Biology Reference
In-Depth Information
7.1.2 Active versus Passive Bindings
Based on the thermodynamics of binding processes, we can divide all
ligand-protein interactions into three classes designated as Types I through III in
Table
7.1
. Alternative names for these three types of ligand-protein interactions are
also indicated in the table. Although most binding experiments focus on Type I
binding, it is very likely that Types II and III also play important roles in living
cells. In theory, there are two kinds of bindings - “active (also called 'downhill' or
'exergonic') binding (AB),” and “passive (also called 'uphill' or 'endergonic')
binding (PB).” AB is defined as the binding process which cannot occur (due to
the endergonic nature of the binding process as depicted in the third row of
Table
7.1
) without being coupled to some exergonic process, including PB depicted
in the first row of Table
7.1
. AB can occur if Type III binding is coupled to Type I
such that
D
D
G
1
is more negative than
G
3
is positive so that their sum is negative,
that is,
0.
As evident in Table
7.1
, if binding is exergonic, de-binding must be endergonic;
if binding is endergonic, the associated de-binding should be exergonic. Combining
these elements, we can formulate the following general statement:
D
G
1
+
D
G
3
<
No molecular machines can be driven by the free energy of binding alone; All molecular
machines must be driven by chemical reactions. (7.7)
We may refer to Statement 7.7 as the Chemical Reaction Requirement for
Molecular Machines (CRRMM).
The proteins that bind ligands actively (ABPs) are predicted to have the follow-
ing properties:
1. ABPs have at least two binding sites, each specific for a unique ligand, L
1
or L
3
,
say, with the associated free energy of bindings
D
G
1
and
D
G
3
.
2. ABPs bind L
1
avidly, that is,
D
G
1
<
0.
3. ABPs do not bind L
3
, that is,
0.
4. However, when both L
1
and L
3
are present together, ABPs can bind L
3
as well
asL
1
,if
D
G
3
>
G
3
.
The proteins that actively de-bind ligands, to be called the active de-binding
proteins (ADP), are predicted to have the following properties:
D
G
1
< D
G
3
, that is,
D
G
1
< D
1. ADPs have at least two binding sites, each specific for a unique ligand, L
1
or L
3
,
say, with the associated free energy of bindings
D
G
1
and
D
G
3
.
2. ADPs bind both L
1
and L
3
avidly, that is,
0.
3. In the presence of L
1
, ADPs bind L
3
, despite the fact that
D
G
3
>
0, because
binding of L
1
increases the binding affinity of ADPs for L
3
if
D
G
1
< D
G
3
, that
is,
D
G
1
<
0 and
D
G
3
<
G
3
.
Active de-binding process may occur during oxidative phosphorylation as pro-
posed by Boyer (2002).
D
G
1
< D
