Two-dimensional gel electrophoresis, abbreviated as 2-DE or 2-D electrophoresis, is a form of gel electrophoresis commonly used to analyze proteins. Mixtures of proteins are separated by two properties in two dimensions on 2D gels.
Basis for separation
2-D electrophoresis begins with 1-D electrophoresis but then separates the molecules by a second property in a direction 90 degrees from the first. In 1-D electrophoresis, proteins (or other molecules) are separated in one dimension, so that all the proteins/molecules will lie along a lane but be separated from each other by a property (eg isoelectric point). The result is that the molecules are spread out across a 2-D gel. 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. However 1-D gel electrophoesis eg SDS-PAGE is more commonly used.
To separate the proteins by isoelectric point, a gradient of pH is applied to a gel and an electric potential is applied across the gel, making one end more positive than the other. At all pHs other than their isoelectric point, proteins will be charged. If they are positively charged, they will be pulled towards the more negative end of the gel and if they are negatively charged they will be pulled to the more positive end of the gel. The proteins applied in the first dimension will move along the gel and will accumulate at their isoelectric point. That is, the point at which the overall charge on the protein is 0 (i.e a neutral charge).
Before separating the proteins by mass, they are treated with sodium dodecyl sulfate (SDS) along with other reagents (SDS-PAGE in 1-D). This denatures the proteins (that is, it unfolds them into long, straight molecules) and binds a number of SDS molecules roughly proportional to the protein's length. Because a protein's length (when unfolded) is roughly proportional to its mass, this is equivalent to saying that it attaches a number of SDS molecules roughly proportional to the protein's mass. Since the SDS molecules are negatively charged, the result of this is that all of the proteins will have approximately the same mass-to-charge ratio as each other. In addition, proteins will not migrate when they have no charge (a result of the isoelectric focusing step) therefore the coating of the protein in SDS (negatively charged) allows migration of the proteins in the second dimension (NB SDS is not compatible for use in the first dimension as it is charged and a nonionic or zwitterionic detergent needs to be used). In the second dimension, an electric potential is again applied, but at a 90 degree angle from the first field. The proteins will be attracted to the more positive side of the gel proportionally to their mass-to-charge ratio. As previously explained, this ratio will be nearly the same for all proteins. The proteins' progress will be slowed by frictional forces. The gel therefore acts like a molecular sieve when the current is applied, separating the proteins on the basis of their molecular weight with larger proteins being retained higher in the gel and smaller proteins being able to pass through the sieve and reach lower regions of the gel.
The result of this is a gel with proteins spread out on its surface. These proteins can then be detected by a variety of means, but the most commonly used stains are silver and coomassie staining. In this case, a silver colloid is applied to the gel. The silver binds to cysteine groups within the protein. The silver is darkened by exposure to ultra-violet light. The darkness of the silver can be related to the amount of silver and therefore the amount of protein at a given location on the gel. This measurement can only give approximate amounts, but is adequate for most purposes.
Other traits than nucleophilicity may be used to separate species. In supercoiling assays, DNA is separated by electrophoresis in one dimension and by a DNA intercalator (such as ethidium bromide or the less carcinogenic chloroquine) in the second. In summary 2D provides resolution according to two traits, whereof one is most often molecular charge. The investigated molecule needs not be protein.
2D Gel Analysis Software
In quantitative proteomics, these tools primarily analyze biological markers by quantifying individual markers, and showing the separation between one or more protein "spots" on a scanned image of a 2-DE product. These tools may also be used to match spots between gels of similar samples to show, for example, proteomic differences between early and advanced stages of an illness. However, though some tools tend to agree on the quantification and analysis of well-defined, well-separated protein spots, they deliver different results and tendencies with less-defined, less-separated spots.
Warping: Images of two 2D electrophoresis gels, overlaid with Delta2D, another leading 2-DE image analysis software package. First image is colored in orange, second one colored in blue. Due to running differences, corresponding spots do not overlap.
Warping: Images of two 2D electrophoresis gels, overlaid and warped with Delta2D. First image is colored in orange, second one colored in blue. Corresponding spots overlap after warping. Common spots are colored black, orange spots are only present (or much stronger) on the first image, blue spots are only present (or much stronger) on the second image.
Modern day 2-DE research often utilizes software-based image analysis tools. These tools primarily analyze bio-markers by quantifying individual proteins, and showing the separation between one or more protein "spots" on a scanned image of a 2-DE product. Additionally, these tools match spots between gels of similar samples to show, for example, proteomic differences between early and advanced stages of an illness. Software packages include Delta2D, PDQuest and Progenesis among others. While this technology is widely utilized, the intelligence has not been perfected. For example, while PDQuest and Progenesis tend to agree on the quantification and analysis of well-defined well-separated protein spots, they deliver different results and analysis tendencies with less-defined less-separated spots.
Challenges for automatic software-based analysis include:
running differences between gels (e.g., protein migrates to different positions on different gels)
differences in software algorithms and therefore analysis tendencies
Modern software packages include advanced features, such as image warping, to try to compensate for running differences between gels. However, as noted above, 2-DE automated image analysis technology has not been perfected a fact which keeps manual visual analysis as the "gold standard" for validation. More advanced methods of discovery include the use of mass spectrometry.