QM/MM MD simulations reveal an asynchronous PCET mechanism for nitrite reduction by copper nitrite reductase

Ronny Cheng, Chun Wu, Zexing Cao, Binju Wang

Research output: Contribution to journalArticle

Abstract

Nitrite reductases are enzymes that aid in the denitrification process by catalyzing the reduction of nitrite to nitric oxide gas. Since this reaction is the first committed step that involves gas formation, it is regarded to be a vital step for denitrification. However, the mechanism of copper-containing nitrite reductase is still under debate due to the discrepancy between the theoretical and experimental data, especially in terms of the roles of secondary shell residues Asp98 and His255 and the electron transfer mechanism between the two copper sites. Herein, we revisited the nitrite reduction mechanism of A. faecalis copper nitrite reductase using QM(B3LYP)/MM-based metadynamics. It is found that the intramolecular electron transfer from T1-Cu to T2-Cu occurs via an asynchronous proton-coupled electron transfer (PCET) mechanism, with electron transfer (ET) preceding proton transfer (PT). In particular, we found that the ET process is driven by the conformation conversion of Asp98 from the gatekeeper to the proximal one, which is much more energy-demanding than the PCET itself. These results highlight that the inclusion of an electron donor is vital to investigate electron-transfer related processes such as PCET.

Original languageEnglish (US)
Pages (from-to)20922-20928
Number of pages7
JournalPhysical Chemistry Chemical Physics
Volume22
Issue number36
DOIs
StatePublished - Sep 23 2020

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Fingerprint Dive into the research topics of 'QM/MM MD simulations reveal an asynchronous PCET mechanism for nitrite reduction by copper nitrite reductase'. Together they form a unique fingerprint.

  • Cite this