What happens to the smallest proteins during SDS-PAGE?

During SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis), small proteins are able to travel further through the gel matrix compared to larger proteins. The gel consists of a network of polymerized acrylamide that creates pores through which proteins migrate when an electric current is applied. The size of these pores allows smaller proteins to move more easily, while larger proteins encounter more resistance and move more slowly.

As a result, the smallest proteins will generally travel the furthest distance towards the positive pole. This migration pattern enables the separation of proteins based on their molecular weight, with smaller proteins appearing towards the bottom of the gel and larger proteins remaining closer to the starting point. This principle is essential for the analysis of protein size and can be observed in the bands formed on the gel after electrophoresis.