Biology Reference
In-Depth Information
The GFCP-based transport mechanism shown in Fig.
7.2
appears to be supported
in part by the crystal structural data of the sodium-galactose transporter described in
(Faham et al. 2008), which exhibit one half cycle of the opening and closing of
the ion channel/gate while the ligands move through it across the membrane. Three
differences are noteworthy between Fig.
7.2
and the mechanism described in
(Faham et al. 2008):
1. Figure
7.2
is based on a well-known physical principle, that is, GFCP or PSFP,
whereas the Fanham et al. mechanism is devoid of any principle to account for
the action of the transporter.
2. Figure
7.2
has eight states of the channel protein and 16 steps underlying the
selective transmembrane ligand transport, whereas the Fanham et al. mechanism
shows only two states of the transporter protein.
3. Thermal fluctuations play an essential mechanistic role in the transmembrane
ligand movement as depicted in Fig.
7.2
, whereas thermal fluctuations are not
explicitly implicated or mentioned in the Fanham et al. mechanism.
7.1.5 Scalar and Vectorial Catalyses:
A Classification of Enzymes
Enzymes can be divided into two groups depending on whether or not one or more
of the products of enzymic catalysis undergo any net displacement (beyond thermal
fluctuations) in space - the
scalar enzymes
if the product does not undergo any net
displacement, and the
vectorial enzymes
if the product produced undergoes a net
displacement in space. The vectorial enzymes in turn divide into two groups - the
linear vectorial enzymes
and the
rotary vectorial enzymes
. Some examples of the
enzymes belonging to these different classes are given in Table
7.2
.
It is interesting to note that the minimum number of the active sites needed for
the various types of catalyses are one, two, and three for
scalar
,
linear,
and
nonlinear
(or rotary or circular) catalyses, respectively, in agreement with the
geometric principle that
two points
are needed to define a
line
and
three points
are needed to define a nonlinear line or a
circle
.
A clear example of the
rotary catalysis
was recently reported by Uchihashi et al.
(2011; Junge and M
uller 2011) who used a high-speed AFM (atomic force micros-
copy) to measure the propagation speed of the
conformational waves
(~ 1 s per
cycle) of the
€
a
3
b
3
stator ring (see Figs. 1 and 2 in
Uchihashi et al. 2011). The authors concluded that the “structural basis of the
unidirectionality” of the rotary conformational waves “is programmed in the stator
ring” but they did not provide any molecular mechanisms for the unidirectional
wave propagation. One possible such mechanism is suggested below that is based
on the
pre-fit hypothesis
, which is in turn rooted in the
generalized Franck-Condon
principle
or the
Principle of Slow and Fast Processes
discussed in Sect.
7.1.3
.
b
subunit around the isolated
