Paween Mahinthichaichan, Robert B. Gennis, and Emad Tajkhorshid.
Bacterial denitrifying nitric oxide reductases and aerobic
respiratory terminal oxidases use similar delivery pathways for their
molecular substrates.
Biochimica et Biophysica Acta - Bioenergetics, 1859:712-724,
2018.
(PMC: PMC6078787)
MAHI2018B-ET
The superfamily of heme-copper oxidoreductases (HCOs) include both NO
and O reductases.
Nitric oxide reductases (NORs) are bacterial membrane enzymes that
catalyze an intermediate step of denitrification by reducing nitric oxide (NO)
to nitrous oxide (NO).
They are structurally similar to heme-copper oxygen reductases (HCOs),
which reduce O to water.
The experimentally observed apparent bimolecular rate constant of NO
delivery to the deeply buried catalytic site of NORs was previously reported
to approach the diffusion-controlled limit (10-10
Ms).
Using the crystal structure of cytochrome-c dependent NOR (cNOR) from
Pseudomonas aeruginosa, we employed several protocols of
molecular dynamics (MD) simulation, which include flooding simulations of
NO molecules, implicit ligand sampling and umbrella sampling simulations,
to elucidate how NO in solution accesses the catalytic site of this cNOR.
The results show that NO partitions into the membrane, enters the enzyme
from the lipid bilayer and diffuses to the catalytic site via a hydrophobic
tunnel that is resolved in the crystal structures.
This is similar to what has been found for O diffusion through the
closely related O reductases.
The apparent second order rate constant approximated using the simulation
data is 5Ms, which is optimized by
the dynamics of the amino acid side chains lining in the tunnel.
It is concluded that both NO and O reductases utilize well defined
hydrophobic tunnels to assure that substrate diffusion to the buried catalytic
sites is not rate limiting under physiological conditions.
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