Walk and Check along a Viral RNA Polymerase Transcription Elongation Path

Abstract

Gene transcription is a fundamental step in the central dogma of molecular biology. The essential protein enzymes that direct the process are RNA polymerases (RNAPs). The viral RNAP from bacteriophage T7 serves a self-sufficient transcription engine and is widely used for lab gene expression and engineering, although its operational mechanisms remain controversial. We have systematically studied mechano-chemical coupling and fidelity control mechanisms of T7 RNAP during its elongation. Based on single molecule measurements and high-resolution structures, we had demonstrated that a small translocation free energy bias aids nucleotide selection in T7 RNAP [1]. Accordingly, we performed atomistic molecular dynamics (MD) simulation and discovered how a critical tyrosine residue aids the nucleotide selection for selective Brownian ratcheting of the RNAP [2]. In addition, we also built a theoretical framework to analyze efficient stepwise nucleotide selection of the RNAP in the absence of proofreading [3]. Recently, we constructed the Markov state model for the PPi product release and translocation of T7 RNAP implementing extensive MD simulations. In particular, we noticed a universal module in which an essential lysine/arginine residue greatly assists a jump-from-cavity activation process of the PPi release [4]. The activated PPi release is unlikely to drive the RNAP translocation, thus ruling out a power stroke mechanism during the RNAP elongation. Overall, our work demonstrates how physical modeling and large-scale simulations can be combined to reveal underlying mechanisms of a key physiological process that may not be easily accessible from experimental approaches.[1] J Yu, G Oster. Biophys J, 102, 532, 2012.[2] B Duan et al., J Yu. Biophys J, 107, 2130, 2014.[3] J Yu. Mol Based Math Biol, 2,141, 2014.[4] LT Da et al., J Yu. ms under review 2015.