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

2020 ◽  
Vol 22 (36) ◽  
pp. 20922-20928
Author(s):  
Ronny Cheng ◽  
Chun Wu ◽  
Zexing Cao ◽  
Binju Wang
Keyword(s):  
Electron Transfer ◽  
Proton Transfer ◽  
Nitrite Reductase ◽  
Md Simulations ◽  
Nitrite Reduction ◽  
Proton Coupled Electron Transfer

The nitrite reduction in copper nitrite reductase is found to proceed through an asynchronous proton-coupled electron transfer (PCET) mechanism, with electron transfer from T1-Cu to T2-Cu preceding the proton transfer from Asp98 to nitrite.

scholarly journals Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography

2016 ◽  
Vol 113 (11) ◽  
pp. 2928-2933 ◽  
Author(s):  
Yohta Fukuda ◽  
Ka Man Tse ◽  
Takanori Nakane ◽  
Toru Nakatsu ◽  
Mamoru Suzuki ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Proton Transfer ◽  
Nitrite Reductase ◽  
Transient State ◽  
Carbonyl Oxygen ◽  
Nitrite Reduction ◽  
Hydroxyl Group ◽  
Intramolecular Electron Transfer ◽  
Metal Centers ◽  
Substrate Complex

Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. Analyses of the nitrite reduction mechanism in CuNiR with conventional synchrotron radiation crystallography (SRX) have been faced with difficulties, because X-ray photoreduction changes the native structures of metal centers and the enzyme–substrate complex. Using serial femtosecond crystallography (SFX), we determined the intact structures of CuNiR in the resting state and the nitrite complex (NC) state at 2.03- and 1.60-Å resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-Å resolution. Comparison between SRX and SFX structures revealed that photoreduction changes the coordination manner of the substrate and that catalytically important His255 can switch hydrogen bond partners between the backbone carbonyl oxygen of nearby Glu279 and the side-chain hydroxyl group of Thr280. These findings, which SRX has failed to uncover, propose a redox-coupled proton switch for PCET. This concept can explain how proton transfer to the substrate is involved in intramolecular electron transfer and why substrate binding accelerates PCET. Our study demonstrates the potential of SFX as a powerful tool to study redox processes in metalloenzymes.

scholarly journals Atomically manipulated proton transfer energizes water oxidation on silicon carbide photoanodes

2018 ◽  
Vol 6 (47) ◽  
pp. 24358-24366 ◽  
Author(s):  
Hao Li ◽  
Huan Shang ◽  
Yuchen Shi ◽  
Rositsa Yakimova ◽  
Mikael Syväjärvi ◽  
...  
Keyword(s):  
Silicon Carbide ◽  
Electron Transfer ◽  
Proton Transfer ◽  
Water Oxidation ◽  
Proton Coupled Electron Transfer ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

Preferential exposure of Si-face of SiC will mechanistically shift the rate limiting step of water oxidation from sluggish proton-coupled electron transfer on C-face to a more energy-favorable electron transfer.

Proton-Coupled Electron Transfer in the Catalytic Cycle ofAlcaligenes xylosoxidansCopper-Dependent Nitrite Reductase

Biochemistry ◽  
2011 ◽  
Vol 50 (19) ◽  
pp. 4121-4131 ◽  
Author(s):  
Nicole G. H. Leferink ◽  
Cong Han ◽  
Svetlana V. Antonyuk ◽  
Derren J. Heyes ◽  
Stephen E. J. Rigby ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Nitrite Reductase ◽  
Catalytic Cycle ◽  
Proton Coupled Electron Transfer

scholarly journals Proton-Coupled Electron Transfer in the Reaction of 3,4-Dihydroxyphenylpyruvic Acid with Reactive Species in Various Media

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
J. J. Fifen ◽  
Z. Dhaouadi ◽  
M. Nsangou ◽  
O. Holtomo ◽  
N. Jaidane
Keyword(s):  
Electron Transfer ◽  
Proton Transfer ◽  
Activation Barrier ◽  
Bond Cleavage ◽  
Hydrogen Atom Transfer ◽  
Free Energies ◽  
Solvent Interactions ◽  
Proton Coupled Electron Transfer ◽  
Nonpolar Solvents ◽  
One Step

