Correction factors for membrane protein molecular weight readouts on sodium dodecyl sulfate-polyacrylamide gel electrophoresis

Membrane proteins are known to migrate anomalously on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to relative molecular mass (Mr) values larger or smaller than formula molecular weight. We constructed a database from literature Mr values reported for 168 nonredundant helical membrane proteins with structures determined to high resolution and found that more than three-quarters of them exhibit this behavior on gels calibrated with commercial standards. Further analysis of the database indicated that the direction of anomalous migration is not a consequence of membrane protein net charge or hydrophobicity. Plots of observed versus formula Mr values showed that membrane proteins migrating slower than expected read out at 1.13 × Mr, whereas those that migrate faster than expected read out at 0.82 × Mr (R2 ∼ 0.98, P < 0.0001). These robust trends imply that division of the Mr readouts of slower or faster migrating analytes by 1.13 or 0.82, respectively, should enhance SDS-PAGE accuracy. Applying this correction procedure to SDS-PAGE readouts of four fast-migrating helical transmembrane (TM) proteins significantly reduced Mr errors from approximately 20% to 8% (P < 0.0001). Our results suggest that hydrophobic standards for SDS-PAGE would significantly improve the performance of the technique applied to membrane proteins.