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Simpson Joseph - Publications

Affiliations: 
Chemistry University of California, San Diego, La Jolla, CA 
Area:
Molecular Mechanism of Protein Synthesis
Website:
https://www-chem.ucsd.edu/faculty/profiles/joseph_simpson.html
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62 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Cruz A, Joseph S. Interaction of the Influenza A Virus NS1 Protein with the 5'-m7G-mRNA·eIF4E·eIF4G1 Complex. Biochemistry. PMID 35797022 DOI: 10.1021/acs.biochem.2c00019  0.306
2022 Edwards M, Huang M, Joseph S. The Fragile X Protein Disordered Regions Bind a Novel RNA Target. Biochemistry. 61: 1199-1212. PMID 35653700 DOI: 10.1021/acs.biochem.2c00228  0.344
2021 Edwards M, Joseph S. The Fragile X Proteins Differentially Regulate Translation of Reporter mRNAs with G-quadruplex Structures. Journal of Molecular Biology. 434: 167396. PMID 34896112 DOI: 10.1016/j.jmb.2021.167396  0.417
2020 de Rozières CM, Joseph S. Influenza A Virus NS1 Protein Binds as a Dimer to RNA-Free PABP1 but Not to the PABP1·Poly(A) RNA Complex. Biochemistry. PMID 33172261 DOI: 10.1021/acs.biochem.0c00666  0.376
2020 Athar YM, Joseph S. The Human Fragile X Mental Retardation Protein Inhibits the Elongation Step of Translation through its RGG and C-terminal domains. Biochemistry. PMID 32945655 DOI: 10.1021/Acs.Biochem.0C00534  0.751
2020 Athar YM, Joseph S. RNA-Binding Specificity of the Human Fragile X Mental Retardation Protein. Journal of Molecular Biology. PMID 32343993 DOI: 10.1016/J.Jmb.2020.04.021  0.758
2018 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, et al. Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions. Nature Communications. 9: 4865. PMID 30451861 DOI: 10.1038/S41467-018-07321-8  0.487
2018 Arias-Mireles BH, de Rozieres CM, Ly K, Joseph S. RNA Modulates the Interaction Between Influenza A Virus NS1 and Human PABP1. Biochemistry. PMID 29782795 DOI: 10.1021/Acs.Biochem.8B00218  0.452
2018 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. Scientific Reports. 8: 3488. PMID 29472573 DOI: 10.1038/S41598-018-21739-6  0.617
2018 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 29298914 DOI: 10.1073/Pnas.1714554115  0.465
2016 Katz FE, Shi X, Owens CP, Joseph S, Tezcan FA. Determination of NTPase activities from measurement of true inorganic phosphate in the presence of labile phosphate compounds. Analytical Biochemistry. PMID 28017740 DOI: 10.1016/J.Ab.2016.12.012  0.308
2016 Shi X, Joseph S. Mechanism of Translation Termination: RF1 Dissociation follows RF3 Dissociation from the Ribosome. Biochemistry. PMID 27779391 DOI: 10.1021/Acs.Biochem.6B00921  0.376
2016 Shi X, Joseph S. Translocation: lights, camera, and action. Nature Structural & Molecular Biology. 23: 367-8. PMID 27142323 DOI: 10.1038/Nsmb.3219  0.416
2016 Trappl K, Joseph S. Ribosome Induces a Closed to Open Conformational Change in Release Factor 1. Journal of Molecular Biology. PMID 26827724 DOI: 10.1016/J.Jmb.2016.01.021  0.434
2015 Chen E, Joseph S. Fragile X mental retardation protein: A paradigm for translational control by RNA-binding proteins. Biochimie. 114: 147-54. PMID 25701550 DOI: 10.1016/J.Biochi.2015.02.005  0.441
