Despite myriad challenges, clinicians see room for progress.
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Edited by Bettie Sue Masters, Duke University Medical Center, Durham, NC, and accepted by Editorial Board Member Gregory A. Petsko July 19, 2017 (received for review December 26, 2016)
Significance
Denitrification, a form of microbial anaerobic respiration where nitrate is sequentially reduced (NO3− → NO2− → NO → N2O → N2) is environmentally, biologically, and chemically interesting, as well as being medically significant. Some pathogenic bacteria, including the major opportunistic pathogen Pseudomonas aeruginosa, can survive in oxygen-limited environments such as biofilms and the lungs of cystic fibrosis patients, owing to denitrification. The current proposal of a complex formation of NO-generating nitrite reductase and NO-decomposing nitric oxide reductase for rapid elimination of NO, a cytotoxic intermediate, in denitrification contributes to further understanding of denitrification and to the design of antimicrobial drugs. This paper also provides an idea of how biological systems control the dynamics of cytotoxic diffusible compounds such as NO in cells.
Abstract
Nitric oxide (NO) plays diverse and significant roles in biological processes despite its cytotoxicity, raising the question of how biological systems control the action of NO to minimize its cytotoxicity in cells. As a great example of such a system, we found a possibility that NO-generating nitrite reductase (NiR) forms a complex with NO-decomposing membrane-integrated NO reductase (NOR) to efficiently capture NO immediately after its production by NiR in anaerobic nitrate respiration called denitrification. The 3.2-Å resolution structure of the complex of one NiR functional homodimer and two NOR molecules provides an idea of how these enzymes interact in cells, while the structure may not reflect the one in cells due to the membrane topology. Subsequent all-atom molecular dynamics (MD) simulations of the enzyme complex model in a membrane and structure-guided mutagenesis suggested that a few interenzyme salt bridges and coulombic interactions of NiR with the membrane could stabilize the complex of one NiR homodimer and one NOR molecule and contribute to rapid NO decomposition in cells. The MD trajectories of the NO diffusion in the NiR:NOR complex with the membrane showed that, as a plausible NO transfer mechanism, NO released from NiR rapidly migrates into the membrane, then binds to NOR. These results help us understand the mechanism of the cellular control of the action of cytotoxic NO.
Footnotes
- ↵1To whom correspondence may be addressed. Email: yshiro{at}sci.u-hyogo.ac.jp or ttosha{at}spring8.or.jp.
Author contributions: E.T., Y. Sugita, Y. Shiro, and T.T. designed research; E.T., K. Yamada, P.-H.W., K.H., R.Y., K.M., S.I., T.M., K. Yagi, H. Sawai, H.A., H. Sugimoto, and T.T. performed research; E.T., K. Yamada, P.-H.W., K.H., R.Y., K.M., S.I., T.M., K. Yagi, H. Sawai, H.A., H. Sugimoto, and T.T. analyzed data; and E.T., Y. Sugita, Y. Shiro, and T.T. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission. B.S.M. is a guest editor invited by the Editorial Board.
Data deposition: Atomic coordinates and structure factors have been deposited in the Protein Data Bank (PDB ID code 5GUW for the cd1NiR:cNOR complex and 5GUX for the xenon derivative of cNOR).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1621301114/-/DCSupplemental.
Dynamics of NO controlled by protein complex
Article Classifications
- Biological Sciences
- Biophysics and Computational Biology
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