Biology Reference
In-Depth Information
Table 11.10 The suggested explanations of the single-molecule enzymological observations on
cholesterol oxidase based on the conformon theory of molecular machines. Extensive footnotes are
provided below, numbered 1-10
Explanations based on the Conformon Theory of Molecular
Machines (Ji 1974b, 2000)
Observations of Lu et al. 1998
A
Asymmetric waiting time
distribution, or dynamic
disorder
(Zwanzig 1990)
1. The enzymic activity of COx is supported in part by the heat
absorbed by its covalent and non-covalent bonds acting as
molecular oscillators just as the blackbody radiation is
supported by a system of molecular oscillators, both
obeying the Bose-Einstein statistics rather than the
Boltzmann statistics (see 5)
2. The
deterministic
shape (or the smooth portion) of the
waiting time distribution is due to different content of the
mechanical energy
stored in the conformons of the COx
molecule in its ground state (Fig.
11.28
)
3.
The nondeterministic
shape (or the rugged portion) of the
waiting time distribution (see Fig.
11.24
) is attributed to the
different
catalytic negentropy
(Ji 1974a) encoded in the
evolutionarily conserved amino acid residues constituting
conformons (see 2)
B
Concentration dependence
of waiting times
4. The formation of the
real
conformons in COx at the Franck-
Condon state depends on the substrate binding-induced
stabilization of
virtual
conformons, an example of the
Circe
effect (Jencks 1975) (see Fig.
11.30
), and binding
interactions are concentration dependent
C
Autocorrelation among
waiting times
5. Within the lifetime of a conformer, more than one cycle of
catalysis can take place, each cycle involving the thermal
activation of a ground-state (or
static
) conformon to
dynamic
conformons at the Franck-Condon (FC) state and
the relaxation of the
dynamic
conformon back to its original
or closely related
static
conformons or to another
conformer. “Static” and “dynamic” conformons are defined
in (7) below
D
Fluctuations of the spectral
mean
6. The fluorescence efficiencies of FAD and FADH
2
(Fig.
11.16
) depend on the conformational states of FAD
and FADH
2
which are in turn influenced by the
conformational state of the binding pocket of the COx
molecule
E
Similarity between the
autocorrelation functions
of waiting times and
spectral means
7. The conformational state of the binding pocket of the COx
molecule affects not only the spectral means of the
fluorophores but also the cycling between
static
and
dynamic
conformons at the active site of the COx molecule
DNA) deemed
necessary
and
sufficient
to drive all goal-directed molecular motions
inside the cell (see Chap.
8
and Sect.
11.3.2
).
1. Lu et al. (1998) derived a mathematical equation, Eq.
11.25
, to fit the waiting time
distribution data of cholesterol oxidase shown in Figs.
11.17
,
11.18
, and
11.24
.
More recently Prakash andMarcus (2007) attempted to provide possible molecular
mechanisms underlying the
dynamic disorder
phenomenon and the similarity