2015 Joseph S. Modification interference analysis of the ribosome. Methods in Molecular Biology (Clifton, N.J.). 1240: 113-23. PMID 25352140 DOI: 10.1007/978-1-4939-1896-6_8  0.43
2014 Chen E, Sharma MR, Shi X, Agrawal RK, Joseph S. Fragile X mental retardation protein regulates translation by binding directly to the ribosome. Molecular Cell. 54: 407-17. PMID 24746697 DOI: 10.1016/J.Molcel.2014.03.023  0.472
2014 Trappl K, Mathew MA, Joseph S. Thermodynamic and kinetic insights into stop codon recognition by release factor 1. Plos One. 9: e94058. PMID 24699820 DOI: 10.1371/Journal.Pone.0094058  0.41
2014 Alverdi V, Hetrick B, Joseph S, Komives EA. Direct observation of a transient ternary complex during IκBα-mediated dissociation of NF-κB from DNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 225-30. PMID 24367071 DOI: 10.1073/Pnas.1318115111  0.684
2013 Sahu B, Khade PK, Joseph S. Highly conserved base A55 of 16S ribosomal RNA is important for the elongation cycle of protein synthesis. Biochemistry. 52: 6695-701. PMID 24025161 DOI: 10.1021/Bi4008879  0.469
2013 Khade PK, Shi X, Joseph S. Steric complementarity in the decoding center is important for tRNA selection by the ribosome. Journal of Molecular Biology. 425: 3778-89. PMID 23542008 DOI: 10.1016/J.Jmb.2013.02.038  0.42
2012 Sahu B, Khade PK, Joseph S. Functional replacement of two highly conserved tetraloops in the bacterial ribosome. Biochemistry. 51: 7618-26. PMID 22938718 DOI: 10.1021/Bi300930R  0.487
2012 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. Journal of Molecular Biology. 419: 125-38. PMID 22459262 DOI: 10.1016/J.Jmb.2012.03.016  0.469
2011 Khade PK, Joseph S. Messenger RNA interactions in the decoding center control the rate of translocation. Nature Structural & Molecular Biology. 18: 1300-2. PMID 22020300 DOI: 10.1038/Nsmb.2140  0.479
2010 Field A, Hetrick B, Mathew M, Joseph S. Histidine 197 in release factor 1 is essential for a site binding and peptide release. Biochemistry. 49: 9385-90. PMID 20873815 DOI: 10.1021/Bi1012047  0.764
2010 Hetrick B, Khade PK, Lee K, Stephen J, Thomas A, Joseph S. Polyamines accelerate codon recognition by transfer RNAs on the ribosome. Biochemistry. 49: 7179-89. PMID 20666453 DOI: 10.1021/Bi1009776  0.776
2010 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 Research. 38: 4108-19. PMID 20215430 DOI: 10.1093/Nar/Gkq151  0.507
2010 Khade P, Joseph S. Functional interactions by transfer RNAs in the ribosome. Febs Letters. 584: 420-6. PMID 19914248 DOI: 10.1016/J.Febslet.2009.11.034  0.367
2009 Hetrick B, Lee K, Joseph S. Kinetics of stop codon recognition by release factor 1. Biochemistry. 48: 11178-84. PMID 19874047 DOI: 10.1021/Bi901577D  0.734
2009 Shi X, Chiu K, Ghosh S, Joseph S. Bases in 16S rRNA important for subunit association, tRNA binding, and translocation. Biochemistry. 48: 6772-82. PMID 19545171 DOI: 10.1021/Bi900472A  0.459
2008 Garcia-Ortega L, Stephen J, Joseph S. Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation. Molecular Cell. 32: 292-9. PMID 18951096 DOI: 10.1016/J.Molcel.2008.09.012  0.451
2007 Studer SM, Joseph S. Binding of mRNA to the bacterial translation initiation complex. Methods in Enzymology. 430: 31-44. PMID 17913633 DOI: 10.1016/S0076-6879(07)30002-5  0.712
