Biology Reference
In-Depth Information
characterized by a distinct pattern of hydrogen-bonding interaction, creates
differences in the local polarity and affects the stabilization of the haem-bound
ligand, the behaviour of each residue being affected by the other residues.
Therefore, the oxygen-binding affinity (which in
C. jejuni
2/2HbP is very
high due to a low dissociation rate constant of 0.0041 s
1
)istheresultofa
cooperative property (
Arroyo Ma˜ez et al., 2011; Lu, Egawa, Wainwright,
Poole, & Yeh, 2007
). Furthermore, in the crystal structure of the
C. jejuni
2/2HbP-cyanide complex, residue HisE7 occurs in two distinct conforma-
tions, corresponding to side-chain orientations that point towards the solvent
or towards the haem distal site, respectively. Alternative position for the
strictly conserved HisE7 suggests a ligand-gating mechanism similar to that
described in
P. caudatum
2/2HbN (
Das et al., 2000; Nardini et al., 2006
).
4. TUNNELS AND CAVITIES THROUGH 2/2Hb
PROTEIN MATRIX
Despite the high-density packing of residues in the protein core, inner
cavities or tunnels are often found in the protein matrix. Although such res-
idue packing 'defects' may hamper the thermodynamic stability of a folded
protein, their presence offers an evolutionary, possibly functional, advantage
to the hosting protein. For instance, in enzymes they may provide preferred
paths or intramolecular docking stations for the diffusion of substrates and
products (
Milani et al., 2003; Raushel, Thoden, & Holden, 2003; Weeks,
Lund, & Raushel, 2006
). In globins, the haem site is often buried inside
the protein chain, which prevents direct contact with solvent. Therefore,
the ligand has to trace its way to the haem by traversing the globin helical
fold. The migration pathways are commonly believed to result from thermal
fluctuations of the protein molecular structure, and the ligand access sites are
located in (what are held to be) evolutionarily optimized well-defined
regions of proteins that can be identified with systematic experimental
and computational efforts (
Brunori et al., 1999
).
The analysis of the three-dimensional structures of 2/2Hbs have shown
that the group I 2/2HbN fold is characterized by the presence of inter-
connected protein matrix apolar cavities, or a continuous tunnel, which
connect the protein surface to an inner region merging with the haem distal
site (
Milani, Pesce, et al., 2004; Pesce, Milani, Nardini, & Bolognesi, 2008
).
Such peculiar feature may be related to the orientation of the CD-D region
that forces positioning of the E-helix close to the haem distal face, thus
preventing ligand access to the distal site cavity through the classical E7.
