Biology Reference
In-Depth Information
(c) A
conformer
is associated with one waiting time as indicated in Column (2)
and hence with one value of the probability of occurrence, p(w), as shown in
Column (4), thus giving rise to the deterministic component of Eq.
11.27
.
In contrast,
conformons
, depending on their amino acid residues shown in
Column (3), can modulate the probability of the occurrence of w either
positively (Rows 2 and 4 in Column 5), negatively (Rows 8 and 10, Column
5), or not at all (Rows 5 and 7, Column 5), thus engendering the nondeter-
ministic term in Eq.
11.27
. That is, it is suggested here that
conformers
account for the deterministic term while the genetic information determines
the non-deterministic term. This introduces an
extra degree of freedom
for
an enzyme to regulate its activity and this extra degree of freedom is
identified as a part of the “evolutionary information” discussed by Socolich
et al. (2005), “catalytic information,” or “catalytic negentropy” discussed in
Ji (1974a) (more at (7) below).
(d) The similarities among the numbers in Column (4) of Table
11.11
reflect the
similarities among the amino acid sequences of the conformons in Column (3).
Thus the amino acid sequence constituting the core of conformons belonging
to Conformer A (i.e., 35, 60, 100) is more similar in structure (or closer in what
may be referred to as the
conformon space
, an abstract space wherein each
point represents one conformon within an enzyme) to Conformon B (i.e., 55,
60, 111) than is Conformon C (i.e., 10, 60, 125), and so are the corresponding
p(w) values given in Column (4), i.e., 20 is closer to 18 than is 15. Similar
correlations hold between Column (3) and Column (5): The amino acid
residues constituting conformons belonging to Conformer A are more tightly
centered on (35, 60, 100) than are those constituting the conformons belonging
to Conformer C around (10, 60, 125). Consequently, the values of the nonde-
terministic component of Eq.
11.27
due to the conformons belonging to
Conformer A are more tightly centered around +2.0 than are those due to the
conformons belonging to Conformer C centered around
2.0.
(e) In calculating the numerical values given in Columns (4) and (5) in
Table
11.11
, it is assumed that
The closer the
conformers
are in the
conformon space
, so are the values of the
deterministic
component
of p(w); the closer the
conformons
are in the conformon space, so are the values
of the
non-deterministic
component of p(w). (11.29)
The
conformon space
is characterized by both
energy
(expressed in terms of
the familiar Gibbs free energy, G
TS) and
information
(expressed in terms of the “evolutionary information” of the kind discussed
by Socolich et al. (2005), i.e., “sequence information”, or “genetic informa-
tion”) and hence belong to the general class of what was referred to as
Gnergy Space, gnergy being defined as a complementary union of informa-
(f) The amino acid sequences given in Column (3) specify the conformons
belonging to a conformer, C
i
, of an enzyme at its ground state, which undergoes
thermal excitation/activation in the time span of t
ie
(e standing for excitation or
¼
E+PV