2007 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 (New York, N.Y.). 13: 817-23. PMID 17416634 DOI: 10.1261/Rna.367307  0.501
2006 Feinberg JS, Joseph S. A conserved base-pair between tRNA and 23 S rRNA in the peptidyl transferase center is important for peptide release. Journal of Molecular Biology. 364: 1010-20. PMID 17045291 DOI: 10.1016/J.Jmb.2006.09.040  0.778
2006 Ali IK, Lancaster L, Feinberg J, Joseph S, Noller HF. Deletion of a Conserved, Central Ribosomal Intersubunit RNA Bridge Molecular Cell. 23: 865-874. PMID 16973438 DOI: 10.1016/J.Molcel.2006.08.011  0.806
2006 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. The Journal of Biological Chemistry. 281: 32303-9. PMID 16950778 DOI: 10.1074/Jbc.M607058200  0.45
2006 Phelps SS, Gaudin C, Yoshizawa S, Benitez C, Fourmy D, Joseph S. Translocation of a tRNA with an extended anticodon through the ribosome. Journal of Molecular Biology. 360: 610-22. PMID 16787653 DOI: 10.1016/J.Jmb.2006.05.016  0.529
2006 Studer SM, Joseph S. Unfolding of mRNA secondary structure by the bacterial translation initiation complex. Molecular Cell. 22: 105-15. PMID 16600874 DOI: 10.1016/J.Molcel.2006.02.014  0.71
2006 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 (New York, N.Y.). 12: 580-8. PMID 16489185 DOI: 10.1261/Rna.2290706  0.801
2005 Sanbonmatsu KY, Joseph S, Tung CS. Simulating movement of tRNA into the ribosome during decoding. Proceedings of the National Academy of Sciences of the United States of America. 102: 15854-9. PMID 16249344 DOI: 10.1073/Pnas.0503456102  0.457
2005 Phelps SS, Joseph S, Draper DE. Non-bridging phosphate oxygen atoms within the tRNA anticodon stem-loop are essential for ribosomal a site binding and translocation Journal of Molecular Biology. 349: 288-301. PMID 15890196 DOI: 10.1016/J.Jmb.2005.03.079  0.483
2005 Ghosh S, Joseph S. Nonbridging phosphate oxygens in 16S rRNA important for 30S subunit assembly and association with the 50S ribosomal subunit. Rna (New York, N.Y.). 11: 657-67. PMID 15811917 DOI: 10.1261/Rna.7224305  0.417
2004 Phelps SS, Malkiewicz A, Agris PF, Joseph S. Modified nucleotides in tRNA(Lys) and tRNA(Val) are important for translocation. Journal of Molecular Biology. 338: 439-44. PMID 15081802 DOI: 10.1016/J.Jmb.2004.02.070  0.537
2003 Sanbonmatsu KY, Joseph S. Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs. Journal of Molecular Biology. 328: 33-47. PMID 12683995 DOI: 10.1016/S0022-2836(03)00236-5  0.439
2003 Studer SM, Feinberg JS, Joseph S. Rapid kinetic analysis of EF-G-dependent mRNA translocation in the ribosome. Journal of Molecular Biology. 327: 369-81. PMID 12628244 DOI: 10.1016/S0022-2836(03)00146-3  0.784
2003 Joseph S. After the ribosome structure: how does translocation work? Rna (New York, N.Y.). 9: 160-4. PMID 12554856 DOI: 10.1261/Rna.2163103  0.319
2002 Phelps SS, Jerinic O, Joseph S. Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation. Molecular Cell. 10: 799-807. PMID 12419224 DOI: 10.1016/S1097-2765(02)00686-X  0.499
2002 Tung CS, Joseph S, Sanbonmatsu KY. All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nature Structural Biology. 9: 750-5. PMID 12244297 DOI: 10.1038/Nsb841  0.362
