Simpson Joseph

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc After the ribosome structure: how does translocation work?
    Simpson Joseph
    Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    RNA 9:160-4. 2003
  2. pmc Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis
    Xinying Shi
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 0314, USA
    J Mol Biol 419:125-38. 2012
  3. pmc Steric complementarity in the decoding center is important for tRNA selection by the ribosome
    Prashant K Khade
    Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    J Mol Biol 425:3778-89. 2013
  4. pmc Polyamines accelerate codon recognition by transfer RNAs on the ribosome
    Byron Hetrick
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0314, USA
    Biochemistry 49:7179-89. 2010
  5. pmc Histidine 197 in release factor 1 is essential for a site binding and peptide release
    Andrew Field
    Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    Biochemistry 49:9385-90. 2010
  6. doi request reprint Highly conserved base A55 of 16S ribosomal RNA is important for the elongation cycle of protein synthesis
    Bhubanananda Sahu
    Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093 0314, United States
    Biochemistry 52:6695-701. 2013
  7. doi request reprint Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation
    Lucia Garcia-Ortega
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    Mol Cell 32:292-9. 2008
  8. ncbi request reprint A conserved base-pair between tRNA and 23 S rRNA in the peptidyl transferase center is important for peptide release
    Jason S Feinberg
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 0314, USA
    J Mol Biol 364:1010-20. 2006
  9. pmc Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding
    Lucia Garcia-Ortega
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
    Nucleic Acids Res 38:4108-19. 2010
  10. ncbi request reprint Translocation of a tRNA with an extended anticodon through the ribosome
    Steven S Phelps
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0314, USA
    J Mol Biol 360:610-22. 2006

Research Grants

  1. Molecular Mechanism of Translation
    Simpson Joseph; Fiscal Year: 2010
  2. Molecular Role of 16S Ribosomal RNA in Translocation
    Simpson Joseph; Fiscal Year: 2006
  3. Molecular Mechanism of Translation
    Simpson Joseph; Fiscal Year: 2009

Collaborators

  • Satoko Yoshizawa
  • Paul F Agris
  • Chang Shung Tung
  • Harry F Noller
  • KEVIN SANBONMATSU
  • VENKATRAMAN RAMAKRISHNAN
  • Prashant K Khade
  • Steven S Phelps
  • Byron Hetrick
  • Xinying Shi
  • Sean M Studer
  • Bhubanananda Sahu
  • Jason S Feinberg
  • Lucia Garcia-Ortega
  • Srikanta Ghosh
  • Vera Alverdi
  • Prashant Khade
  • Andrew Field
  • Kristin Lee
  • Jenise Stephen
  • Christine M Dunham
  • Tsutomu Suzuki
  • Iraj K Ali
  • Taeko Komoda
  • Elizabeth A Komives
  • Elisa Alvarez-García
  • Jose G Gavilanes
  • Merrill Mathew
  • Alex Thomas
  • Alvaro Martínez-del-Pozo
  • Katie Chiu
  • Maria Selmer
  • Ann C Kelley
  • Jason Feinberg
  • Cesar Benitez
  • Cyril Gaudin
  • Neuza S Sato
  • Dominique Fourmy
  • Naoki Namba
  • Laura Lancaster
  • Andrzej Malkiewicz
  • Olga Jerinic

