Molecular Mechanisms: From Enzymes to Evolution - Molecular Theory of the Living Cell - page 209

Table 7.2 A classification of enzymic catalysis based on mechanisms and principles

Minimum
number of
active sites

Motion
of products Catalysis Examples Mechanisms Principles

Scalar 1( Basic

catalysis )

None Most enzymes

(e.g., histidine
decarboxylase;
Fig. 7.5 )

Pre-fit
mechanism
(Sect. 7.1.3 )

Generalized
Franck-
Condon
principle
(GFCP),
also
called the
Principle
of Slow
and Fast
Processes
(PSFP)
(Sect. 2.2.3 )

Vectorial 2( Linear
catalysis )

Linear (or
translational )

Pre-fit
mechanism

GFCP/PSFP

Ion channels
(Fig. 7.2 )

3( Rotary
catalysis )

Circular (or
rotary )

F 1 -ATPase Pre-fit

mechanism

GFCP/PSFP

The pre-fit mechanism of the rotary catalytic activity of the F 1 -ATPase stator
ring consists of the following key elements:

1. In the absence of ATP, the three subunits of the F 1 stator exist in (or assume)

only one ground-state conformation designated as O (from “open”), and since
there are three

b

subunits per F 1 stator, the ground conformational state of the F 1
stator as whole can be designated as (O/O/O), which is characterized by the
presence of an opening in its center (see Fig. 1A in Uchihashi et al. 2011). The
red bold letters symbolize the conformational state of the

b

subunits and the
slash indicates the subunit which may also undergo conformational changes but
these changes are not detectable with the high-speed AFM method employed by
Uchihashi et al. (2011). ( It should be noted here that the hole in the center of the
F 1 stator ring disappears when two of the three

b

subunits bind ATP and ADP
(see Fig. 1D in Uchihashi et al . 2011 ) and undergo conformational transition
from the O to the C and C' states. )
2. The ground-state F 1 stator is in thermal equilibrium with (or thermally fluctuate
among) three different conformational states designated as (O/C/C'),(C'/O/C),
and (C/C'/O) (see the top row in Fig. 7.3 ).
3. In the presence of ATP, the F 1 stator binds ATP to its

b

b subunit in the C'

conformation, ADP (produced from ATP hydrolysis) to its b subunit in the C

subunit is left empty in the O conformation.
4. The structure of the ligand-bound F 1 stator has been selected by biological
evolution because of its ability to select, out of all the theoretically possible
conformational transitions, only those states that obey the generalized
Franck-Condon principle (or the Principle of Slow and Fast Processes):
5. The essence of the pre-fit mechanism (in contrast to the induced-fit mechanism
of Koshland (1958)) is that conformational transitions of enzymes precede the

conformation, and the third b