2002 Ma C, Baker NA, Joseph S, McCammon JA. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. Journal of the American Chemical Society. 124: 1438-42. PMID 11841313 DOI: 10.1021/Ja016830+  0.395
2001 Feinberg JS, Joseph S. Identification of molecular interactions between P-site tRNA and the ribosome essential for translocation. Proceedings of the National Academy of Sciences of the United States of America. 98: 11120-5. PMID 11562497 DOI: 10.1073/Pnas.211184098  0.8
2000 Jerinic O, Joseph S. Conformational changes in the ribosome induced by translational miscoding agents. Journal of Molecular Biology. 304: 707-713. PMID 11124020 DOI: 10.1006/Jmbi.2000.4269  0.362
2000 Joseph S, Noller HF. [13] Directed hydroxyl radical probing using iron(II) tethered to RNA Methods in Enzymology. 318: 175-190. PMID 10889988 DOI: 10.1016/S0076-6879(00)18052-8  0.545
2000 Joseph S, Whirl ML, Kondo D, Noller HF, Altman RB. Calculation of the relative geometry of tRNAs in the ribosome from directed hydroxyl-radical probing data Rna. 6: 220-232. PMID 10688361 DOI: 10.1017/S1355838200992112  0.675
1999 Samaha RR, Joseph S, O'Brien B, O'Brien TW, Noller HF. Site-directed hydroxyl radical probing of 30S ribosomal subunits by using Fe(II) tethered to an interruption in the 16S rRNA chain Proceedings of the National Academy of Sciences of the United States of America. 96: 366-370. PMID 9892639 DOI: 10.1073/Pnas.96.2.366  0.654
1998 Joseph S, Noller HF. EF-G-catalyzed translocation of anticodon stem-loop analogs of transfer RNA in the ribosome Embo Journal. 17: 3478-3483. PMID 9628883 DOI: 10.1093/Emboj/17.12.3478  0.673
1997 Joseph S, Weiser B, Noller HF. Mapping the inside of the ribosome with an RNA helical ruler Science. 278: 1093-1098. PMID 9353184 DOI: 10.1126/Science.278.5340.1093  0.64
1996 Joseph S, Noller HF. Mapping the rRNA neighborhood of the acceptor end of tRNA in the ribosome. The Embo Journal. 15: 910-6. PMID 8631311 DOI: 10.1002/J.1460-2075.1996.Tb00425.X  0.635
1996 Noller HF, Green R, Heilek G, Hoffarth V, Hüttenhofer A, Joseph S, Lee I, Lieberman K, Mankin A, Merryman C, Powers T, Puglisi EV, Samaha RR, Weiser B. Erratum: Structure and function of ribosomal RNA Biochemistry and Cell Biology. 74: 417-417. DOI: 10.1139/O96-045  0.702
1995 Noller HF, Green R, Heilek G, Hoffarth V, Hüttenhofer A, Joseph S, Lee I, Lieberman K, Mankin A, Merryman C. Structure and function of ribosomal RNA. Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire. 73: 997-1009. PMID 8722015 DOI: 10.1139/O95-107  0.782
1993 Berzal-Herranz A, Joseph S, Chowrira BM, Butcher SE, Burke JM. Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme. The Embo Journal. 12: 2567-73. PMID 8508779 DOI: 10.1002/J.1460-2075.1993.Tb05912.X  0.723
1993 Joseph S, Berzal-Herranz A, Chowrira BM, Butcher SE, Burke JM. Substrate selection rules for the hairpin ribozyme determined by in vitro selection, mutation, and analysis of mismatched substrates. Genes & Development. 7: 130-8. PMID 7678568 DOI: 10.1101/Gad.7.1.130  0.692
1992 Berzal-Herranz A, Joseph S, Burke JM. In vitro selection of active hairpin ribozymes by sequential RNA-catalyzed cleavage and ligation reactions Genes and Development. 6: 129-134. PMID 1730406 DOI: 10.1101/Gad.6.1.129  0.576
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