title: Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation.
abstract: Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a preinsertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection. We calculated the relative binding free energy between a noncognate nucleotide and a cognate one at a preinsertion configuration via alchemical simulations, showing that a small selection free energy or the binding free energy difference (∼3 kBT) exists between the two nucleotides. Indeed, another preinsertion configuration favored by the noncognate nucleotides was identified, which appears to be off path for further nucleotide insertion and additionally assists the nucleotide selection. By chemical master equation (CME) approach, we show that the small selection free energy at the preinsertion site along with the off-path noncognate nucleotide filtering can help substantially to reduce the error rate and to maintain the elongation rate high in the T7 RNAP transcription.
authors.affiliation: Beijing Computational Science Research Center , Beijing 100193, China.
authors.forename: Chao
authors.initials: C
authors.lastname: E
authors.affiliation: Beijing Computational Science Research Center , Beijing 100193, China.
authors.forename: Baogen
authors.initials: B
authors.lastname: Duan
authors.affiliation: Beijing Computational Science Research Center , Beijing 100193, China.
authors.forename: Jin
authors.identifier: 0000-0001-8224-1374
authors.initials: J
authors.lastname: Yu
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009711:Nucleotides / Q000737:chemistry / Q000378:metabolism*; D013816:Thermodynamics; D061805:Transcription Elongation, Genetic; D014764:Viral Proteins / Q000378:metabolism*
chemical_list: D009711:Nucleotides; D014764:Viral Proteins; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases