Universally Conserved Interactions between the Ribosome and the Anticodon Stem- Loop of A Site tRNA Important for Translocation  Steven S. Phelps, Olga Jerinic, Simpson Joseph  Molecular Cell  Volume 10, Issue 4, Pages 799-807 (October 2002) DOI: 10.1016/S1097-2765(02)00686-X

Figure 1 Translocation of 2′-O-Methyl Substituted ASL4Phe Bound to the Ribosomal A Site (A) Secondary structure of ASL4Phe and ribose 2′-hydroxyl group analogs. The nucleotides in ASL4Phe are numbered according to the full-length E. coli tRNAPhe sequence. The ribose 2′-hydroxyl groups in ASL4Phe were substituted with 2′-O-methyl, 2′-deoxy, 2′-amino, or 2′-fluoro analogs. (B) Toeprinting assay to monitor translocation. Arrows indicate toeprints before (Pre) and after (Post) translocation. Lanes show ribosomal complexes containing unmodified ASL4Phe, fully 2′-deoxy substituted ASL4Phe (DNA), or having single 2′-O-methyl substitutions at positions 28–42 within ASL4 as indicated. (C) Extent of translocation of ASL4Phe having single 2′-O-methyl substitutions. The fraction of translocation of the fully 2′-deoxy substituted ASL4Phe was considered to be background and was subtracted from the translocation value for the unmodified and single 2′-O-methyl substituted ASL4Phe. Gels were quantified with a Molecular Dynamics PhosphorImager, and the results are the average of at least three experiments. Molecular Cell 2002 10, 799-807DOI: (10.1016/S1097-2765(02)00686-X)

Figure 2 Time Course of Translocation of 2′-Deoxy Substituted ASL4Phe Bound to the Ribosomal A Site Translocations of unmodified ASL4Phe and single 2′-deoxy substituted ASL4Phe were performed in parallel for the indicated time points. The percent translocation in the absence of EF-G (lane C, control) was considered to be background and was subtracted from the translocation value for the remaining time points. Values were normalized with respect to translocation of the unmodified ASL4Phe, which was set to 100% at the 60 min time point. Molecular Cell 2002 10, 799-807DOI: (10.1016/S1097-2765(02)00686-X)

Figure 3 Interaction of ASL with the 30S Subunit P Site The ASL residues are in red, and 16S rRNA residues that are within a radius of 5 Å from the respective 2′-hydroxyl groups (2′-OH) in the ASL are color coded: A790 (purple), C1230 (orange), G1338 (light green), A1339 (blue), and A1340 (golden). Molecular Cell 2002 10, 799-807DOI: (10.1016/S1097-2765(02)00686-X)

Figure 4 Interaction of ASL with the 30S Subunit A Site The ASL residues are in red, and 16S rRNA residues that are within a radius of 5 Å from the respective 2′-hydroxyl groups in the ASL are color coded: G530 (blue), U955 (light green), U956 (dark green), A1492 (magenta), and A1493 (cyan). Lysine 120 at the carboxy terminus of small subunit protein S13 is shown in yellow. Molecular Cell 2002 10, 799-807DOI: (10.1016/S1097-2765(02)00686-X)