Biology Reference
In-Depth Information
volume, with the short tunnel being only 13
˚
long with the surface entry
occurring between the G and H helices and defined by PheG5, AlaG9,
LeuH8 and AlaH12 (
Daigle, Guertin, & Lag
¨
e, 2009
). This tunnel system
may function as a way to create high concentrations of ligands in a local envi-
ronment; its hydrophobicity also slows the access of water to the haem
pocket (
Dantsker et al., 2004
). As Bidon-Chanal et al. comment, ligand dif-
fusion appears to be a limiting factor in the reaction of trHbN and certain
aspects of the protein appear to have evolved to ensure that gaseous ligands
can access the haem cavity. For example, the TyrB10-GlnE11 pair
undergoes a conformation change upon binding of O
2
to the haem, accessed
via the short tunnel, which causes the main tunnel to open via movement of
the PheE15 gate (
Bidon-Chanal, Marti, Estrin, & Luque, 2007
).
Molecular dynamics studies have shown that the long tunnel provides
the lowest energy pathway for NO migration to the haem (
Lama et al.,
2009
). The proposed mechanism—that the main tunnel opens only after
O
2
has bound to the haem—suggests that the protein may have evolved this
control to ensure that NO can enter the protein only after O
2
has bound to
the haem, resulting in the NOD reaction and the production of nitrate (see
Section 5.1
). The coordination state of the haem is the ultimate factor con-
trolling the positions of key residues which allow or block ligand binding:
when the protein is in the deoxy form, molecular dynamics show that the
long tunnel is completely closed (
Bidon-Chanal et al., 2006
). A paper from
2011 proposes some additional conclusions about the tunnel system in
trHbN, suggesting the presence of two extra tunnels, termed EH and BE,
that lead from the surface of the protein to the haem distal pocket that
are not seen in the crystal structure (
Daigle et al., 2009
). The EH tunnel
is located between the E and H helices and the entrance is defined by the
residues PheE14, AlaE18, ValH10 and LeuH14. It is 15
˚
long and access
by ligands is controlled by PheE15 (
Crespo et al., 2005
). In the open state,
this tunnel can merge with the long tunnel and the authors suggest that
ligands gain access to the haem via a two-stage process, first moving from
the substrate into the protein itself, and then across the PheE15 barrier into
the haem distal pocket (
Daigle et al., 2009
). The BE tunnel, between B and
E helices, has its entrance defined by TyrB10, LeuB14 and MetE4. It is
10.5
˚
long and has two conformations determined by the positioning of
TyrB10, and movements only appear to occur when simulations were done
with deoxy trHbN (
Daigle et al., 2009
). The paper is in variance with
another molecular dynamics study on the tunnel system: results here show
that in the open state, PheE15 is parallel to the long tunnel axis and in the
