Fig. 4: Modulation of the interaction between unfolded nascent chains and the ribosome by uL23 and uL24 loop truncation.

a Schematic of the WT + 31 RNC (L = 31) with sequence and domain landmarks indicated. Three regions of the NC whose dynamics was monitored by NMR and all-atom MD simulations (residues 648–717, 724 and 735–758) are shown in black rectangles. b Relative intensities (I) of ¹H-¹⁵N cross-peaks from the spectra of an isolated unfolded FLN5 Δ12 (grey circles, I_ref), WT + 21 (black circles), 23^ΔL + 21(blue circles), 24^ΔL + 21(red circles) and 23^ΔL24^ΔL + 21 (turquoise circles) RNCs. A four-point moving average is plotted as a guide. Yellow-shaded region indicates the residues that interact with ribosomal outer surface. Errors are derived from spectral noise from a single measurement. c Cross-correlated relaxation rates of FLN5Δ12, WT + 21 and 23^ΔL24^ΔL + 21. A four-point moving average is plotted as a guide. Errors are derived from the spectral noise for FLN5 Δ12 and WT, while the mean and standard error from two biological repeats are shown for 23^ΔL24^ΔL. d ¹H-¹⁵N cross-peaks of E724 of the A₃A₃ variant of FLN5 of the WT (L = 31, 42 and 67) and 23^ΔL, 24^ΔL, 23^ΔL24^ΔL (L = 31) RNCs with that of the isolated unfolded protein. All spectra are recorded at a ¹H frequency of 950 MHz. The changes in the free energy of binding (ΔΔG_binding) in 23^ΔL, 24^ΔL and 23^ΔL24^ΔL RNCs are calculated using the populations of unbound state NC (P_Ub, Supplementary Fig. 10b). Errors are s.d. and calculated by propagating the s.d. of P_Ub. e S² order parameters determined from simulated ensembles of the unfolded NCs on WT, 23^ΔL, 24^ΔL and 23^ΔL24^ΔL RNCs (L = 31). The salmon pink-shaded region indicates the FLN6 linker residues between FLN5 and SecM.