Fig. 9: Derivation of the promoter binding free energy using molecular dynamics.
From: Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase
a Thermodynamic cycle of promoter binding. The PPC superscript (e.g. DNAPPC) stands for Promoter Pocket Conformation in regard to the structure of the 3′-−11UUG−9-5′ DNA trinucleotide. b Equilibration and relaxation of the cryo-EM derived atomic model of the AR9 nvRNAP holoenzyme with the 3′-−11UUG−9-5′ DNA trinucleotide bound to the promoter pocket. c Equilibration and relaxation of the 3′-−11UUG−9-5′ trinucleotide in bulk water. d, e Energetics of forward and backward alchemical transformations of the 3′-−11UUG−9-5′ DNA trinucleotide in the promoter pocket of the AR9 nvRNAP holoenzyme and in the PPC in bulk water, respectively. f–l Entropic cost of applying seven harmonic constraints to the 3′-−11UUG−9-5′ DNA trinucleotide to maintain it in the promoter pocket-bound state. m Entropic cost of the harmonic RMSD constraint on the 3′-−11UUG−9-5′ DNA trinucleotide to maintain the PPC.
