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

• Published in: Biomolecules (Basel, Switzerland) Vol. 10; no. 9; p. 1289
• Main Authors: Génin, Nicolas E J, Weinzierl, Robert O J
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 07.09.2020; MDPI
• Subjects: Catalysis; Catalytic Domain; Deoxyribonucleic acid; Diffusion; DNA; DNA - chemistry; DNA-directed RNA polymerase; downstream bubble; Enzymes; Humans; Hypotheses; Investigations; Isomerization; main channel; Models, Molecular; Molecular Conformation; Molecular dynamics; Molecular Dynamics Simulation; Nucleic Acid Conformation; nucleoside triphosphate; Nucleotides - chemistry; Nucleotides - metabolism; Physiological aspects; Polymerization; Protein Conformation; Proteins; RNA - chemistry; RNA polymerase; RNA Polymerase II - chemistry; RNA Polymerase II - metabolism; RNA polymerases; secondary channel; Simulation; tertiary channel; Transcription Factors, TFII - chemistry; Transcription, Genetic; France; entry; secondary channel; diffusion; TFIIF; nucleoside triphosphate; downstream bubble; RNA polymerase; tertiary channel; loading; main channel
• ISSN: 2218-273X; 2218-273X
• DOI: 10.3390/biom10091289

Mapping the route of nucleoside triphosphate (NTP) entry into the sequestered active site of RNA polymerase (RNAP) has major implications for elucidating the complete nucleotide addition cycle. Constituting a dichotomy that remains to be resolved, two alternatives, direct NTP delivery via the secondary channel (CH2) or selection to downstream sites in the main channel (CH1) prior to catalysis, have been proposed. In this study, accelerated molecular dynamics simulations of freely diffusing NTPs about RNAPII were applied to refine the CH2 model and uncover atomic details on the CH1 model that previously lacked a persuasive structural framework to illustrate its mechanism of action. Diffusion and binding of NTPs to downstream DNA, and the transfer of a preselected NTP to the active site, are simulated for the first time. All-atom simulations further support that CH1 loading is transcription factor IIF (TFIIF) dependent and impacts catalytic isomerization. Altogether, the alternative nucleotide loading systems may allow distinct transcriptional landscapes to be expressed.