Biology Reference
In-Depth Information
closed state is orthogonal (
Daigle et al., 2009
); however, Bidon-Chanal et al.
propose that the open state occurs when the phenyl ring of PheE15 is parallel
to the axis of the tunnel and the closed state when it is closer to the haem
(
Bidon-Chanal et al., 2006
). This disagreement could be due to the pre-A
region, which appears to behave differently in the two simulations and will
be discussed later.
More recent work, using solution NMR and molecular dynamics to fur-
ther probe the structure of trHbN, has added to our understanding. These
authors propose that the F and G helices provide flexibility to the protein,
with the B and E helices being more rigid (
Savard et al., 2011
). The molec-
ular dynamics study identified that helices B, G and H and residue TyrB10
have slow motions, and that residues in helices G and H, through which the
short tunnel passes, are orientated away from the solvent. This could perhaps
slow ligands passing through the tunnel or the movement of this part of the
protein, which is potentially vital for the release of the relatively bulky
nitrate once the reaction is complete (
Savard et al., 2011
). Their data suggest
that this mixture of flexibility and rigidity is required for the formation of the
four hydrophobic tunnels, allowing ligand migration that links the haem
centre to the solvent. This agrees with the conclusions reached in Daigle
et al., which showed that protein rigidity is required to generate and main-
tain the tunnels with the flexibility of the protein able to reshape the tunnels
to allow passage of various ligands (
Daigle et al., 2009
). A previous study also
commented on the complexity of
the flexibility of
trHbN (
Crespo
et al., 2005
).
The control of ligand binding, and ligand access to the haem, has been
studied extensively. One important residue conserved among Mycobacterial
trHbs (
Fig. 5.1
) is TyrB10, which is located buried in the haem distal pocket
and forms hydrogen bonds with GlnE11, thereby creating a polar environ-
ment in the haem pocket (
Mukai, Ouellet, Ouellet, Guertin, & Yeh, 2004
).
TyrB10 is unique to the Mycobacterial Hbs, and Resonance Raman spectral
analysis of Mtb trHbN mutants (where TyrB10 was mutated to Leu or Phe)
showed that a change in this residue gives the globin similar properties to
other haem-containing proteins, suggesting that TyrB10 plays an important
role in ligand binding by Mycobacterial trHbN (
Yeh, Couture, Ouellet,
Guertin, & Rousseau, 2000
). Data also showed that the binding properties
between bound O
2
and TyrB10 in the haem pocket are unique. The haem
group of Mtb trHbN can form H-bonds with many ligands (
Yeh et al.,
2000
) including O
2
(
Crespo et al., 2005
), and NO (
Mukai et al., 2004
)
and TyrB10 has been shown to stabilise bound O
2
at the distal site
