Mathematical model development and numberical simulation of Laemmli SDS-page

Ashfaq Mohammad Ansery

This thesis presents a mathematical model which illustrates the behavior of proteins and buffer constituents in Laemmli SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). A 1-D numerical simulation based on the Nernst-Planck equations, which describes the transport of ions in an electric field, is implemented through the COMSOL Multiphysics v4.2a finite element solver to illustrate the behavior of two virtual proteins with molecular weights of 100 kDa and 25 kDa respectively. SDS-PAGE is simulated for a 10% polyacrylamide gel concentration using the Laemmli system that stacks proteins at a pH of 6.8 and resolves them at a pH of 8.8. Our numerical simulation demonstrates stacking and migration of proteins and dye behind a leading electrolyte and in front of a terminating electrolyte, and shows the formation of discrete, contiguous zones by the proteins and the dye in the stacking region of the gel. The predicted electric field is not constant during the separation of proteins: it varies along the length of the gel. This simulation shows a sharp peak for the high molecular weight protein, Pr2 and a more diffuse peak for the lower molecular weight protein, , in the resolving gel. The distance between the two proteins predicted by this numerical simulation shows qualitative agreement with reported experiments. The numerical simulation illustrates changes in the concentration of the terminating ion (glycine) and leading ion (chloride), and pH excursions throughout the sample, stacking and resolving regions of the gel. The simulation also reveals anomalous dispersion of proteins as they enter the resolving section of the gel. It is found that the dispersion of the protein peaks is not due solely to diffusive spreading but, instead, is the result of peak dispersive processes that take place inside the gel because of the mismatch in conductivities between concentrated proteins and the resolving gel buffer. Mismatch in conductivities between the leading ionic species, chloride and concentrated proteins also affects dispersion of the protein peaks. This simulation helps to explain artifacts such as the smearing of protein peaks in Laemmli SDS-PAGE, and can be used to eliminate performance bottlenecks in Laemmli SDS-PAGE gels.

Mathematical model development and numberical simulation of Laemmli SDS-page

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