Protein Gel Electrophoresis
1. Native PAGE
2. Native Gradient PAGE
3. Urea PAGE
4. SDS PAGE
5. SDS Gradient PAGE
6. IEF
7. 2D PAGE
8. Western Blot
Principle
Proteins move in the
electric field. Their relative
speed depends on the
charge, size, and shape of
the protein
From large to small and simple
Protein visualization on gels
Immediately after electrophoresis proteins in the gels are
precipitated by either adding alcohol containing solutions or
strong acids (e.g. TCA).
Protein are often stained by Coomassie Blue dye or by
photography-like treatment with AgNO3 (silver staining)
There are many other stains available (e.g. Stains-all,
fluorescence probes etc.)
Example of silver stained gel
Silver staining is usually
10-100 times more
sensitive than Coomassie
Blue staining, but it is
more complicated.
Faint but still visible bands
on this gel contain less
than 0.5 ng of protein!
Native PAGE
Separates folded proteins and proteinprotein or protein-ligand complexes by
charge, size, and shape
Useful for:
1. Examining protein-protein protein-ligand
interactions
2. Detecting protein isoforms/conformers
Native PAGE examples
In the absence of phospholipids, both
twinfilins run as a single sharp band on this
gel. PI(4,5)P2 causes twinfilin-1 and
twinfilin-2 to move more rapidly toward the
anode, indicating a net increase in the
negative charge and thus a binding
interaction.
Vartiainen et al. JBC 2003
Dimerization of
KIR2DL1 in the
presence of Co2
Qing R. Fan et al. JBC 2000
Native gradient PAGE
Separate native proteins by
size – proteins stop moving
when they reach a sertain gel
density (but this may take a
very long time ...)
A great technique to study
protien oligomerization!
Native gradient PAGE example
Native 4-15% gradient PAGE
Zavialov et al. Mol. Microbiol. 2002
Urea PAGE
Separates denatured
proteins by size/charge
Typically 6-8 M urea is
added into the gel
A great technique to study
protein modifications!
Example of Urea PAGE
Urea PAGE of samples of
heat shock protein 25
Zavialov et al. BBA 1998
SDS PAGE
Due to high density of binding of
SDS to proteins, the ratio
size/charge is nearly the same
for many SDS denatured
proteins. Hence proteins are
separated only by length of their
polypeptide chains (but not by
differences in charge).
Great separation. Allows
estimation of the size of
polypeptide chains
SDS gradient PAGE
12.5% SDS PAGE
Bands in SDS gradient gel
are usually sharper than in
homogeneous SDS PAGE
5-20% SDS PAGE
SDS-PAGE
Sodium Dodecyl Sulfate Polyacrylamid Gel
Electrophoresis
Sodium Dodecyl Sulfate
• SDS is a common ingredient in detergents
• Other names for SDS include laurel sulfate
and sodium laurel sulfate
• As a detergent SDS destroys protein
secondary, tertiary and quaternary structure
• This makes proteins rod shaped
• SDS also sticks to proteins in a ratio of
approximately 1.4 g of SDS for each gram of
protein
• Negative charge on the sulfate groups of
SDS mask any charge on the protein
SDS
Sodium Dodecyl Sulfate
C12H25NaO4
S
HHHHHHHHHHHH O
H-C-C-C-C-C-C-C-C-C-C-C-C-O-S-O
HHHHHHHHHHHH O
Non-polar
Hydrophobic tail
Polar
Hydrophilic head
• Because it is amphipathic, SDS is a potent detergent
SDS and Proteins
SDS
Protein
SDS and Proteins
SDS nonpolar chains arrange themselves on
proteins and destroy secondary tertiary and
quarternary structrure
Thus shape is no longer an issue as the protein SDS
complex becomes rod shaped
In aqueous solutions, SDS polarizes releasing Na+
and retaining a negative charge on the sulfate head
So much SDS binds to proteins that the negative
charge on the SDS drowns out any net charge on
protein side chains
In the presence of SDS all proteins have uniform
shape and charge per unit length
Polyacrylamide Gels
• Polyacrilamide is a polymer made of
acrylamide (C3H5NO) and bis-acrilamide
(N,N’-methylene-bis-acrylamide C7H10N2O2)
CH2 CH
O
C
O
C
NH2
CH2 CH
Acrylamide
Acrylamide
NH2
CH2
O
C
CH2 CH
NH2
Acrylamide
bis-Acrylamide
Polyacrylamide Gels
• Acrylamide polymerizes in the presence of free
radicals typically supplied by ammonium
persulfate
O
C
CH2 CH
O
NH2
C
CH2 CH
SO4-.
NH2
Polyacrylamide Gels
1. Acrylamide polymerizes in the presence of
free radicals typically supplied by ammonium
persulfate
2.TMED
(N,N,N’,N’tetramethylethylenediamine) serves as a
catalyst in the reaction
O
C
CH2 CH
O
NH2
C
CH2 CH
SO4-.
O
NH2
C
CH2 CH
O
NH2
C
CH2 CH
NH2
Polyacrylamide Gels
• bis-Acrylamide polymerizes along with
acrylamide forming cross-links between
O
O
O
acrylamide
chains
C
CH2 CH
NH2
C
CH2 CH
O
O
C
C
CH2 CH
CH2 CH
NH2
C
NH2
CH2 CH
NH2
CH2
O
NH2
C
CH2 CH
bis-Acrylamide
O
NH2
C
CH2 CH
O
NH2
C
CH2 CH
NH2
Polyacrylamide Gels
• bis-Acrylamide polymerizes along with
acrylamide forming cross-links between
acrylamide chains
Polyacrylamide Gels
• Pore size in gels can be varied by varying the
ratio of acrylamide to bis-acrylamide
Protein separations typically use a 29:1 or
37.5:1 acrylamide to bis ratio
Lots of bis-acrylamide
Little bisacrylamide
SDS-PAGE
1
2
3
3
1
Addition
2 of SDS
Protein becomes
rod-shaped with
uniform charge
IEF
Separates proteins by their
isoelectric points (pI)
Each protein has own pI = pH
at which the protein has equal
amount of positive and
negative charges (the net
charge is zero)
IEF
Mixtures of ampholytes, small
amphoteric molecules with high
buffering capacity near their pI, are
used to generate the pH gradient.
Positively and negatively charged
proteins move to – and +,
respectively, until they reach pI.
PI of proteins can be theoretically
predicted. Therefore, IEF can also
be used for protein identification.
IEF example
IEF 4-6.5 pH gradient
Zavialov A.
2D PAGE
2D PAGE
Lung V79 cells
from chinese
hamster
Guillermo Senisterra
Dept. of PhysicsUniversity of WaterlooWaterloo-Ontario N2L
3G1-Canada
Proteomics Pathway
Proteomics Pathway
Western Blotting (WB)
WB is a protein detection technique that combines
the separation power of SDS PAGE together with
high recognition specificity of antibodies
An antibody against the target protein could be
purified from serum of animals (mice, rabbits, goats)
immunized with this protein
Alternatively, if protein contains a commonly used
tag or epitope, an antibody against the tag/epitope
could be purchase from a commercial source (e.g.
anti-6 His antibody)
WB: 4 steps
1. Separation of proteins using SDS PAGE
2. Transfer of the proteins onto e.g. a
nitrocellulose membrane (blotting)
3. Immune reactions
4. Visualization
WB, Step 2: Blotting
WB, Steps 3-4: Detection