Biology Reference
In-Depth Information
The protein matrix tunnel, linking the protein surface to the haem distal
site, appears to be conserved in group I 2/2Hbs, with the exception of the
hexacoordinated
Synechocystis
sp. 2/2HbN, likely because of the conforma-
tional transitions required in this protein distal site region to achieve haem
hexacoordination (
Hoy et al., 2004
). An alternative haem distal site access
through the exposed 8-methyl edge of the haem group and near the propi-
onates has been proposed (
Falzone et al., 2002; Scott et al., 2010
).
In agreement with the availability of cavities in the protein matrix, it has
been shown that at least three group I 2/2Hbs, from
C. eugametos
,
M. tuberculosis
, and
P. caudatum
, can bind Xe atoms in the crystalline state.
The Xe atoms map experimentally at multiple sites and with comparable
topology within the tunnel/cavity path in these 2/2Hbs (
Milani, Pesce,
et al., 2004
). In particular, in
C. eugametos
2/2HbN and in
M. tuberculosis
2/2HbN, the tunnel is composed of two roughly orthogonal branches con-
verging at the haem distal site from two distinct protein surface access sites.
On one hand, a 20
˚
long tunnel branch connects the protein region nestled
between the AB and GH hinges to the haem distal site. On the other, a short
tunnel branch of about 8
˚
connects an opening in the protein structure
between G- and H-helices to the haem (
Fig. 2.2
). In
P. caudatum
2/2HbN, the haem site is connected to the solvent region by a three-cavity
system, topologically distributed along the tunnel's long branch described
above (
Milani, Pesce, et al., 2004
). A similar, but more open, tunnel system
is also present in
T. pyriformis
2/2HbN, where the exit of the short branch
differs slightly in orientation relative to
M. tuberculosis
2/2HbN. The tunnel
volume of
T. pyriformis
2/2HbN is about 380
˚
3
, which is similar to that of
C. eugametos
2/2HbN (400
˚
3
), but larger than that of
M. tuberculosis
and
P. caudatum
HbNs (265
˚
3
and 180
˚
3
, respectively) (
Igarashi et al.,
2011
). Although protein cavity volumes vary among 2/2HbNs, these values
are not correlated with O
2
association rate constants (
Couture, Das, et al.,
1999; Couture, Yeh, et al., 1999; Das et al., 2000; Igarashi et al., 2011;
Ouellet et al., 2008
).
Residues lining the tunnel branches are hydrophobic and are substan-
tially conserved throughout group I (
Vuletich & Lecomte, 2006
). PheE15,
a well-conserved residue, adopts two conformations in
M. tuberculosis
2/2HbN (
Fig. 2.2
). In one, PheE15 benzene side chain blocks the
longer channel of the tunnel path (the so-called closed state) and in the other
it does not (the open state) (
Milani et al., 2001; Milani, Pesce, et al., 2004
).
M. tuberculosis
2/2HbN is endowed with a potent nitric oxide dioxygenase
activity which allows it to relieve nitrosative stress and enhance
in vivo
