In SDS-PAGE it shows the molecular weight range of the protein. But, if my information is correct, native PAGE gives information about the native structure of the protein. Then what information would the ladder give in native PAGE?
It completely depends on the nature of your desired protein, in terms of molecular weight (kDa). If I were you I would run the native SDS-PAGE using standard proteins along with the sample. Examples of good standard proteins are albumin from bovine serum (or bovine serum albumin; BSA), egg albumin, and some other commercially-available enzymes such as tyrosinase from Agaricus bisporus (Sigma sells the enzyme, from what I know).
These standard proteins had a defined tertiary and/or quaternary structures so they are suitable for native SDS-PAGEs. They can tell you exactly the kDa of band(s) formed on your gel after running. Then only decide a suitable protein marker to run along with your protein samples. Hope these information could help you.
No, it is not incredibly necessary; however, it does depend on what information you'd like to obtain from your native PAGE gel. They do sell commercially available standards (http://www.lifetechnologies.com/order/catalog/product/LC0725), but again, they will only show molecular weights, whereas your proteins may oligomerize or have different shapes that would change their migration in a native PAGE environment. Then the ladder isn't incredibly useful. Personally I would use several internal standards/controls based upon what questions you're hoping to answer with your native PAGE analysis.
Native gels are run of many purposes but rarely for calculating molecular weights of protein samples,so loading a conventional SDS-PAGE ladder will not serve much purpose.As Tyler suggested companies do sell commercial native gel ladders.
During native runs,i prefer to load a protein whose behavior is already known,that just helps me observe if everything is fine with the gel and the running setup,but one may need to work around with the concentrations of the standard protein.
You can run the mixture of known molecular protein proteins along with your proteins..just make sure which protein you are using as ladder. (you should know the oligomeric form of that protein..)
Thank you for your answers. Gaurav can you please tell me what you mean by knowin the oligomeric form of my protein? Also how would that help?
It completely depends on the nature of your desired protein, in terms of molecular weight (kDa). If I were you I would run the native SDS-PAGE using standard proteins along with the sample. Examples of good standard proteins are albumin from bovine serum (or bovine serum albumin; BSA), egg albumin, and some other commercially-available enzymes such as tyrosinase from Agaricus bisporus (Sigma sells the enzyme, from what I know).
These standard proteins had a defined tertiary and/or quaternary structures so they are suitable for native SDS-PAGEs. They can tell you exactly the kDa of band(s) formed on your gel after running. Then only decide a suitable protein marker to run along with your protein samples. Hope these information could help you.
@ Shashwati: oligomer means protein can be in any form such as monomer Dimers, trimers, or tetramers..while doing SDS PAGE all these forms will become monomer but in case of NATIVE PAGE all the proteins will be in its native form so while running the protein as marker you should know their oligomer form..hope you understood this
Native PAGE is run to know the activity of the protein in its native form. If we really want to know the molecular weight (as asked for ladder) of our protein, then we need to run SDS-PAGE. In this technique, we will have both information about the number of peptides that constitute our protein and also the molecular weight. The same ladder won't help you in native PAGE.
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