RNAPs (RNA polymerases) are complex molecular machines that contain a highly conserved catalytic site surrounded by conformationally flexible domains. High-throughput mutagenesis in the archaeal model system Methanocaldococcus jannaschii has demonstrated that the nanomechanical properties of one of these domains, the bridge–helix, exert a key regulatory role on the rate of the NAC (nucleotide-addition cycle). Mutations that increase the probability and/or half-life of kink formation in the BH-HC (bridge–helix C-terminal hinge) cause a substantial increase in specific activity (‘superactivity’). Fully atomistic molecular dynamics simulations show that kinking of the BH-HC appears to be driven by cation–π interactions and involve amino acid side chains that are exceptionally highly conserved in all prokaryotic and eukaryotic species.
Cation–π interactions induce kinking of a molecular hinge in the RNA polymerase bridge–helix domain
Hans Heindl, Pamela Greenwell, Noam Weingarten, Tamas Kiss, Gabor Terstyanszky, Robert O.J. Weinzierl; Cation–π interactions induce kinking of a molecular hinge in the RNA polymerase bridge–helix domain. Biochem Soc Trans 1 February 2011; 39 (1): 31–35. doi: https://doi.org/10.1042/BST0390031
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