Figure 4. Mechanochemical reaction scheme for the nucleotide addition cycle of the SARS-CoV-2 core RTC alone or in complex with nsp13 helicase.
(A and B) Schematic representations of the different elongating RTCs without (A) and with (B) nsp13 helicase at saturating concentration.
(C–F) Characteristic timescales (C and D) and probabilities (E and F) for the different nucleotide addition pathways (VFNA, FNA, SNA, and VSNA) and long-lived pause (LLP) state versus tension applied to the non-template RNA strand and without (C and E) or with (D and F) saturating nsp13-helicase concentration (20 nM). The circles with error bars represent the mean ± SEM from 100 bootstraps of the individual dwell-time fits. The solid lines and shaded areas represent the mean ± SEM of the global fit, with the mechanochemical reaction scheme shown in (G) (STAR Methods).
(G) Mechanochemical reaction scheme underlying the timescales and probabilities (green box) for the VFNA pathway, which is only entered by the RTC-nsp13.1,2* complex, and (blue box) for the nucleotide addition pathways entered by the core RTC, RTC-nsp13.1, and RTC-nsp13.1,2. The solid and dashed arrows represent kinetic steps for which rates could either be extracted or not, respectively, from the global fit.