Biology Reference
In-Depth Information
E and E' refer to the two conformational states of the enzyme molecule in the
“unbound” and “binding” conformations, respectively. The concept of
conforma-
tion
, in contrast to that of
configuration
, plays a fundamental role in my theoretical
reasoning in molecular biology (Ji 1997a). As explained in Sect.
3.2
,c
onformations
are three-dimensional structures of a molecule that can be altered without breaking
or forming any covalent bonds. When such bonds need to be broken or formed
during structural or shape changes, we are now dealing with “configurations” and
not “conformations.” There are two distinct mechanisms of
ligand-binding
processes:
Induced Fit Hypothesis
(IFH)
:
L
þ
E
$
L
E
$
L
E'
(7.8)
Pre
-
Fit Hypothesis
(PFH)
:
L
þ
E
$
L
þ
E'
$
L
E'
(7.9)
The following differences exist between these two mechanisms:
1. IFH predicts that E cannot assume E' without first binding L. In contrast, PFH
predicts that E can assume E' in the absence of L, the probability P(E') of
observing E' being dependent only on the Gibbs free energy difference,
D
G,
between E and E', that is,
G(E') - G(E), obeying the Boltzmann distribu-
tion law (Moore 1963, p. 621; Andrews 1963, p. 33),
D
G
¼
P(E)e
D
G
=
RT
P (E'
Þ¼
(7.10)
where R is the universal gas constant and T the absolute temperature.
2. The conformational change of E to E'
follows
ligand binding according to IFH,
whereas it precedes ligand binding according to PFH.
3. The energy required for the conformational transition from E to E' is provided
by the substrate binding energy in IFH, whereas, in PFH, it is “borrowed”
temporarily
from thermal environment to be “paid back” subsequently from
the free energy of binding of L to E' rapidly enough to avoid violating the
Second Law of thermodynamics (Ji 1974a, pp. 29-30) (see Sect.
2.1.4
). This
mechanism is consistent with the theory of enzymic catalysis proposed by
Jencks (1975) based on the
Circe effect
in which a part of the free energy of
substrate binding is stored in the enzyme-substrate complex as conformational
deformations of the enzyme to be utilized later to lower the activation free
energy barrier for catalysis.
4. Another way to describe the difference between IFH and PFH is that, in the
former, L “instructs” E to change its conformation to E', while, in the latter, L
“selects” E' over E which are both available to L due to the thermal equilibration
between the two conformers (or conformational isomers). Thus, it can be stated
that IFH is based on
instruction
, whereas PFH is based on
selection.
An indirect evidence for PFH was recently reported by K. Ravindranathan
(2005) who used X-ray crystallographic data on the
ribose-binding protein
(RBP)
