Biology Reference
In-Depth Information
active site, as long as domain A is allosteric (i.e., mechanically coupled) to
domain B. Because of their postulated role in catalysis, it can be predicted that
these
NR residues
in domain A will be evolutionarily conserved and coevolve
with the
catalytic residues
in domain B, similar to the critical residues found in
the WW domain proteins (Lockless and Ranganathan 1999; Suel et al 2003;
Socolich et al. 2005, and Poole and Ranganathan 2006). It is postulated here
that the NR residues are responsible for the
ruggedness
of the waiting time
histograms (Fig.
11.24
). Therefore
it can be predicted that mutating one or
more of the NR residues of COx will remove the ruggedness of the waiting time
histograms
(see the lower panel of Fig.
11.24
)
.
(This prediction was suggested
to me on July 28, 2009, by one of my undergraduate students at Rutgers,
Ms. Julie Bianchini.)
(b) The
iso-entropic nature
(i.e., no change in
D
S
{
) postulated for the negentropy
transfer process from NR to the active site of the enzyme (Row 4, Table
11.12
)
is the most salient feature of the
garage-door postulate
. Lumry and Gregory
(1986, p. 23) discussed enzymic mechanisms similar to the garage-door mech-
anism described here (Lumry 1974; Lumry and Gregory 1986).
If these conjectures are correct, we can conclude that
blackbody radiation
and
the waiting time distribution of COx
are isomorphic with each other as summarized
in Row (10) of Table
11.9
.
9. Armed with the conclusions drawn above, we can return to Eq.
11.7
with a new
perspective, namely, the view that the X(w) factor does not merely reflect
experimental noise but also carries biological (i.e., genetic or evolutionary)
information. We will refer to this view as the “X factor hypothesis,” which
may be expressed as follows, among others:
The waiting time distribution of COx contains both deterministic and non-deterministic (or
stochastic) components. (11.50)
The waiting time distribution of COx contains the deterministic and non-deterministic
components, the former being constrained by, and the latter harnessing, the laws of physics
and chemistry. (11.51)
The waiting time distribution of COx contains the deterministic and non-deterministic
components, the former being constrained by the
laws of physics and chemistry
and the
latter embodying the
evolutionary information
that harness the laws of physics and chem-
istry. (11.52)
Enzymic catalysis embodies two complementary aspects - the
energy/matter aspect
obey-
ing the laws of physics and chemistry and the
bioinformatic aspect
embodying the
evolutionarily selected amino acid residues capable of harnessing the laws of physics and
chemistry.
(11.53)
It should be noted that the adjectives “deterministic” and “nondeterministic”
appearing in the above statements can be replaced by their synonyms, “synchronic”
and “diachronic,” respectively, as already indicated (see Row 3 in Table
4.1
).
10. The
waiting time distribution
of COx measured by Xie and his colleagues in Lu
et al. (1998) may be comparable to the
blackbody spectrum
measured by Otto
Lummer and Ernst Pringsheim in 1899 (Kragh 2000). Also the probability
