Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations

Abstract

Polymerases are protein enzymes that move along nucleic acid chains and catalyze template--based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non--equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano--chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We keep away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while address only statistical physics modeling approach and all--atom molecular dynamics simulation approach. We organize this review around our own modeling and simulation practices on a single--subunit T7 RNA polymerase, and summarize commensurate studies on structurally similar DNA polymerases. For multi--subunit RNA polymerases that have been intensively studied in recent years, we leave detailed discussions on the simulation achievements to other computational chemical surveys, while only introduce very recently published representative studies, including our own preliminary work on structure--based modeling on yeast RNA polymerase II. In the end, we quickly go through kinetic modeling on elongation pauses and backtracking activities. We emphasize the fluctuation and control mechanisms of the polymerase actions, highlight the non--equilibrium physical nature of the system, and try to bring some perspectives toward understanding replication and transcription regulation from single molecular details to a genome--wide scale.

Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation

“…Additionally, in multisubunit RNAPs, there exists an entry (E) site for the nucleotide binding prior to the binding into the preinsertion site. , It would actually be interesting to probe how the nucleotide selection proceeds at an early or preinsertion stage for both types of RNAPs. Nevertheless, detailed computational studies focused on the preinsertion nucleotide selection were still lack of, though substantial amount of work had been devoted to study overall conformational dynamics throughout the RNAP elongation cycle. − Current work would fill the gap then by implementing atomistic molecular dynamics (MD) simulations to the comparatively simple single-subunit T7 RNAP to provide structural and quantitative basis for the preinsertion nucleotide selection.…”

A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control

“…We have recently studied transcription elongation of T7 RNAP by combining physical modeling and all-atom MD simulations, addressing both mechano-chemical coupling and fidelity control mechanisms during elongation [ [28] , [29] , [30] , [31] , [32] , [33] , [34] , [35] , [36] ]. The mechanochemistry concerns about how the protein machine utilizes chemical free energy to generate mechanical or directional motions, referring to how the chemical synthesis of RNA couples with the polymerase translocation along DNA in the RNAP system.…”

Balancing Non-Equilibrium Driving with Nucleotide Selectivity at Kinetic Checkpoints in Polymerase Fidelity Control

“…Basically, the polymerization can happen without the enzyme at very low speeds and with low fidelity. The enzymes essentially accelerate the polymerization chemical cycles, and often significantly improve the fidelity [ 1 , 2 , 3 , 4 , 5 ]. No matter whether it is under the enzyme catalysis or not, continuous polymerization or elongation process needs to be supported by the chemical potentials of the reactants over that of the products, so that the growth of the polymer chain is sustained under chemical non-equilibrium [ 6 , 7 , 8 ].…”