Collective coordinates and facilitated translocation of human mitochondrial RNA polymerase (POLRMT) translocation from atomic simulations

Collective coordinate (CV) identification is challenging in many complex dynamical systems; physical, chemical, and biological. To study translocation of a single-subunit RNA polymerase (RNAP) during transcription, we employ all-atom molecular dynamics (MD) as a vehicle to illustrate CV refinement. RNAP translocation is an essential step of the transcription elongation that dictates gene expression. It generally follows from polymerization product release and proceeds to the initial binding of incoming nucleotides. Human mitochondrial DNA-dependent RNA polymerase (POLRMT) has a fundamental role in mitochondrial gene expression and cell metabolism. POLRMT is also a key molecular target of concern in the design of nucleotide analogue antiviral and antitumor drugs. While POLRMT shares high structural similarity to viral T7 RNAP, previous experimental studies and our current simulations suggest POLRMT's mechano-chemical coupling may be distinct. In our current research, we constructed and performed equilibrium MD simulations of pre- and post-translocation models of POLRMT and along different potential translocation paths (with or without coupling of the fingers subdomain conformational change). We then conducted dimension reduction data analyses, comparing time-lagged independent component analysis (tICA) and the neural network implementation of the variational approach for Markov processes (VAMPnets), and comparing differing relevant atomic CV sets to best represent the sampled MD simulations. Our results indicate that POLRMT translocation is facilitated by NTP binding to enable fingers subdomain opening in post-translocation and by the inclusion NTP binding/catalytic motifs. Thusly, our results suggest a novel mechano-chemical coupling mechanism in single-subunit RNAPs which may guide antiviral or antitumor drug design.