Ultrafast dynamics of diatomic ligand binding to nitrophorin 4

Abdelkrim Benabbas, Xiong Ye, Minoru Kubo, Zhenyu Zhang, Estelle M. Maes, William "Bill" Montfort, Paul M. Champion

Research output: Contribution to journalArticle

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Abstract

Nitrophorin 4 (NP4) is a heme protein that stores and delivers nitric oxide (NO) through pHsensitive conformational change. This protein uses the ferric state of a highly ruffled heme to bind NO tightly at low pH and release it at high pH. In this work, the rebinding kinetics of NO and CO to NP4 are investigated as a function of iron oxidation state and the acidity of the environment. The geminate recombination process of NO to ferrous NP4 at both pH 5 and pH 7 is dominated by a single ∼7 ps kinetic phase that we attribute to the rebinding of NO directly from the distal pocket. The lack of pH dependence explains in part why NP4 cannot use the ferrous state to fulfill its function. The kinetic response of ferric NP4NO shows two distinct phases. The relative geminate amplitude of the slower phase increases dramatically as the pH is raised from 5 to 8. We assign the fast phase of NO rebinding to a conformation of the ferric protein with a closed hydrophobic pocket. The slow phase is assigned to the protein in an open conformation with a more hydrophilic heme pocket environment. Analysis of the ultrafast kinetics finds the equilibrium off-rate of NO to be proportional to the open state population as well as the pHdependent amplitude of escape from the open pocket. When both factors are considered, the off-rate increases by more than an order of magnitude as the pH changes from 5 to 8. The recombination of CO to ferrous NP4 is observed to have a large nonexponential geminate amplitude with rebinding time scales of ∼10 -11-109 s at pH 5 and ∼10 10-108 s at pH 7. The nonexponential CO rebinding kinetics at both pH 5 and pH 7 are accounted for using a simple model that has proven effective for understanding CO binding in a variety of other heme systems (Ye, X.; et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14682).

Original languageEnglish (US)
Pages (from-to)2811-2820
Number of pages10
JournalJournal of the American Chemical Society
Volume132
Issue number8
DOIs
StatePublished - Feb 24 2010

Fingerprint

Nitric oxide
Nitric Oxide
Ligands
Carbon Monoxide
Kinetics
Heme
Proteins
Conformations
Hemeproteins
Genetic Recombination
nitrophorin
Acidity
Protein Conformation
Iron
Oxidation

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Benabbas, A., Ye, X., Kubo, M., Zhang, Z., Maes, E. M., Montfort, W. B., & Champion, P. M. (2010). Ultrafast dynamics of diatomic ligand binding to nitrophorin 4. Journal of the American Chemical Society, 132(8), 2811-2820. https://doi.org/10.1021/ja910005b

Ultrafast dynamics of diatomic ligand binding to nitrophorin 4. / Benabbas, Abdelkrim; Ye, Xiong; Kubo, Minoru; Zhang, Zhenyu; Maes, Estelle M.; Montfort, William "Bill"; Champion, Paul M.

In: Journal of the American Chemical Society, Vol. 132, No. 8, 24.02.2010, p. 2811-2820.

Research output: Contribution to journalArticle

Benabbas, A, Ye, X, Kubo, M, Zhang, Z, Maes, EM, Montfort, WB & Champion, PM 2010, 'Ultrafast dynamics of diatomic ligand binding to nitrophorin 4', Journal of the American Chemical Society, vol. 132, no. 8, pp. 2811-2820. https://doi.org/10.1021/ja910005b
Benabbas, Abdelkrim ; Ye, Xiong ; Kubo, Minoru ; Zhang, Zhenyu ; Maes, Estelle M. ; Montfort, William "Bill" ; Champion, Paul M. / Ultrafast dynamics of diatomic ligand binding to nitrophorin 4. In: Journal of the American Chemical Society. 2010 ; Vol. 132, No. 8. pp. 2811-2820.
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