Biology Reference
In-Depth Information
Fig. 7.6 Mechanism of enzymic catalysis based on the generalized Franck-Condon principle
transitions of the active site accompanying enzymic catalysis are schematically indicated by the
rearrangements of the Arabic numerals identifying different catalytic residues (Reproduced from
Ji 1974a, 1979)
between two aspartic acid residues (see residues D198 and D53'), thus holding two
chains close together. As HDC's product, histamine, accumulates, the pH rises and the
protons are pulled off from D198 to D53', which triggers conformational changes in
the B helix, leading to dissolution of the helical structure and rearrangements of
catalytic residues away from the catalytic center, including D53', I59', and Y62'.
In the process, residue D53' is found to be displaced by up to 5-10
´
(10
8
cm).
The structural information contained in Fig.
7.5
does not reveal the dynamic
nature of enzymic catalysis or the geometry of the active site at the transition state
(lasting no longer than perhaps 10
9
-10
12
s). Therefore, the overall dynamics of
enzymic catalysis (and of bionetworks in general) must be inferred based on
theoretical principles and structural and kinetic data available on the network
under consideration.
The overall sequence of steps involved in an enzyme-catalyzed chemical reaction
can be represented briefly as shown in Process
7.17
:
$
S
þ
E
$½
ES
$
EP
E
þ
P
(7.17)
where S, E, and P are, respectively, the substrate, the enzyme, and the product, and
ES and EP represent the enzyme-substrate and enzyme-product complexes. The
symbol [
]* indicates the transition state (also called the Franck-Condon state)
in which the E assumes such an unusual conformational state (i.e., mechanically
strained state often referred to as the Franck-Condon state) that S and P becomes
indistinguishable (see
b
and
c
in Fig.
7.6
). Figure
7.6
schematically represents the
...