Detail Information

Publications29

  1. pmc After the ribosome structure: how does translocation work?
    Simpson Joseph
    Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    RNA 9:160-4. 2003
    ..Translocation of the tRNA-mRNA complex is one of the most fascinating tasks performed by the ribosome. The impact of the crystal structures in understanding the molecular mechanism of translocation is highlighted in this review...
  2. pmc Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis
    Xinying Shi
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 0314, USA
    J Mol Biol 419:125-38. 2012
    ..The SRL also is not essential for peptide bond formation. Our results, instead, suggest that the SRL is crucial for anchoring EF-G on the ribosome during mRNA-tRNA translocation...
  3. pmc Steric complementarity in the decoding center is important for tRNA selection by the ribosome
    Prashant K Khade
    Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    J Mol Biol 425:3778-89. 2013
    ..These results suggest that steric complementarity in the decoding center is more important than the hydrogen bonds between the A site codon and G530, A1492 and A1493 for tRNA selection. ..
  4. pmc Polyamines accelerate codon recognition by transfer RNAs on the ribosome
    Byron Hetrick
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0314, USA
    Biochemistry 49:7179-89. 2010
    ..Polyamines may accelerate codon recognition by altering the structure and dynamics of the anticodon arm of the aminoacyl-tRNA...
  5. pmc Histidine 197 in release factor 1 is essential for a site binding and peptide release
    Andrew Field
    Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    Biochemistry 49:9385-90. 2010
    ..The rate of peptidyl-tRNA hydrolysis was also reduced significantly, more than the binding data would suggest, implying a defect in the orientation of the GGQ domain without the histidine residue...
  6. doi request reprint Highly conserved base A55 of 16S ribosomal RNA is important for the elongation cycle of protein synthesis
    Bhubanananda Sahu
    Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093 0314, United States
    Biochemistry 52:6695-701. 2013
    ..These results indicate that A55 is important for fine-tuning the activity of the ribosome during the elongation cycle of protein synthesis...
  7. doi request reprint Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation
    Lucia Garcia-Ortega
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    Mol Cell 32:292-9. 2008
    ....
  8. ncbi request reprint A conserved base-pair between tRNA and 23 S rRNA in the peptidyl transferase center is important for peptide release
    Jason S Feinberg
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 0314, USA
    J Mol Biol 364:1010-20. 2006
    ....
  9. pmc Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding
    Lucia Garcia-Ortega
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
    Nucleic Acids Res 38:4108-19. 2010
    ..These results suggest that the SRL is more critical in EF-G than ternary complex binding to the ribosome implicating different requirements in this region of the ribosome during protein elongation...
  10. ncbi request reprint Translocation of a tRNA with an extended anticodon through the ribosome
    Steven S Phelps
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0314, USA
    J Mol Biol 360:610-22. 2006
    ..Flexibility within the loop may allow conformational adjustment upon A site binding and for interacting with the four nucleotide codon in order to shift the mRNA reading frame...
  11. ncbi request reprint Non-bridging phosphate oxygen atoms within the tRNA anticodon stem-loop are essential for ribosomal A site binding and translocation
    Steven S Phelps
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0314, USA
    J Mol Biol 349:288-301. 2005
    ..Our results correlate with structural data, indicating that position 34 interacts with the highly conserved 16S rRNA base G966 and position 36 interacts with the universally conserved tRNA base U33 during translocation to the P site...
  12. ncbi request reprint Unfolding of mRNA secondary structure by the bacterial translation initiation complex
    Sean M Studer
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    Mol Cell 22:105-15. 2006
    ..We show that unfolding of structured mRNAs requires a SD sequence, the start codon, fMet-tRNA(fMet), and the GTP bound form of initiation factor 2 bound to the 30S subunit...
  13. pmc Nonbridging phosphate oxygens in 16S rRNA important for 30S subunit assembly and association with the 50S ribosomal subunit
    Srikanta Ghosh
    4102 Urey Hall, Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    RNA 11:657-67. 2005
    ..Interestingly, however, several of the phosphate oxygens identified in this study do not participate in any interaction in the mature 30S subunit, suggesting that they play a role in the early steps of the 30S subunit assembly...
  14. pmc Bases in 16S rRNA important for subunit association, tRNA binding, and translocation
    Xinying Shi
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0314, USA
    Biochemistry 48:6772-82. 2009
    ..These results show that conserved bases located as far as 100 A from the tRNA binding sites can be important for translation...
  15. ncbi request reprint Rapid kinetic analysis of EF-G-dependent mRNA translocation in the ribosome
    Sean M Studer
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla 92093 0314, USA
    J Mol Biol 327:369-81. 2003
    ....
  16. doi request reprint Messenger RNA interactions in the decoding center control the rate of translocation
    Prashant K Khade
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
    Nat Struct Mol Biol 18:1300-2. 2011
