Research on Biomolecular Machines

Structure-based modeling and simulation of RNA polymerases

RNA polymerase (RNAP) is the key enzyme that transcribes DNA into messenger RNA for protein expression. Bacteriophage T7 RNAP is widely utilized in lab gene expression system and synthetic circuit due to its simplicity, high promoter specificity, and high productivity. We have studied fidelity control (Duan et al, Biophys J 2014; Yu, Mol Based Math Biol 2014) and mechano-chemical properties of T7 RNAP (Yu & Oster, Biophys J 2012), as well as general elongation kinetics of yeast Polymerase II (Yu et al Phys Biol 2015). Recently, we conducted extensive all-atom molecular dynamics (MD) simulations on the PPi product release and translocation of T7 RNAP, constructing the Markov state model (MSM). Meanwhile, we are quantifying the stepwise selectivity of T7 RNAP by calculating differentiation free energies between right and wrong nucleotides along the reaction path. We also try to design viral RNAP mutants that may furnish with functions of the RNAPs from higher organisms.

Modeling gene transcription from molecule to circuit

We study generic transcription initiation from the RNAP binding to promotor opening, from abortive escaping to persistent elognation. We want to build a coherent model of transcription with interaction and feedback control between the RNAP and DNA, with bursting kinetics of mRNA production (Chong et al., Cell 2014), possibly with multiple RNAP functioning and with celluar impacts.

Molecular cooperativity: neighbor intearction and allosteric propagation

Currently, we study coordination and control inside ring-shaped molecular motors on top of previous work of a viral DNA packaging motor (Yu et al., J Mol Biol 2010). We first focus on studying F1-ATPase ring that performs sequential hydrolysis among three active sites even in the absence of the central subunit (Uchihashi et al., Science 2011). We implemented stochastic simulations to predict essential inter-subunit couplings that lead to the sequential performance. We then conducted MD simulations to substantiate our findings. Coarse-grained approaches describing relaxation dynamics of the motor ring are performed additionally. Comparative studies on V1-ATPase, T7 helicase, ClpX, or other viral packaging motors are feasible. More general long-range molecular control generated from neighbor-neighbor interactions can be investigated similarly.