PMC

Model of helices IV and V in lac permease. Helices IV and V are represented as light blue ribbons. The charge pair (Glu-126 and Arg-144; dark blue), as well as the relevant Gly (G115, G121, G141, G147, and G150; red) and Ala (A120, A122, A124, and A127; yellow) residues are indicated.

(a) Participation of the GNRA loop in multiple tertiary contacts involves non-native tetraloop conformations, such as the C4 conformation seen in the crystal structure of the 23S rRNA from D. radiodurans (PDB 1P9X). Expansion of the tetraloop and its multiple tertiary interactions is shown in (b) and a schematic version of this interaction is shown in (c). Note that the coloring of bases and hydrogen bonds is consistent throughout, and that each oval represents both base and corresponding backbone in the schematic representation. The GAAA tetraloop and closing base pair residues are shown in cyan (G), violet (A) and lime (C), with the hydrogen bonds of the closing G121•C126 base pair in yellow. Intraloop hydrogen bonding is evident between G122 and A124 (green), and G121 and G122 (pink). Furthermore, interaction of A124 and A125 in the tetraloop with C114 and G54, respectively, provides for two tertiary contacts between the tetraloop and the nearby pink helical region. Additionally, G121 forms a third tertiary contact (black) with C1389 in the adjacent orange helical region.

(a) The same GNRA tetraloop from D. radiodurans also takes on a C5 conformation (PDB 2O45) while participating in multiple tertiary contacts. The overall hydrogen bonding scheme both within the tetraloop and between the tetraloop and nearby helical regions, as illustrated in (b), is significantly different than in the docking conformation shown in Figure 8. Within the tetraloop and stem, hydrogen bonding is evident between A124 and A125 (orange), and between C126 and C127 (blue). While the G121–C1389 tertiary contact (black) is formed in the same manner as in the C4 conformation pictured in Figure 8, the other tertiary contacts are different. In this C5 conformation, C128 of the stem forms a tertiary contact with A1362 of the nearby helical region (orange). Additionally, both A125 and C126 form contacts with the pink helical region via interactions with C113 and C114 of the stem, respectively, giving a total of four tertiary contacts.

Panel A shows a two dimensional map of Rho where amino acid residues modified following exposure to high flux X rays are shown as red filled circles. The complete list of residues unambiguously identified as being modified following X–ray exposure includes: W³⁵, M⁴⁴, M⁴⁹, P⁷¹, M⁸⁶, A¹¹⁷, A¹²⁴, M¹⁴³, M¹⁵⁵, M¹⁶³, M¹⁸³, P¹⁹⁴, M²⁵³, P²⁸⁵, M²⁸⁸, P³⁰³, M³¹⁷ and Ala³⁴⁶. Panel B shows the X–ray crystal structure of Rho (PDB entry 1u19 (Okada et al., 2004)) represented as gray cartoons. Amino acid residues M⁸⁶, M¹⁶³, M²⁸⁸, P³⁰³, M²⁵³, and A³⁴⁶ are represented by spheres. The color coding represents percent of differences between rates of Rho* and Rho*–G_t labeling normalized to Rho*–G_t rates. Panel C tabulates modified amino acid residues (shown in red letters) with their modification rates in Rho, Rho* and the Rho*–G_t complex.