    ..These results provide insight into the molecular mechanism of translocation...
  17. pmc Kinetics of stop codon recognition by release factor 1
    Byron Hetrick
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0314, USA
    Biochemistry 48:11178-84. 2009
    ..These results suggest that sense codons inhibit conformational changes necessary for RF1 to stably bind to the ribosome and catalyze peptide release...
  18. pmc Functional replacement of two highly conserved tetraloops in the bacterial ribosome
    Bhubanananda Sahu
    Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    Biochemistry 51:7618-26. 2012
    ..Our results suggest that the tetraloops in helices 8 and 14 are highly conserved mainly for their structural stability and the precise sequences of these tetraloops are not critical for protein synthesis...
  19. ncbi request reprint Binding of mRNA to the bacterial translation initiation complex
    Sean M Studer
    Department of Chemistry and Biochemistry, University of California, San Diego, USA
    Methods Enzymol 430:31-44. 2007
    ..These methods are important for quantitatively analyzing the effects of mRNA secondary structure and the role of the initiation factors in recruitment of mRNA by the bacterial initiation complex...
  20. pmc Functional interactions by transfer RNAs in the ribosome
    Prashant Khade
    Department of Chemistry and Biochemistry, University of California, 4102 Urey Hall, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, United States
    FEBS Lett 584:420-6. 2010
    ..Both high-resolution structures and functional studies are essential for fully appreciating the complex process of protein synthesis...
  21. pmc Ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of P-site tRNA are not essential for EF-G catalyzed translocation
    Jason S Feinberg
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0314, USA
    RNA 12:580-8. 2006
    ..This suggests that either these 2'-hydroxyl groups are not important for translocation or they are redundant and the three-dimensional shape of the P-site tRNA is more important for translocation...
  22. ncbi request reprint Modified nucleotides in tRNA(Lys) and tRNA(Val) are important for translocation
    Steven S Phelps
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0314, USA
    J Mol Biol 338:439-44. 2004
    ..Thus, naturally occurring modifications in tRNA contribute functional groups and conformational dynamics that are critical for accurate decoding of mRNA and for translocation to the P site during protein synthesis...
  23. ncbi request reprint Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation
    Steven S Phelps
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Mol Cell 10:799-807. 2002
    ..Furthermore, these interactions are also essential for the decoding process, indicating a functional relationship between decoding and translocation...
  24. doi request reprint Direct observation of a transient ternary complex during IκBα-mediated dissociation of NF-κB from DNA
    Vera Alverdi
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92092 0378
    Proc Natl Acad Sci U S A 111:225-30. 2014
    ..This mutant associates with NF-κB more rapidly than wild-type IκBα, but it associates with the NF-κB-DNA complex more slowly and also is less efficient at mediating dissociation of the NF-κB-DNA complex. ..
  25. pmc Simulating movement of tRNA into the ribosome during decoding
    Kevin Y Sanbonmatsu
    Department of Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Proc Natl Acad Sci U S A 102:15854-9. 2005
    ..This study serves as a template for simulating conformational changes in large (>10(6) atoms) biological and artificial molecular machines...
  26. pmc Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit
    Christine M Dunham
    MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom
    RNA 13:817-23. 2007
    ..Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center...
  27. ncbi request reprint Deletion of a conserved, central ribosomal intersubunit RNA bridge
    Iraj K Ali
    Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Mol Cell 23:865-74. 2006
    ..However, Deltah69 50S subunits are unable to associate with 30S subunits in the absence of tRNA, are defective in RF1-catalyzed peptide release, and can be recycled in the absence of RRF...
  28. ncbi request reprint The A-site finger in 23 S rRNA acts as a functional attenuator for translocation
    Taeko Komoda
    Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 8656, Japan
    J Biol Chem 281:32303-9. 2006
    ....
  29. ncbi request reprint All-atom homology model of the Escherichia coli 30S ribosomal subunit
    Chang Shung Tung
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Nat Struct Biol 9:750-5. 2002
    ..The hypervariable regions in our structure, which differ from the structure of the 30S ribosomal subunit from Thermus thermophilus, are consistent with the cryo-EM map of the E. coli ribosome...

Research Grants10

  1. Molecular Mechanism of Translation
    Simpson Joseph; Fiscal Year: 2010
    ..Furthermore, this proposal will have a broad impact on fields such as RNA catalysis, origin of life, RNA structure and function, mechanism of eukaryotic protein synthesis, cancer, and neuroscience. ..
  2. Molecular Role of 16S Ribosomal RNA in Translocation
    Simpson Joseph; Fiscal Year: 2006
    ..Understanding the mechanism of translocation will provide insights for developing more effective antibiotics that target the ribosome of these drug-resistant strains of bacteria. ..
  3. Molecular Mechanism of Translation
    Simpson Joseph; Fiscal Year: 2009
    ..Furthermore, this proposal will have a broad impact on fields such as RNA catalysis, origin of life, RNA structure and function, mechanism of eukaryotic protein synthesis, cancer, and neuroscience. ..