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Native polyacrylamide gel electrophoresis is an electrophoretic separation method typically used in proteomics and metallomics.
Native PAGE separations are run in non-denaturing conditions. Detergents are used only to the extent that they are necessary to lyse lipid membranes in the cell. Complexes remain--for the most part--associated and folded as they would be in the cell. One downside, however, is that complexes may not separate cleanly or predictably, since they cannot move through the polyacrylamide gel as quickly as individual, denatured proteins.
Take care not to confuse Native PAGE with SDS-PAGE. SDS-PAGE uses a detergent, sodium dodecyl sulfate, to transfer a negative charge dependent on the mass to the proteins and allow the electrophoretic separation. Due to the repulsion of equal charges, proteins are denatured and protein complexes are separated, reducing the dependence of protein mobility on folding and allowing for a reproducible separation after the mass of the proteins.
There are three popular methods of native PAGE, clear native (CN-PAGE), blue native (BN-PAGE), and quantitative preparative native continuous (QPNC-PAGE).
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Blue Native PAGE
BN-PAGE is the oldest native PAGE technique, where the Coomassie blue dye procures the necessary charges to the protein complexes for the electrophoretic separation. The disadvantage of coomassie is that in binding to proteins it can act like a detergent causing complexes to dissociate. Another drawback is the potential quenching of chemoluminescence (e.g. in subsequent western blot detection or activity assays) or fluorescence of proteins with prosthetic groups (e.g. heme or chlorophyll) or labelled with fluorescent dyes.
Clear Native PAGE
CN-PAGE uses no dye, which makes it necessary to use other means to transfer sufficient charge to the proteins, like the use of SLS. CN-PAGE separates acidic water-soluble and membrane proteins (pI < 7) in an acrylamide gradient gel, and usually has lower resolution than BN-PAGE. However, this method is arguably the most useful for examining protein-protein interactions, particularly in conjunction with mass spectrometry (MS).
Quantitative Preparative Native Continuous PAGE
In contrast to CN and BN-PAGE the protein complexes of interest (metalloproteins) may separate cleanly and predictably, since they move through the polyacrylamide gel as quickly as individual, denatured proteins due to the pH value of the applied electrophoresis buffer and specific properties of the gel column and electrophoresis chamber. QPNC-PAGE may be coupled off-line to size exclusion chromatography (SEC), ICP-MS and NMR for structural determination of metallobiomolecules in complex protein mixtures.
Downstream processing
In a typical native PAGE experimental procedure, the complexes will be separated with CN or BN-PAGE. An additional separation method may then be used, such as isoelectric focusing or SDS-PAGE. The gel will then be physically cut, and the protein complexes extracted from each portion separately. Each extract may then be analysed, such as by peptide mass fingerprinting or de novo sequencing after in-gel digestion. This can provide a great deal of information about the identities of the proteins in a complex.
See also
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