Biology Reference
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As expected from this reported data, the protein is six-coordinated and the
haem is in the high-spin form when in the ferric state. However, compared
with Mtb trHbN, Ms trHbN shows a faster rate of autoxidation (
Lama
et al., 2006
).
The NOD reaction of trHbN has also been studied using molecular
dynamics. Briefly, the reaction is as follows: when the protein is in the
oxy form, NO binds which leads to a peroxynitrite intermediate. This is
rearranged to the nitrato complex, with nitrate finally dissociating, leaving
trHbN in the ferric form (
Mishra & Meuwly, 2010
). This reaction is
facilitated by the side chains TyrB10 and GlnE11, which act to orientate
the ligands in the correct position via the dynamic hydrogen bonding
network, especially in the third step where GlnE11 stops the ligand from
moving too much and allowing the reaction to continue with all the ligands
in the correct place. The second step disagrees with the accepted mechanism
which predicts a dissociated state; molecular dynamics simulations on
this scale suggest that this is energetically unfavourable and the new
mechanism, involving simply a rearrangement, is more likely (
Mishra &
Meuwly, 2010
). During the final step, the haem changes to a six-coordinate
species from five-coordinated. This study therefore shows that the protein
environment plays a role in the NOD reaction, in agreement with a study
which showed that upon NO binding, the protein undergoes a large-scale
conformational change that extends to the E and B helices (
Mukai et al.,
2004
). However, both of these are in contrast with another study
(
Crespo et al., 2005
) which suggests that the protein environment is
not important.
3.2. Group II trHbs: trHbO
3.2.1 Structural features and dynamics
Less is known about the structure and dynamics of trHbO. As shown in
Fig. 5.2
, as for trHbN, there is extensive structural conservation of the
important residues required for the formation of the 2-over-2 globin fold;
these include PheB9 and TyrB10, PheE14 and HisF8 but not CD1, which is
often Phe in other globins but here it is Tyr (
Mukai, Savard, Ouellet,
Guertin, &Yeh, 2002
). Unlike trHbN, trHbO does not have a pre-A region
but does have an EF-loop region which is highly conserved within the group
and contains a highly charged, polar sequence motif (
Pathania, Navani,
Rajamohan, et al., 2002
), potentially important to the function of trHbO,
which is probably different to that of trHbN (see
Section 5
). Resonance
Raman spectroscopy showed that the proximal ligand is His and analysis
