Brownian ratchet mechanism of translocation in T7 RNA polymerase facilitated by a post-translocation energy bias arising from the conformational change of the enzyme
(color online) Free-energy profiles of translocation. (a) The potential of mean force (PMF) during the process of Tyr639 moving from PRE to POST positions in system 7 where only the enzyme is present. The x axis is the moving distance of Tyr639 from PRE to POST positions and the y axis is PMF. The PRE position corresponds to d = 0, with PMF = −0.5 kcal/mol, and the POST position corresponds to d = 0.4 nm, with PMF = −2.5 kcal/mol. (b) The potential of mean force (PMF) during the process of Tyr639 moving from PRE to POST positions in system 3 where the αβ methylene ATP and the template nucleotide i + 1 are removed in the insertion complex (PDB 1S76). The x axis is the moving distance of Tyr639 from PRE to POST positions and the y axis is PMF. The PRE position corresponds to d = 0, with PMF = −2 kcal/mol, and the POST position corresponds to d = 0.4 nm, with PMF = −6.5 kcal/mol.
