A density gradient is formed in a centrifuge tube, and a mixture of

proteins in solution is placed on top of the gradient.

To identify the estradiol receptor, the protein mixture is first incubated

with radioactive estradiol, which is readily detected. Only the estradiol
receptor will bind to the steroid. Moreover, the steroid alone is too
small to be influenced by the centrifugal force.

After the centrifugation is complete, a small hole is made in the bottom

of the centrifuge tube and portions of the gradient are collected and
tested for radioactivity.
An antibody is a protein synthesized in response to the presence of a foreign
substance called an antigen.

The antibody recognizes a particular structural feature on the antigen called the
antigenic determinant or epitope.
Any antibody-producing cell synthesizes antibodies that recognize only one epitope.
Each antibody-producing cell thus synthesizes a monoclonal antibody.

Any antigen may have multiple epitopes. The antibodies produced to the antigen by
different cells are said to be polyclonal.
Immortal cell lines producing monoclonal
antibodies can be generated by fusing
normal antibody producing cells with cells
from a type of cancer called multiple
myeloma.

A monoclonal cell line is isolated by

screening for the antibody of interest.
A monoclonal antibody for the estrogen receptor can be isolated by searching for cell
lines that produce an antibody that binds to the receptor.

If an antibody for the receptor is present, it will bind to the receptor and alter the
sedimentation constant of the receptor.
Once the monoclonal cell line is isolated, the antibody can be used to purify
the estrogen receptor.
Antibodies are used as a reagent to determine the amount of a protein or other antigen
present. Enzyme-linked immunosorbent Assay (ELISA) quantifies the amount of protein
present because the antibody is linked to an enzyme whose reaction yields a readily
identified colored product.
In western blotting or immunoblotting, proteins are separated in an SDS-
PAGE gel, transferred to a sheet of polymer, and then stained with a
fluorescent antibody.
A key step in understanding protein function is to determine the primary
structure, or the amino acid sequence, of the protein. A preliminary step is to
determine the amino acid composition of the protein.

The protein is hydrolyzed, and the constituent amino acids are separated on an
ion-exchange column. The amino acids are visualized by reaction with
fluorescamine.
The amino acid sequence can be determined by Edman degradation.
The protein is exposed to phenyl isothiocyanate (PTH), which reacts
with the N-terminal amino acid to form a PTH-derivative. The PTH-
amino acid can be released without hydrolyzing the remainder of the
protein, and the degradation is subsequently repeated.
Because the reactions of the Edman degradation procedure are not 100%
effective, it is not possible to sequence polypeptides longer than 50 amino
acids.

In order to sequence the entire protein, the protein is chemically or

enzymatically cleaved to yield peptides of fewer than 50 amino acids.

The peptides are then ordered by performing a different cleavage

procedure in order to generate overlapping peptides.
 Mass Spectrometry Can Be Used to Determine a Protein’s Mass,
Identity, and Sequence

Two mass spectrometry techniques can be used to determine a proteins mass:

matrix-assisted laser desorption (MALDI) and electrospray ionization (ESI). In
MALDI, proteins are precipitated onto a matrix and a laser flash releases negatively
charged ions.

Time of flight (TOF) analysis is used to measure how rapidly the ions move toward a
detector.

Only picomoles or femtomoles of a protein are required for MALDI-TOF analysis.

Mass spectrometry allows determination of a protein’s identity. For instance, an
unknown protein visible in a two-dimensional gel can be removed from the gel.

The protein is then cleaved in some fashion and subjected MALDI-TOF, revealing a
series of peptides with known masses.

These peptide masses are then compared to proteins in a data base that are
“electronically cleaved” by a computer using the same cleavage technique used to
generate the protein fragments.
A proteins sequence can be determined with the use of tandem mass spectrometry.
1. Primary structures from different proteins can be compared to infer
knowledge about structure and function.
2. Primary structure comparison of similar proteins from different
species provides information about evolution.
3. Primary structure can be searched for internal repeats that may
yield information on the history of the individual protein.
4. Primary structure can reveal the presence of amino acid sequences
that regulate protein function and location.
5. Primary structure can provide insight into the molecular basis of
disease.
6. Primary structure can be used as a guide to explore nucleic acid
information.