One
measurement of ligand binding is called the "saturation
fraction" or the "association fraction."
- Ya
simply equals the fraction of
all receptor ligand binding sites occupied by that ligand under a given set of conditions. In some
cases, a protein will only bind one ligand of given kind whereas other proteins,
especially multi-subunited proteins, may bind several ligand molecules of the
same type. In fact, many proteins bind multiple different kinds of ligands, each being characterized by its
own saturation fraction under specified conditions.
- By convention, Ya varies in value from 0 to 1 (or 0% to 100%). For example,
if a protein with two
binding sites for the one type of ligand is "50% saturated," only 1 out of the 2
ligand binding sites
-- on average -- will be occupied by ligand in the entire
protein population. Specifically, different protein molecules in the
population will have 0, 1 or 2 ligand molecules bound, but only half of all of
the potential ligand binding sites will be occupied if Ya = 0.5, or 50%.
How is the saturation
fraction used to determine quantities or amounts?
- In order to determine the amount saturated, simply multiply Ya
by the total capacity, i.e., "amount "= Ya
* "capacity."
- For example:
The amount of water held by a sponge
equals the product of the saturation
fraction with the total liquid capacity of the sponge.
The amount of water held by a cup
equals the product of the saturation
fraction with the total liquid capacity of the cup.
The amount of acid saturated with
protons (in moles per liter, or moles) equals the product of the saturation
fraction with the total concentration of acid (in moles per
liter, or moles).
The amount of oxygen bound to
hemoglobin (in moles per liter, or moles) equals the product of the saturation
fraction with the total concentration of hemoglobin (in moles per
liter, or moles) and the valence or number of
oxygen-binding sites, which equals 4 for each hemoglobin molecule.
Through precise quantitative measurements, the dynamics of a protein-mediated process
can reasonably be related to temporal changes
in the saturation fraction for a ligand that participates in and/or regulates the protein's activity.
Essentially three requirements
must be met to quantitate ligand binding processes:
- A protein's activity must be quantitatively related to the
saturation binding fraction of a given ligand, which can be a substrate and/or regulatory molecule.
- The biological range of the ligand concentration variations in
the cell or in the organism must be known.
- The temporal fluctuations of the ligand concentration must
also be known.
Ligand binding systems are examined
on this site with several exercises appearing with an increasing order of complexity as listed below:
- Monovalent ligand binding
systems
- Bivalent, non-interactive ligand binding
systems
- Trivalent, semi-interactive ligand binding
systems
- Bivalent, interactive ligand binding
systems
- Multivalent, interactive ligand binding
systems
- Michaelis-Menten enzyme kinetics
- Ligand-regulated enzyme kinetics