title: A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation.
abstract: Pyrophosphate ion (PPi) release during transcription elongation is a signature step in each nucleotide addition cycle. The kinetics and energetics of the process as well as how it proceeds with substantial conformational changes of the polymerase complex determine the mechano-chemical coupling mechanism of the transcription elongation. Here we investigated detailed dynamics of the PPi release process in a single-subunit RNA polymerase (RNAP) from bacteriophage T7, implementing all-atom molecular dynamics (MD) simulations. We obtained a jump-from-cavity kinetic model of the PPi release utilizing extensive nanosecond MD simulations. We found that the PPi release in T7 RNAP is initiated by the PPi dissociation from two catalytic aspartic acids, followed by a comparatively slow jump-from-cavity activation process. Combining with a number of microsecond long MD simulations, we also found that the activation process is hindered by charged residue associations as well as by local steric and hydrogen bond interactions. On the other hand, the activation is greatly assisted by a highly flexible lysine residue Lys472 that swings its side chain to pull PPi out. The mechanism can apply in general to single subunit RNA and DNA polymerases with similar molecular structures and conserved key residues. Remarkably, the flexible lysine or arginine residue appears to be a universal module that assists the PPi release even in multi-subunit RNAPs with charge facilitated hopping mechanisms. We also noticed that the PPi release is not tightly coupled to opening motions of an O-helix on the fingers domain of T7 RNAP according to the microsecond MD simulations. Our study thus supports the Brownian ratchet scenario of the mechano-chemical coupling in the transcription elongation of the single-subunit polymerase.
authors.affiliation: Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America.
authors.forename: Lin-Tai
authors.initials: LT
authors.lastname: Da
authors.affiliation: Beijing Computational Science Research Center, Beijing, China.
authors.forename: Chao
authors.initials: C
authors.lastname: E
authors.affiliation: Beijing Computational Science Research Center, Beijing, China.
authors.forename: Baogen
authors.initials: B
authors.lastname: Duan
authors.affiliation: School of Physics, University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Chuanbiao
authors.initials: C
authors.lastname: Zhang
authors.affiliation: School of Physics, University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Beijing Computational Science Research Center, Beijing, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Yu
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism*; D011756:Diphosphates / Q000737:chemistry / Q000378:metabolism*; D008239:Lysine / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment; D014764:Viral Proteins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D011756:Diphosphates; D014764:Viral Proteins; C107241:diphosphoric acid; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases; D008239:Lysine