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. Author manuscript; available in PMC: 2019 Apr 18.
Published in final edited form as: J Am Chem Soc. 2018 Apr 6;140(15):5077–5087. doi: 10.1021/jacs.7b11044

Figure 6. The influence of the unstructured nascent chain pulling force on the free energy of peptide bond formation.

Figure 6

(A) The atoms shown were treated quantum mechanically in the QM/MM simulations. (B) A pictorial representation of the reaction that was simulated quantum mechanically. Red arrows denote the movement of electrons. Note well that the final structure depicted represents the rate limiting transition intermediate of the peptidyl transfer and not the final product. (C) The free energy as a function of the reaction coordinate for peptide bond formation for the 95-residue (green dots) and 190-residue (magenta dots) 3Ala10 RNC. Error bars represent the 95% confidence intervals. Because we modeled the reaction only up to the transition state (panel b), reaction coordinate values greater than 0.5 Å result in exploration of what is no longer the relevant free energy pathway and, consequently, larger error bars.