RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation.

摘要: RNA polymerase II is the central eukaryotic enzyme in transcription from DNA to RNA. The dynamics of described molecular-dynamics simulations started two crystal structures with open and closed trigger loop (TL) forms. Dynamic transitions between neutral forward translocated states were observed, especially for downstream duplex. rearrangements also seen active site environment, including conformations which nucleotide assumed a possibly precatalytic conformation close proximity terminal 3′-hydroxyl nascent Because nucleic acid translocation was observed primarily an TL structure, whereas approach ribose predominantly occurred modified Brownian ratchet mechanism proposed whereby thermally driven only possible TL, fidelity control catalysis require closing.