depends on the reversible adsorption/desorption of
the proteins, which have varying degrees of hydro-
phobicity, to a hydrophobic stationary matrix. The
nature of the hydrophobic binding interaction is
thought to be the result of a favorable entropy effect
in areas adjacent to the hydrophobic regions where
there is a higher degree of organized water structure,
although the actual mechanism has yet to be fully
elucidated. The matrices are generally silica-based or
synthetic organic polymers and contain covalently
bound alkyl chains of different lengths such as n-
octadecyl (C18), n-butyl (C4), or phenyl groups.
The strength of the hydrophobic interaction increases
as the alkyl chain size increases.
0032 Proteins are initially introduced on to the chroma-
tographic matrix in conditions that promote binding,
e.g., 5% organic modifier (acetonitrile) containing a
weak hydrophobic ion-pairing reagent such as tri-
fluoroacetic acid (0.1%, pH * 2), and then eluted
with an aqueous gradient of the organic modifier
(5–60% v/v). The resulting separations are generally
quick, and the proteins are usually highly resolved.
0033 RPC has only recently become the method of
choice for the separation and characterization of
proteins/peptides. This is because of concerns that
the organic solvents, e.g., acetonitrile, routinely used
for the mobile phase can lead to protein denaturation
and loss of biological activity. Strategies such as using
short columns of short alkyl chain length, e.g., C4,
organic modifiers such as ethanol or isopropanol, and
omitting trifluoroacetic acid have been developed to
allay these apprehensions.
0034 Hydrophobic interaction chromatography Separa-
tion of proteins by hydrophobic interaction chroma-
tography (HIC) is similar to RPC and utilizes
hydrophobic interactions between the proteins in a
mixture and the hydrophobic ligands (usually butyl,
octyl, or phenyl groups) attached to an immobile
matrix. HIC is different to RPC, however, in its use
of aqueous mobile phases of high ionic strength and
neutral pH that do not denature proteins. The
ligands in HIC are also less hydrophobic and less
densely bound to the solid matrix than in RPC
matrices.
0035 Proteins are bound to the column in a mobile phase
that contains a high salt concentration, e.g., 1–3M
ammonium sulfate, and then eluted with a descending
salt gradient that resolvates the proteins and makes
binding thermodynamically unfavorable. This differs
from RPC, where an organic solvent gradient is used
to neutralize hydrophobic binding interactions. The
protein-binding selectivity and strength can be ma-
nipulated by the mobile-phase pH and temperature,
and elution of strongly adsorbed hydrophobic
proteins can be achieved using ethylene glycol to
lower the polarity of the mobile phase.
0036Affinity chromatography Affinity chromatography
uses unique aspects of the biological or individual
chemical structure of a protein to affect its purifica-
tion. By selecting an interacting ligand which has a
high natural specificity to the target protein, highly
selective separations can be achieved. The protein to
be purified or quantified is specifically and reversibly
adsorbed by the complementary ligand immobilized
on an insoluble matrix. Purification factors of up to
several thousand can be achieved, together with fur-
ther concentration during the elution step and high
recoveries of the initial active protein.
0037Whilst the method is now routinely used for the
purification of monoclonal antibodies and their cor-
responding antigens, receptor proteins, DNA-binding
proteins, and ‘tagged‘ recombinant proteins, its use in
protein analysis is less prevalent.
0038Immobilized metal affinity chromatography Immo-
bilized metal affinity chromatography (IMAC) is a
specialized variant of affinity chromatography
where the proteins or peptides are separated
according to their affinity for metal ions that have
been immobilized by chelation to an insoluble matrix.
At pH values around neutral, the amino acids histi-
dine, tryptophan, and cysteine form complexes with
the chelated metal ions (e.g., Zn
2þ
,Cu
2þ
,Cd
2þ
,
Hg
2þ
,Co
2þ
,Ni
2þ
, and Fe
2þ
). They can then be eluted
by reducing the pH, increasing the mobile phase ionic
strength, or adding ethylenediaminetetraacetic acid
(0.05 M) to the mobile phase. This technique is espe-
cially suited for purifying recombinant proteins as
poly-histidine fusions and for membrane proteins
and protein aggregates where detergents or high-
ionic-strength buffers are required.
0039Size-exclusion chromatography Size exclusion (or
gel filtration) chromatography (SEC or GFC) separ-
ates proteins in solution according to differences in
their size and shape as they travel through a solid
phase (gel) matrix. As most proteins are spherical,
their shape, or radius of gyration, will approximate
to their M
r
. The gel matrices are usually cross-
linked three-dimensional polymers of dextran, agar-
ose, or silica that contain pores of controlled size
ranges to allow free transfer of the liquid phase and
limited diffusion of the proteins to be separated. By
using matrices with pores of carefully controlled
sizes, different M
r
ranges of proteins can be separ-
ated.
0040Separation of a mixture of proteins occurs when
the passage of the smaller proteins, peptides, and
4828 PROTEIN/Determination and Characterization