PMC

(A) Conformational states of the RNAP clamp (two orthogonal views) [,]. Structure of RNAP showing open (red), partly closed (yellow), and fully closed (green) clamp conformations, as observed in crystal structures (PDB 1I3Q, PDB 1HQM, PDB 1I6H). Circle, switch region; dashed circle, binding site for rifamycins; violet sphere, active-center Mg²⁺.
(B) Conformational states of the RNAP switch region (stereoview) [,]. Structure of RNAP switch 1 and RNAP switch 2 (β’ residues 1304–1329 and β’ residues 330–349; residues numbered as in E. coli RNAP) showing conformational states associated with open (red), partly closed (yellow), and fully closed (green) clamp conformations, as observed in crystal structures (PDB 1I3Q, PDB 1HQM, PDB 1I6H). Gray squares, points of connection of switch 1 and switch 2 to the RNAP main mass. Colored circles, points of connection of switch 1 and switch 2 to the RNAP clamp.

(A) Conformational states of the RNAP clamp (two orthogonal views). Structure of RNAP showing open (red), partly closed (yellow), and fully closed (green) clamp conformations, as observed in crystal structures (PDB 1I3Q, PDB 1HQM, PDB 1I6H). Circle, switch region; dashed circle, binding site for rifamycins; violet sphere, active-center Mg²⁺.
(B) Conformational states of the RNAP switch region (stereoview). Structure of RNAP switch 1 and RNAP switch 2 (β′ residues 1304–1329 and β′ residues 330–349; residues numbered as in E. coli RNAP) showing conformational states associated with open (red), partly closed (yellow), and fully closed (green) clamp conformations, as observed in crystal structures (PDB 1I3Q, PDB 1HQM, PDB 1I6H). Gray squares, points of connection of switch 1 and switch 2 to the RNAP main mass. Colored circles, points of connection of switch 1 and switch 2 to the RNAP clamp.
(C) Structures of myxopyronin A (Myx), corallopyronin A (Cor), and ripostatin A (Rip).

After ternary complex binds to the 30S subunit, the 30S domain closes at the A-site to dock EF-Tu onto the SRL and 50S. Codon-anticodon interactions are then formed completing the GTPase activated state. Once in the GTPase activated state GTP is hydrolyzed, Pi release, allowing switch I to undergo a conformational change from an α-helix to a β-hairpin. This initial rearrangement of EF-Tu allows aa-tRNA to undergo an initial ~5Å movement (A/T’). After the A/T’ movement switch I interacts with the acceptor stem of the aa-tRNA. Switch I has to pass by the aa-tRNA to allow for accommodation. Stalling in aa-tRNA accommodation prevents switch I from passing by the aa-tRNA. Once switch I has passed by the aa-tRNA it can pack with domain III. Finally, when switch I packs against domain III EF-Tu can undergo a conformational change leading to EF-Tu dissociation and aa-tRNA accommodation.

In each case the system is allowed to reach equilibrium under a constant level of input. The concentrations of R1, R2, R3 and R4 are represented by pink, black, orange and green lines respectively. A. Switch from [R1 & R2 high, R3 & R4 low] to [R3 & R4 high, R1 & R2 low], at an input of 0.1 nM. B. Switch from [R3 & R4 high, R1 & R2 low] to [R1 & R2 high to R3 & R4 low], at an input of 0.1 nM. C. Switch from [R2 & R3 high, R1 & R4 low] to [R1 & R4 high, R2 & R3 low], at an input of 50 nM. D. Switch from [R1 & R4 high, R2 & R3 low] to [R2 & R3 high, R1 & R4 low], at an input of 50 nM. In A and C the switch is performed by increasing the for R1 and R2 binding from M to M ( exactly) between the times and seconds. In B and D the switch is performed by increasing the for R3 and R4 binding by the same amount and duration. Initial conditions of nM, nM for A and C, and nM, nM for B and D. Parameters from are used.