Understanding the functioning of the respiratory enzyme nitric oxide reductase through computer simulations

• Project/Area Number: 22770163
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Biophysics
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: PISLIAKOV Andrei 独立行政法人理化学研究所, 杉田理論生物化学研究室, 国際特別研究員 (70565770)
• Project Period (FY): 2010 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2011: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2010: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: membrane proteins / respiratory enzymes / nitric oxide reductase / MD simulation / water dynamics / proton transfer / enzyme catalysis / denitrification

Research Abstract

We investigated proton pathways in nitric oxide reductases(cNOR and qNOR types), both in wild-type proteins and in silico mutants. Results provide insights into proton uptake mechanism of NORs and shed light on molecular evolution of respiratory enzymes.

Research Products

• [Journal Article] Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus (2012)
  • Author(s): Y. Matsumoto, T. Tosha, A. V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita, and Y. Shiro
  • Journal Title: Nature Structural and Molecular Biology Volume: Vol.19 Pages: 238-245
• [Journal Article] Crystal Structure of Quinol-Dependent Nitric Oxide Reductase from Geobacillus stearithermophilus (2012)
  • Author(s): Y.Matsumoto, T.Tosha, A.V.Pisliakov, T.Hino, H.Sugimoto, S.Nagano, Y.Sugita, Y.Shiro
  • Journal Title: Nat.Strl.Mol.Biol. Volume: 19 Issue: 2 Pages: 238-245
  • DOI: 10.1038/nsmb.2213
  • Peer Reviewed
• [Journal Article] Structural insights into electron transfer in caa3-type cytochrome oxidase (2012)
  • Author(s): JA Lyons, D Aragao, O Slattery, AV Pisliakov, T Soulimane, M Caffrey
  • Journal Title: Nature Volume: 487 Issue: 7408 Pages: 514-518
  • DOI: 10.1038/nature11182
  • Peer Reviewed
• [Journal Article] Molecular dynamics simulations reveal proton transfer pathways in cytochrome c-dependent nitric oxide reductase (2012)
  • Author(s): A.V Pisliakov, T.Hino, Y.Shiro, Y.Sugita
  • Journal Title: PLoS Computational Biology Volume: 8
  • Peer Reviewed
• [Journal Article] Structural insights into electron transfer in caa3-type cytochrome oxidase
  • Author(s): J. A. Lyons, D. Aragao, O. Slattery, A. V. Pisliakov, T. Soulimane, and M. Caffrey
  • Journal Title: Nature Volume: (in press)
• [Presentation] Computational studies of nitric oxide reductases (2012)
  • Author(s): A. V. Pisliakov
  • Organizer: Biophysical Society Annual Meeting
  • Place of Presentation: San Diego, CA, USA.
  • Year and Date: 2012-02-25
• [Presentation] Mechanism of proton of proton uptake in nitric oxide reductases (2012)
  • Author(s): A. V. Pisliakov
  • Organizer: Gordon Conference"Protons and Membrane Reactions"
  • Place of Presentation: Ventura, CA, USA.
  • Year and Date: 2012-02-20
• [Presentation] Mechanism of proton of proton uptake in nitric oxide reductases (2012)
  • Author(s): Pisliakov A.V.
  • Organizer: Gordon Conference "Protons and Membrane Reactions"
  • Place of Presentation: Ventura, CA, USA
  • Year and Date: 2012-02-20
• [Presentation] Computer Simulations Reveal Proton Transfer Pathways in Nitric Oxide Reductases (2011)
  • Author(s): Pisliakov A.V.
  • Organizer: 49th Annual Meeting of the Biophysical Society of Japan
  • Place of Presentation: Himeji
  • Year and Date: 2011-09-17
• [Presentation] Computer simulations of proton transfer in cytochrome c oxidase and nitric oxide reductase (2011)
  • Author(s): A. V. Pisliakov
  • Organizer: 8th European Biophysics Congress
  • Place of Presentation: Budapest, Hungary.(oral)
  • Year and Date: 2011-08-25
• [Presentation] Computer simulations of proton transfer in cytochrome c oxidase and nitric oxide reductase (2011)
  • Author(s): Pisliakov A.V.
  • Organizer: 8th European Biophysics Congress
  • Place of Presentation: Budapest, Hungary
  • Year and Date: 2011-08-25
• [Presentation] Molecular Dynamics Simulations Reveal Proton Transfer Pathways in NORs (2011)
  • Author(s): Pisliakov A.V.
  • Organizer: Workshop "From Computational Biophysics to Systems Biology"
  • Place of Presentation: Juelich, Germany
  • Year and Date: 2011-07-21
• [Presentation] Water dynamics and proton transfer in cNOR (2011)
  • Author(s): A. V. Pisliakov
  • Organizer: Cold Spring Harbor Conference "Membrane Proteins : Structure and Function"
  • Place of Presentation: Suzhou, China.(oral)
  • Year and Date: 2011-05-17
• [Presentation] Water dynamics and proton transfer in nitric oxide reductase (2011)
  • Author(s): Pisliakov A.V.
  • Organizer: 8th European Biophysics Congress
  • Place of Presentation: Suzhou, China
  • Year and Date: 2011-05-17
• [Presentation] Water channels and proton transfer pathways in nitric oxide reductase (2010)
  • Author(s): Andrei Pisliakov
  • Organizer: Symposium on Hydration Dynamics and Molecular Processes
  • Place of Presentation: Wako
  • Year and Date: 2010-12-01
• [Presentation] Biological proton transfer : simulation methods and applications (2010)
  • Author(s): Andrei Pisliakov
  • Organizer: European Bioenergetics Conference
  • Place of Presentation: Warsaw, Poland
• [Presentation] Proton transfer in cytochrome c oxidase and nitric oxide reductase (2010)
  • Author(s): Andrei Pisliakov
  • Organizer: Gordon Conference on Computational Chemistry
  • Place of Presentation: LesDiablerets, Switzerland
• [Presentation] Proton transfer pathways in cNOR revealed by MD simulations (2010)
  • Author(s): Andrei Pisliakov
  • Organizer: 48th Annual Meeting of the Biophysical Society of Japan
  • Place of Presentation: Sendai
• [Presentation] Molecular dynamics simulations of NORs (2010)
  • Author(s): Andrei Pisliakov
  • Organizer: Frontiers in the Simulations of Macromolecules
  • Place of Presentation: Los Angeles, CA, USA
• [Remarks] Best Poster Award at 2012 RIKEN SPDR and FPR Research Results Session, 2012/01/14, Wako-shi.