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Hi All, Thanks for all of your inputs! Alex On Thu, Oct 4, 2018 at 7:31 PM Zhijie Li <[log in to unmask]> wrote: > Hi, > > At high concentration (1-2%) the published saturating SDS:protein binding > ratio is about 1.4:1 by weight, that is roughly one SDS molecule per two aa > on average. It is dense but not that dense to prevent any further > interaction. More importantly, as a quite hydrophilic small molecule SDS > should have no trouble dissociating from the peptide when its in-solution > concentration drops (therefore you can use SDS gel bands for MS). With > common procedure, during staining the SDS should partially fall off( > especially if the gel is heated), and partially remain with the protein in > the gel, depending on: how hydrophobic the protein is, how low the > environmental SDS concentration becomes, how much organic solvent there is > in the solution, etc.. The coomassie should simply find whatever > hydrophobic/positively charged patch to bind and aggregate. Besides, > coomassie-R is probably slightly more hydrophobic than SDS so it is capable > of competing SDS off if necessary. (The even less hydrophobic Coomassie > G250 definitely binds protein in the presence of detergents - that how Blue > Native gel works for membrane proteins) Finally, since the only thing you > are looking for is some deeper blue to indicate the presence of protein, > even if SDS did prevent dye binding to some extent, your gel still will > work. This is different from when you want to use the dye to do some > quantitative work such as the Bradford assay. It would be interesting to > know the effect of detergents on Bradford. > > Zhijie > > > > On Oct 4, 2018, at 9:26 PM, Alex Lee <[log in to unmask]> wrote: > > Dear All, > > I am thinking that in an SDS-PAGE experiment, if protein samples are > boiled in SDS containing loading dye, and supposedly SDS interacts with > proteins, why the Coomassie Blue dyes could still interact with and stain > the proteins? I am thinking SDS is covering the proteins, making no > room for the Coomassie Blue dyes interaction. I'd appreciate it if any > input from this forum. > > Alex > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1