Distinguishing Nitro vs Nitrito Coordination in Cytochrome c′ Using Vibrational Spectroscopy and Density Functional Theory

Zach N. Nilsson, Brian L. Mandella, Kakali Sen, Demet Kekilli, Michael A. Hough, Pierre Moenne-Loccoz, Richard W. Strange, Colin R. Andrew

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Nitrite coordination to heme cofactors is a key step in the anaerobic production of the signaling molecule nitric oxide (NO). An ambidentate ligand, nitrite has the potential to coordinate via the N- (nitro) or O- (nitrito) atoms in a manner that can direct its reactivity. Distinguishing nitro vs nitrito coordination, along with the influence of the surrounding protein, is therefore of particular interest. In this study, we probed Fe(III) heme-nitrite coordination in Alcaligenes xylosoxidans cytochrome c′ (AXCP), an NO carrier that excludes anions in its native state but that readily binds nitrite (Kd ∼ 0.5 mM) following a distal Leu16 → Gly mutation to remove distal steric constraints. Room-temperature resonance Raman spectra (407 nm excitation) identify ν(Fe-NO2), δ(ONO), and νs(NO2) nitrite ligand vibrations in solution. Illumination with 351 nm UV light results in photoconversion to {FeNO}6 and {FeNO}7 states, enabling FTIR measurements to distinguish νs(NO2) and νas(NO2) vibrations from differential spectra. Density functional theory calculations highlight the connections between heme environment, nitrite coordination mode, and vibrational properties and confirm that nitrite binds to L16G AXCP exclusively through the N atom. Efforts to obtain the nitrite complex crystal structure were hampered by photochemistry in the X-ray beam. Although low dose crystal structures could be modeled with a mixed nitrite (nitro)/H2O distal population, their photosensitivity and partial occupancy underscores the value of the vibrational approach. Overall, this study sheds light on steric determinants of heme-nitrite binding and provides vibrational benchmarks for future studies of heme protein nitrite reactions.

Original languageEnglish (US)
Pages (from-to)13205-13213
Number of pages9
JournalInorganic Chemistry
Volume56
Issue number21
DOIs
StatePublished - Nov 6 2017

Fingerprint

Vibrational spectroscopy
nitrites
cytochromes
Nitrites
Cytochromes c
Density functional theory
density functional theory
spectroscopy
Heme
nitric oxide
Nitric Oxide
Crystal structure
Ligands
Hemeproteins
proteins
Atoms
vibration
ligands
crystal structure
Photosensitivity

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Inorganic Chemistry

Cite this

Distinguishing Nitro vs Nitrito Coordination in Cytochrome c′ Using Vibrational Spectroscopy and Density Functional Theory. / Nilsson, Zach N.; Mandella, Brian L.; Sen, Kakali; Kekilli, Demet; Hough, Michael A.; Moenne-Loccoz, Pierre; Strange, Richard W.; Andrew, Colin R.

In: Inorganic Chemistry, Vol. 56, No. 21, 06.11.2017, p. 13205-13213.

Research output: Contribution to journalArticle

Nilsson, Zach N. ; Mandella, Brian L. ; Sen, Kakali ; Kekilli, Demet ; Hough, Michael A. ; Moenne-Loccoz, Pierre ; Strange, Richard W. ; Andrew, Colin R. / Distinguishing Nitro vs Nitrito Coordination in Cytochrome c′ Using Vibrational Spectroscopy and Density Functional Theory. In: Inorganic Chemistry. 2017 ; Vol. 56, No. 21. pp. 13205-13213.
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AU - Kekilli, Demet

AU - Hough, Michael A.

AU - Moenne-Loccoz, Pierre

AU - Strange, Richard W.

AU - Andrew, Colin R.

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AB - Nitrite coordination to heme cofactors is a key step in the anaerobic production of the signaling molecule nitric oxide (NO). An ambidentate ligand, nitrite has the potential to coordinate via the N- (nitro) or O- (nitrito) atoms in a manner that can direct its reactivity. Distinguishing nitro vs nitrito coordination, along with the influence of the surrounding protein, is therefore of particular interest. In this study, we probed Fe(III) heme-nitrite coordination in Alcaligenes xylosoxidans cytochrome c′ (AXCP), an NO carrier that excludes anions in its native state but that readily binds nitrite (Kd ∼ 0.5 mM) following a distal Leu16 → Gly mutation to remove distal steric constraints. Room-temperature resonance Raman spectra (407 nm excitation) identify ν(Fe-NO2), δ(ONO), and νs(NO2) nitrite ligand vibrations in solution. Illumination with 351 nm UV light results in photoconversion to {FeNO}6 and {FeNO}7 states, enabling FTIR measurements to distinguish νs(NO2) and νas(NO2) vibrations from differential spectra. Density functional theory calculations highlight the connections between heme environment, nitrite coordination mode, and vibrational properties and confirm that nitrite binds to L16G AXCP exclusively through the N atom. Efforts to obtain the nitrite complex crystal structure were hampered by photochemistry in the X-ray beam. Although low dose crystal structures could be modeled with a mixed nitrite (nitro)/H2O distal population, their photosensitivity and partial occupancy underscores the value of the vibrational approach. Overall, this study sheds light on steric determinants of heme-nitrite binding and provides vibrational benchmarks for future studies of heme protein nitrite reactions.

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