mol Biol. 2004 Apr 30; 338(3):439-44. PMID: 15081802.
      View in: PubMed
    38. Studer SM, Feinberg JS, Joseph S. Rapid kinetic analysis of EF-G-dependent mRNA translocation in the ribosome. J Mol Biol. 2003 Mar 21; 327(2):369-81. PMID: 12628244.
      View in: PubMed
    39. Joseph S. After the ribosome structure: how does translocation work? RNA. 2003 Feb; 9(2):160-4. PMID: 12554856; PMCID: PMC1370379.
    40. Tung CS, Joseph S, Sanbonmatsu KY. All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nat Struct Biol. 2002 Oct; 9(10):750-5. PMID: 12244297.
      View in: PubMed
    41. Phelps SS, Jerinic O, Joseph S. Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation. Mol Cell. 2002 Oct; 10(4):799-807. PMID: 12419224.
      View in: PubMed
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