Biology Reference
In-Depth Information
including the TrpG8, LeuE11, TyrCD1, and AlaE7. The initial migration
of the ligand within the distal pocket leads to its rebinding to the haem
iron atom or to its escape into the solvent
via
a hydrophobic tunnel that
coincides with the internal cavities found in the crystallographic structure
of 2/2HbO (
Guallar et al., 2009
). This would indicate that the presence
of the conserved residues in group II and group III, but not in group I, is
responsible for the significantly different migration patterns in 2/2HbO
and 2/2HbN.
Within group II 2/2HbOs, the protein from
B. subtilis
is a peculiar
case, as the presence of a Thr residue at position E7 typically blocks the
E7 path and the X-ray crystallographic structure does not exhibit a clear
tunnel for ligand migration (
Giangiacomo et al., 2005
). However, O
2
asso-
ciation rate constant
k
on
is higher than that found for
M. tuberculosis
2/2HbO, and similar to that of
M. tuberculosis
2/2HbN (
Couture, Yeh,
et al., 1999; Giangiacomo et al., 2005; Pathania, Navani, Rajamohan, &
Dikshit, 2002
). The structural and the kinetic data have been reconciled
by classical molecular dynamics simulations of the oxy, carboxy, and deoxy
proteins which showed that GlnE11 presents an alternate conformation, giv-
ing rise to a wide ligand migration tunnel, topologically related to the long
tunnel branch found in group I 2/2HbNs. In
B. subtilis
2/2HbO, residue
TrpG8 does not block the tunnel, as generally assumed by inspection of
the crystal structure, due to a rearrangement in the distal site involving
GlnE11, and the tunnel is open due to the lack of the bulky PheE15,
the tunnel gating residue in
M. tuberculosis
2/2HbN. On the other hand,
the results for the CO and O
2
bound protein show that GlnE11 is directly
involved in the stabilization of the coordinated ligand, playing a similar
role as TyrB10 and TrpG8 in other 2/2Hbs (
Boechi et al., 2010
). These
results underline once more the plasticity and redundancy of several residues
within the globin fold that account
for
the varied ligand-binding
kinetics observed.
Analysis of group III
C. jejuni
2/2HbP structure shows no evident pro-
tein matrix tunnel/cavity system, mostly due to the peculiar backbone con-
formation of the pre-B helix residues, and to bulky side-chain substitutions
(conserved among members of group III) at residues that define the tunnel/
cavities walls in group I and II 2/2Hbs (
Nardini et al., 2006
). Since HisE7
(conserved in group III) adopts two alternate conformations ('open' and
'closed') in
C. jejuni
2/2HbP, E7 haem-distal-site gating has been proposed
to play a functional role for ligand diffusion to the haem, in the absence of a
protein matrix tunnel/cavity system (
Nardini et al., 2006
).
