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Nitric oxide binding to ferrous nitrobindins: A computer simulation investigation.

Andresa Messias1, Andrea Pasquadibisceglie2, Diego Alonso de Armiño1

  • 1Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.

Journal of Inorganic Biochemistry
|August 12, 2023
PubMed
Summary
This summary is machine-generated.

Nitrobindins (Nbs) exhibit slow nitric oxide (NO) binding due to iron atom displacement, not ligand migration barriers. NO binding also triggers a His-Fe bond shift, forming a stable alternative conformation with water molecules.

Keywords:
Computer simulationHeme-proteinsNitric oxideNitrobindinQM/MM

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biophysics

Background:

  • Nitrobindins (Nbs) are conserved heme-proteins with exposed heme-iron.
  • Nbs show slower ligand binding kinetics than myoglobins (Mbs) despite distal accessibility.
  • Nitric oxide (NO) binding to Nbs weakens or cleaves the proximal histidine-iron bond.

Purpose of the Study:

  • To elucidate the molecular mechanisms behind ligand binding kinetics in Nitrobindins.
  • To investigate the role of ligand migration and bond formation in NO binding.
  • To understand the proximal histidine-iron bond dynamics upon NO interaction.

Main Methods:

  • Classical molecular dynamics simulations with steered molecular dynamics.
  • Jarzinski equality to calculate ligand migration free energy profiles.
  • Quantum-classical (QM-MM) optimizations for His-Fe bond dynamics.

Main Results:

  • Ligand migration in Nbs is largely unhindered.
  • The primary barrier to NO binding is the significant displacement of the iron atom from the heme plane.
  • NO binding induces a stable alternative conformation of the proximal histidine, interacting with water molecules.

Conclusions:

  • The slow NO binding rate in Nbs is attributed to the iron atom's displacement, not ligand migration.
  • Computational simulations reveal the structural basis for altered His-Fe bond stability upon NO binding.
  • A water-mediated alternative conformation of proximal histidine is identified in Nbs.