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SDS-PAGE of Peptides 73<br />

13<br />

SDS-Polyacrylamide<br />

Gel Electrophoresis of Peptides<br />

Ralph C. Judd<br />

1. Introduction<br />

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) has<br />

proven to be among the most useful tools yet developed in the area of molecular biology.<br />

The discontinuous buffer system, first described by Laemmli (1), has made it<br />

possible to separate, visualize, and compare readily the component parts of complex<br />

mixtures of molecules (e.g., tissues, cells). SDS-PAGE separation of proteins and peptides<br />

makes it possible to quantify the amount of a particular protein/peptide in a<br />

sample, obtain fairly reliable molecular mass information, and, by combining SDS-<br />

PAGE with immunoelectroblotting, evaluate the antigenicity of proteins and peptides.<br />

SDS-PAGE is both a powerful separation system and a reliable preparative purification<br />

technique (2; and see Chapter 11).<br />

Parameters influencing the resolution of proteins or peptides separated by SDS-<br />

PAGE include the ratio of acrylamide to crosslinker (bis-acrylamide), the percentage<br />

of acrylamide/crosslinker used to form the stacking and separation gels, the pH of (and<br />

the components in) the stacking and separation buffers, and the method of sample<br />

preparation. Systems employing glycine in the running buffers (e.g., Laemmli [1],<br />

Dreyfuss et al. [3]) can resolve proteins ranging in molecular mass from over 200,000<br />

Daltons (200 kDa) down to about 3 kDa. Separation of proteins and peptides below<br />

3 kDa necessitates slightly different procedures to obtain reliable molecular masses<br />

and to prevent band broadening. Further, the increased use of SDS-PAGE to purify<br />

proteins and peptides for N-terminal sequence analysis demands that glycine, which<br />

interferes significantly with automated sequence technology, be replaced with noninterfering<br />

buffer components.<br />

This chapter describes a modification of the tricine gel system of Schagger and von<br />

Jagow (4) by which peptides as small as 500 Daltons can be separated. This makes it<br />

possible to use SDS-PAGE peptide mapping (see Chapter 80), epitope mapping (5), and<br />

protein and peptide separation for N-terminal sequence analyses (6) when extremely<br />

small peptide fragments are to be studied. Since all forms of SDS-PAGE are denaturing,<br />

they are unsuitable for separation of proteins or peptides to be used in functional<br />

analyses (e.g., enzymes, receptors).<br />

From: The <strong>Protein</strong> <strong>Protocols</strong> Handbook, 2nd Edition<br />

Edited by: J. M. Walker © Humana Press Inc., Totowa, NJ<br />

73

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