Biology Reference
In-Depth Information
the mutant amino acid residue.
Chemical difference
is a measure, originally devised
by Grantham (1974), that combined the three interdependent properties of chem-
ical composition, polarity and molecular volume of an amino acid residue. When
the magnitude of biochemical change upon substitution was measured in this way
and related to the clinical severity of the resulting disease phenotype, nonconser-
vative substitutions (i.e. those characterized by large chemical differences) were
found to result in severe rather than mild or moderate hemophilia B approxi-
mately 1.7 times more often than conservative substitutions. Conversely, conserv-
ative substitutions were 3- to 4-fold more likely to be associated with a moderate
or mild phenotype than their nonconservative counterparts. The possibility was
considered that conservative amino acid substitutions might be more likely to
come to clinical attention in the tightly packed core of the protein as opposed to
the surface of the molecule where they mght be more readily tolerated. However,
since mutations from all chemical difference classes appeared to be scattered over
all domains of the protein and since no one chemical difference class was found to
be associated solely with surface or buried residues, there appeared to be no rela-
tionship between the magnitude of the amino acid exchange and the location of
the affected residue (Wacey
et al
., 1994).
The extent of evolutionary sequence conservation exhibited by amino acid
residues in factor IX was also found to correlate with disease severity. Whilst 71%
of mutations at 'highly conserved' residues (residues conserved in all mammalian
factor IX proteins and in three other serine proteases) caused severe rather than
mild or moderate hemophilia B, this was the case for only 50% of mutations at less
conserved residues. Furthermore, Wacey
et al
. (1994) estimated that missense
mutations at non-conserved residues were 15-20 times less likely than mutations
at conserved residues to result in a disease phenotype at all. Although this implies
that many missense mutations at evolutionarily unconserved residues are toler-
ated by the molecule and do not come to clinical attention, the relative impor-
tance of such residues was considered to be greater than previously claimed by
Bottema
et al
. (1991). Several explanations were suggested for this discrepancy.
Firstly, the sample of mutations used by Wacey
et al
. (1994) was three times larger
than that of Bottema
et al
. (1991). Secondly, Wacey
et al
. (1994) allowed for deter-
minants neglected by Bottema
et al
. (1991) viz. the actual
F9
gene coding sequence
and the redundancy of the genetic code. Finally, the two studies were not directly
comparable since Wacey
et al
. (1994) confined their estimation of clinical obser-
vation likelihoods to severe cases of hemophilia B in order to cope with the prob-
lem of identical-by-descent mutations which are likely to be more prevalent in
cases of mild or moderate disease.
Amino acid residues which are sequence conserved both in mammalian factor
IX proteins and four different human serine proteases are likely to be critical for
functions common to all serine proteases. These residues are located predomi-
nantly in the interior of factor IX, within
-turns, and Wacey
et al
.
(1994) found that substitutions tended to cluster in the Gla domain, the EGF
domains and the serine protease domain (around the reactive site and oxyanion
hole). All but one of the Cys residues known to be involved in disulfide bonding
were affected by mutation as were the reactive site residues, residues involved in
carboxylase recognition and activation peptide cleavage site, and residues which
-helices or
