Extended Data Fig. 6: Trajectories from MD simulations of different monomers in the A site. | Nature Chemistry

Extended Data Fig. 6: Trajectories from MD simulations of different monomers in the A site.

From: Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates

Extended Data Fig. 6

Trajectories illustrating evolution of the distance between the A-site nucleophile (Nα) and the P-site fMet carbonyl electrophile (Csp2) over 300 ns within the 30 Å Reduced Ribosome Model (RRM). a, aminobenzoic acids 2–4; b, β2,3-2-aminocyclopentane−1-carboxylic acids 5–8. We used Schrödinger’s Force Field Builder (Schrödinger release 2022-1) to parametrize the existing OPLS4 force field to accurately describe the conformational dynamics of each new monomer. Maestro’s 3D Builder was then used to assemble the new ester bond and minimize the system to release clashes with surrounding residues.

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