Cell Language Theory, The: Connecting Mind And Matter

The Bhopalator 79

“6x9” b2861 The Cell Language Theory: Connecting Mind and Matter

(E,T/D,E/T,D). As one can see, State 2 is intermediate between

States 1 and 3 in both the conformational states of the proteins and

the associated ligand systems, thus satisfying the principle of micro-

scopic reversibility (PMR; Section 3.2.12). From State 2, the F 1 stator

can go back to State 1 or go forward to State 3, in which case the

ligand binding state spontaneously changes from (E,T/D,E/T,D) to

(T/E/D). The mechanisms of the state transitions from 3 to 5 and

from 5 to 1 as shown in Figure 3.14 are similar to the state transitions

from 1 to 3 in that they obey both the GFCP (Section 2.7), the pre-fit

mechanism (Section 3.2.9), and the PMR (see Section 3.2.12).

3.2.9 The Pre-fit Hypothesis

One interesting consequence of the PSFP, or the GFCP (see Section 2.7), as

applied to enzymic catalysis, is that enzymes must undergo conformational

changes before substrates can bind to their active sites to initiate catalysis.

This conclusion is diametrically opposed to the induced-fit hypothesis of

Koshland [28] widely accepted in biochemistry textbooks and other media

Figure 3.14 The pre-fit molecular mechanism of the rotary catalysis of the F 1 -ATPase (in

the direction of ATP hydrolysis, i.e., the clockwise direction) based on the GFCP or the

PSFP (Section 2.7). The red bold letters symbolize conformational states of the F 1 stator

ring and the blue letters indicate the ligands bound to the b-subunits. The square brackets

indicate the high-energy transition state or activated states called the Franck–Condon state

[70]. The mechanism obeys the PMR (see Section 3.2.12) so that it can be driven forward

(from left to right) or backward (from right to left), depending on whether the Gibbs free

energy change, ∆G, accompanying ATP hydrolysis is negative or positive, respectively.

Reproduced from [25, p. 217].

O(E)/C(D)/C′(T) [OC′(E,T)/CO(D,E)/C′C(T,D)]‡ C′(T)/O(E)/C(D)

CO(D,E)/C′C(T,D)/OC′(E,T)]‡ [C′C(T,D)/OC′(E,T)/CO(D,E)]‡

C(D)/C′(T)/O(E)

1 2 3

4

5

6

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