Biology Reference
In-Depth Information
ligand in the bound-state conformation; and P'
¼
the protein in the bound-state
conformation.
There are two aspects to Scheme 7.2 - (1) the thermodynamic aspect that
determines whether or not the binding process as written will take place under a
given experimental condition and, if so, to what extent, and (2) the kinetic aspect that
determines the rate or speed of the binding process. The thermodynamics of ligand
binding under most biological conditions (i.e., constant pressure and temperature) is
determined by the Gibbs free energy change,
G final -G initial , namely, the
difference in Gibbs free energy levels between the initial and final states of the
system under consideration. Gibbs free energy is defined by Eq. 2.1 . Any binding
process accompanied by a decrease in Gibbs free energy (i.e.,
D
G
¼
0) will occur
spontaneously. In contrast, if the binding free energy change is positive, that is,
D
D
G
<
0, the binding process will not occur spontaneously unless and until coupled
to (or driven by) another process accompanied by a sufficiently large negative Gibbs
free energy change so that the combined Gibbs free energy change becomes nega-
tive. In other words, all spontaneous binding processes, either simple or coupled, are
associated with negative Gibbs free energy changes. More generally, the relation
between the concentrations of the chemical species involved in a binding process
and the accompanying Gibbs free energy change is given by Eq. 7.3 , using
Scheme 7.2 as an example (Kondepudi and Prigogine 1998, pp. 235-237):
G
>
G 0
D
G
¼ D
þ
RT log
ð
½
L'
P'
L
½
P
Þ
(7.3)
Structural effect
Concentration effect
Global control
Covalently
(i.e., biochemically ,
which is slow)
Local control
Covalently
(i.e., transcriptionally ,
which is slow and
post-transcriptionally ,
which is fast)
or
Noncovalently
(which is fastest)
G 0 is the standard Gibbs free energy change (i.e., the Gibbs free energy
change under the standard condition of the unit concentrations of the chemical
species involved), R is the gas constant, T is the absolute temperature, and [L'P']
and[L][P] are the concentrations (or activities, more precisely speaking; Sect. 3.1.7 ) .
Evidently, Eq. 7.3 is consistent with the Le Chatelier's principle (which states that,
when a system at equilibrium is perturbed, the system will readjust itself in the
where
D
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