Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Understanding nucleotide entry into RNA polymerase (RNAP) is crucial for the nucleotide addition cycle.
• Two proposed pathways exist: direct entry via the secondary channel (CH2) or selection in the main channel (CH1).

Purpose of the Study:

• To refine the CH2 model and detail the CH1 model for NTP entry into RNAPII.
• To simulate NTP diffusion, binding to DNA, and transfer to the active site.

Main Methods:

• Accelerated molecular dynamics simulations of freely diffusing NTPs around RNAPII.
• All-atom simulations to analyze specific interactions and dependencies.

Main Results:

• Refined atomic details for the CH2 NTP entry model.
• First-time simulation of NTP diffusion, DNA binding, and active site transfer.
• Demonstrated that CH1 loading is dependent on transcription factor IIF (TFIIF) and affects catalytic isomerization.

Conclusions:

• The study provides atomic insights into two distinct NTP loading mechanisms into RNAP.
• These alternative loading pathways may contribute to expressing diverse transcriptional landscapes.