Biology Reference
In-Depth Information
Chapter 7
Molecular Mechanisms: From Enzymes
to Evolution
7.1 Molecular Mechanisms of Ligand-Protein Interactions
7.1.1 Thermodynamics and Kinetics of Ligand-Protein
Interactions
Binding
is prerequisite for practically all molecular processes occurring inside the
cell, including
messenger (or molecular) recognition
,
enzymic catalysis, transport
processes, and control of gene expression
. Furthermore,
binding
must be followed
by
de-binding
if molecular machines are to work more than one cycle. Otherwise,
molecular machines will get stuck in a substrate- or a product-bound state and not
be able to move on to the next state to perform molecular work in continuous
cycles. Molecular machines stuck in either a substrate- or a product-bound state is
akin to the gear shift of a car stuck in either the drive or the neutral position.
To emphasize the importance of this basic feature of molecular machines, it may be
justified to formulate Statement 7.1 to be referred to as the
Principle of the Binding
and De-binding Requirement of Molecular Machines
(PBDRMM):
All molecular machines must perform at least one cycle of
binding and debinding
of
molecules in order to carry out their functions more than once. (7.1)
The simplest form of ligand-protein interactions can be represented as shown in
Scheme
7.2
:
L
P
$
L
þ
P
$½
L'
P'
Initial
Transisiton
Final
(7.2)
State
State
State
where L
¼
ligand (including proteins, RNA, and DNA); P
¼
proteins; L*
¼
the
ligand in the transition-state conformation; P*
¼
the protein in the transition-state
conformation; [
...
]
¼
the transition state of the ligand-protein complex; L'
¼
the
