Subcellular Systems - Molecular Theory of the Living Cell - page 327

Table 11.7 The relative transition probabilities among the four confor-
mational states of COx-FAD complex predicted on the basis of the
generalized Franck-Condon principle (Sect. 2.2.3 ) . For the definition of
the conformational states, A-D, see Figs. 11.17 and 11.20 . The Arabic
numerals in the table refer to the relative probabilities for the X to Y
transition, where X and Y represent rows and columns, respectively, and
the relative probabilities are in the order of 1 > 2 > 3 > 4 > 5

A B C D

A 1 2 4 5

B 2 1 3 4

C 4 3 1 2

D 5 4 2 1

3. The generalized Franck-Condon principle is postulated to apply to the COx-
FAD and COx-FADH 2 complexes in the sense that the probability of the
fluorescence transitions of these complexes are inversely proportional to the
Euclidean distances between the corresponding conformational states of COx
indicated in Fig. 11.20 .

Although the current state of development of single-molecule mechanics may
not allow measurements to be made of these six transitions predicted in Table 11.7 ,
it may be possible to detect them in the future when the single-molecule mechanics
techniques improve.

11.3.2 Molecules, Conformers, and Conformons

In order to rigorously analyze single-molecule enzymological data such as shown in
Figs. 11.18 and 11.24 , it may be necessary to utilize some of the concepts, theories, and
principles that have been developed in molecular enzymology and biology by various
investigators since the mid-twentieth century, including Widom (1965), Volkenstein
(1972, 1986), Green and Ji (1972a, b), Ji (1974a, b, 1990, 2000), Lumry (1974, 2009),
Lumry and Gregory (1986), Lumry and Biltonen (1969), Northrup and Hynes (1980),
Anderson (1983, 1987), Frauenfelder (1987), Frauenfelder et al. (2001), Welch
and Kell (1986), Benham (1992, 1996a, b), Kurzynski (1993, 1997, 2006), and
Eisenmesser et al. (2002).
In physical organic chemistry, the terms configuration and conformation are
carefully differentiated (see Fig. 3.5 ) (Sect. 3.2 ) unlike in physics and molecular
biology where they are often used interchangeably (Ji 1997a, see Table 4). Strictly
speaking, not distinguishing configurations and conformations in chemistry is equiv-
alent to conflating electrons and protons in physics, since configurations involve the
movement of electrons while conformations entail proton displacement in molecules
secondary to breaking and making H-bonds, the study of which being referred to