184 Part II: Water, Enzymology, Biotechnology, and Protein Cross-linking
several motions and conformational changes of the
various regions always occur (Hammes 2002). The
extent of these motions depends on many factors
including temperature, the properties of the solvating
medium, and the presence or absence of substrate
and product (Hammes 2002). The conformational
changes undergone by the enzyme play an important
role in controlling the catalytic cycle. In some en-
zymes there are significant movements of the binding
residues, usually on surface loops, and in other cases
there are larger conformational changes. Catalysis
takes place in the closed form, and the enzyme opens
again to release the product. This favored model,
which explains enzyme catalysis and substrate inter-
action, is the so-calledinduced-fit hypothesis(An-
derson et al. 1979, Joseph et al. 1990). In this hypoth-
esis the initial interaction between enzyme and sub-
strate rapidly induces conformational changes in the
shape of the active site, which results in a new shape
of the active site that brings catalytic residues close to
substrate bonds to be altered (Fig. 8.8). When bind-
ing of the enzyme to the substrate takes place, the
shape adjustment triggers catalysis by generating
transition-state complexes. This hypothesis helps to
explain why enzymes only catalyze specific reactions
(Anderson et al. 1979, Joseph et al. 1990). This basic
cycle has been seen in many different enzymes
including triosephosphate isomerase (TIM), which
uses a small hinged loop to close the active site
(Joseph et al. 1990), and kinases, which use two large
lobes moving towards each other when the substrate
binds (Anderson et al. 1979).Figure 8.6.A schematic diagram showing the free energy profile of the course of an enzyme-catalyzed reaction
involving the formation of enzyme-substrate (ES) and enzyme-product (EP) complexes. The catalyzed reaction path-
way goes through the transition states TS 1 , TS 2 , and TS 3 , with standard free energy of activation Gc, whereas the
uncatalyzed reaction goes through the transition state TSuwith standard free energy of activation Gu.