Proteomics/Protein Separations- Electrophoresis/Two Dimensional Polyacrylamide gel Electrophoresis(2D-PAGE)

2D-PAGE is a form of gel electrophoresis in which separation and identification of proteins in a sample are done by displacement in 2 dimensions oriented at right angles to one another(orthogonal). This technique is also used to compare two or more samples to find differences in their protein expressions.

Basis for separation
In this technique proteins are separated by two different physicochemical properties. In the first dimension proteins or polypeptides are separated on the basis of their net charges by isoelectric focusing and in the second dimension they are separated on the basis of their molecular masses by electrophoresis. Because it is unlikely that two molecules will be similar in both properties, molecules are more effectively separated in 2-D electrophoresis than in 1-D electrophoresis.

Sample preparation
The goal of sample preparation is to solubilize maximum number of proteins and maintain their solubility throughout the process. The materials for sample should be carefully collected, snap frozen and ground under liquid nitrogen in the presence of protease inhibitors. After extracting proteins from source material they are then solubilized and denatured by means of chaotropes, detergents, and reducing agents. Hydrogen-bonds in the sample proteins are disrupted by chaotropes urea and thiourea. Uncharged detergents are used to disrupt hydrophobic interactions. Detergents such as CHAPS, Triton X-100, sulfobetaine SB3-10, and amidosulfobetaine are IEF-compatible additives. Disulfide bonds are reduced to sulfhydryls by reducing agents dithiothrietol (DTT), dithioerythritol, and tributyl phosphine (TBP).

Sequential extraction is done to categorize proteins based on their solubility. This is an example of pre-fractionation to enrich low abundance proteins. Proteins are sequentially extracted into chaotrope/detergent solutions of increasing solubilization power. First, proteins are treated with an aqueous buffer, the insoluble proteins remaining from this extraction are treated with urea/CHAPS/TBP, and the insoluble proteins remaining from this step are then treated with urea/thiourea/CHAPS/SB 3-10/TBP. 2-D PAGE is then done to separate the proteins in each of the supernatants. The remaining insoluble material from the final extraction can be taken up in SDS-PAGE sample solution and run in a one-dimensional gel.

Isoelectric focusing (IEF)
In IEF, proteins are separated by electrophoresis in a pH gradient based on their isoelectric point(pl). A pH gradient is generated in the gel and an electric potential is applied across the gel. At all pHs other than their isoelectric point, proteins will be charged. If they are positively charged, they will move towards the more negative end of the gel and if they are negatively charged they will move towards the more positive end of the gel. At its isoelectric point, since the protein molecule carry no net charge it accumulates or focuses into a sharp band.

Immobilized pH Gradient (IPG) and IEF run
Immobilized pH gradients are used for IEF because the fixed pH gradients remain stable over extended run times at very high voltages. The pH gradients of IPGs are generated by means of buffering compounds that are covalently bound into polyacrylamide gels. IPGs are cast strips with plastic backing sheets and are commercially available in different pH ranges and lengths. They offer high resolution, great reproducibility, and allow high protein loads. Isoelectric focusing is run in the same solutions that are used to extract or solubalize the proteins. The IPG strips with the protein sample must be rehydrated in the rehydration/sample buffer during with protein samples are loaded into the strips. Rehydration can be active or passive. To load larger proteins active rehydration in small voltage is applied. After the run in IEF cell, the proteins focus as bands on the strip according to their isoelectric points. The focused strips can be frozen for storage

IPG gel strips equilibration
The proteins in the focussed IPG strips are uncharged because they are at their pI and so they will not move into the SDS- PAGE gel. So the strips are treated with SDS (sodium dodecyl sulfate), an anionic detergent which denatures the protein by breaking the disulfide bonds and gives negative charge to each protein in proportion to its mass. Without SDS, different proteins with similar molecular weights would migrate differently due to differences in folding, as differences in folding patterns would cause some proteins to better fit through the gel matrix than others. SDS linearizes the proteins so that they may be separated strictly by molecular weight. The SDS binds to the protein in a ratio of approximately 1.4 g SDS per 1.0 g protein (although binding ratios can vary from 1.1-2.2 g SDS/g protein), giving an approximately uniform mass:charge ratio for most proteins, so that the distance of migration through the gel can be assumed to be directly related to only the size of the protein. Proteins may be further treated with reducing agent, such as dithiothreitol (DTT) or TRP(Tributyl phosphine to break any reformed disulfide bonds and then alkalated with iodoacetamide to prevent reformation of disulfide bonds. A tracking dye like bromophenol blue may be added to the protein solution to track the progress of the protein solution through the gel during the electrophoretic run.

SDS-PAGE run
The equlibrated IPG strip is placed on the top of the SDS-PAGE gel submerged in a suitable buffer and sealed in place with agarose gel. An electric current is applied across the gel, causing the negatively-charged proteins move out of the gel and migrate across the gel. Depending on their size, each protein move differently through the gel matrix. Smaller proteins travel farther down the gel, while larger ones remain closer to the point of origin. The proteins separate roughly according to size and therefore by molecular weight. It is common to run "marker proteins" of known molecular weight in a separate lane in the gel, in order to calibrate the gel and determine the weight of unknown proteins by comparing the distance traveled relative to the marker.

Visualization
After electrophoresis the gel is stained to visualize the separated proteins. Commonly used stains are Coomassie Brilliant Blue or SYPRO Ruby or silver stain. different proteins will appear as distinct spot within the gel. Coomassie Brilliant Blue or SYPRO Ruby are compatible with Mass Spectrometry. Coomassie Brilliant Blue has detection limit about 10ng of proteins per spot and the gel images of spots can be captured by scanning densitometer which operate in visible light[]. SYPRO Ruby can detect 1ng of proteins per spot and since it is fluorescent, the sopts are visualized by a fluorescent imager. Silver stain can detect spots containing proteins less than 1 ng and is the most sensitive non – radioactive protein visualization method.Laser devices for image capturing are useful for fluorescently stained gels.

Analysis
The images can be further analyzed using image –analysis softwares. These softwares quantify proteins spots, match images and compare corresponding spots intensites of related gels, prepare gel data reports, remove background patterns, and integrate image information to databases.Alternately the proteins separated can be obtained from the gel can be analyzed by MS for protein identification. 2D- PAGE can be used to study differential protein expression by comparing images from 2D –PAGE gels samples labeled with stable isotopes or fluorescent dyes.

Advantages and Disadvantages
Using 2D-PAGE,100 –1000’s of polypeptides can be analyzed in a single run. The proteins can be separated in pure form from the spots. The spots can be quantified and also analyzed by MS. In this method polypeptides can be probed with antibodies and also they can be tested for post- translational modifications. The disadvantages may include large amount of sample handling, less reproducibility, difficulty to separate low abundance proteins, acidic and basic proteins, very large and very small proteins and hydrophobic proteins.Also not automated for high throughput analysis.2D-PAGE has limited dynamic range.