The distinction of concerted proton-coupled electron transfer (CPCET) from sequential one as well as proton transfer-electron transfer (PT-ET) from electron transfer-proton transfer (ET-PT) in the O–H bond cleavage reactions in various media has always been a difficult task. In this work, the activation barrier of the CPCET mechanism, its rate constants, and reaction free energies related to ET-PT and PT-ET involving coreactive species were presented as good parameters to attempt the problem. DFT calculations were carried out studying the described pathways subsequent to the scavenging of OH• and OBr- by the 3,4-DHPPA in various media. The solvation was described in a hybrid manner using IEF-PCM model conjointly with a model that takes into account some solute-solvent interactions. As a result, we found that the scavenging of hydroxyl radical by 3,4-DHPPA is thermodynamically governed by a one-step hydrogen atom transfer (CPCET) from the acid to the radical in all media. In kinetic viewpoint, CPCET still dominates in the vacuum and in nonpolar solvents, but in polar solvents it could compete strongly with the ET-PT mechanism so that the latter could slightly dominate.

scholarly journals Nitrite reduction by copper through ligand-mediated proton and electron transfer

2015 ◽  
Vol 6 (6) ◽  
pp. 3373-3377 ◽  
Author(s):  
Cameron M. Moore ◽  
Nathaniel K. Szymczak
Keyword(s):  
Electron Transfer ◽  
Transfer Process ◽  
Copper Complex ◽  
Nitrite Reductase ◽  
Nitrite Reduction ◽  
Electron Transfer Process ◽  
Tripodal Ligand

A copper complex featuring a proton-responsive tripodal ligand reduces nitriteviaa proton/electron transfer process, which parallels copper nitrite reductase.

scholarly journals Design and synthesis of benzimidazole phenol-porphyrin dyads for the study of bioinspired photoinduced proton-coupled electron transfer

2019 ◽  
Vol 23 (11n12) ◽  
pp. 1336-1345
Author(s):  
S. Jimena Mora ◽  
Daniel A. Heredia ◽  
Emmanuel Odella ◽  
Uma Vrudhula ◽  
Devens Gust ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Excited State ◽  
Photosystem Ii ◽  
Proton Transfer ◽  
Water Oxidation ◽  
Oxidation Catalyst ◽  
Design And Synthesis ◽  
Proton Coupled Electron Transfer ◽  
Anchoring Groups ◽  
High Redox Potential

Benzimidazole phenol-porphyrin dyads have been synthesized to study proton-coupled electron transfer (PCET) reactions induced by photoexcitation. High-potential porphyrins have been chosen to model P680, the photoactive chlorophyll cluster of photosynthetic photosystem II (PSII). They have either two or three pentafluorophenyl groups at the meso positions to impart the high redox potential. The benzimidazole phenol (BIP) moiety models the Tyr[Formula: see text]-His190 pair of PSII, which is a redox mediator that shuttles electrons from the water oxidation catalyst to P680[Formula: see text]. The dyads consisting of a porphyrin and an unsubstituted BIP are designed to study one-electron one-proton transfer (E1PT) processes upon excitation of the porphyrin. When the BIP moiety is substituted with proton-accepting groups such as imines, one-electron two-proton transfer (E2PT) processes are expected to take place upon oxidation of the phenol by the excited state of the porphyrin. The bis-pentafluorophenyl porphyrins linked to BIPs provide platforms for introducing a variety of electron-accepting moieties and/or anchoring groups to attach semiconductor nanoparticles to the macrocycle. The triads thus formed will serve to study the PCET process involving the BIPs when the oxidation of the phenol is achieved by the photochemically produced radical cation of the porphyrin.

scholarly journals Visualizing the protons in a metalloenzyme electron proton transfer pathway

2020 ◽  
Vol 117 (12) ◽  
pp. 6484-6490 ◽  
Author(s):  
Hanna Kwon ◽  
Jaswir Basran ◽  
Juliette M. Devos ◽  
Reynier Suardíaz ◽  
Marc W. van der Kamp ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Electron Transfer ◽  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Proton Donor ◽  
Biological Processes ◽  
Proton Coupled Electron Transfer ◽  
Neutron Structure ◽  
Bona Fide ◽  
Electron Proton Transfer

In redox metalloenzymes, the process of electron transfer often involves the concerted movement of a proton. These processes are referred to as proton-coupled electron transfer, and they underpin a wide variety of biological processes, including respiration, energy conversion, photosynthesis, and metalloenzyme catalysis. The mechanisms of proton delivery are incompletely understood, in part due to an absence of information on exact proton locations and hydrogen bonding structures in a bona fide metalloenzyme proton pathway. Here, we present a 2.1-Å neutron crystal structure of the complex formed between a redox metalloenzyme (ascorbate peroxidase) and its reducing substrate (ascorbate). In the neutron structure of the complex, the protonation states of the electron/proton donor (ascorbate) and all of the residues involved in the electron/proton transfer pathway are directly observed. This information sheds light on possible proton movements during heme-catalyzed oxygen activation, as well as on ascorbate oxidation.

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