The purified protein is exhibiting a trimeric state based on my NATIVE PAGE gel and SDS PAGE shows monomeric configuration. Can you recommend detergents to destabilize the H-bonds mediated by sulfate ions (based on literature)? I have already tried BME and DTT and they don't work.
I'm confused about your question.
(1) If the protein is a trimer under native conditions, then why do you want to disrupt the trimer, which is probably the physiologically relevant oligomerization state? Many proteins exist as homotrimers or other homo-oligomers.
(2) If you are trying to disrupt binds using reducing agents, then you should be talking about disulfide bonds, rather than sulfate ions. Disulfide bonds are covalent bonds between cysteine residues, not H-bonds. Reducing agents can usually reduce them, but if they are deeply buried, it may not work. In that case, if you want to reduce them, you have to denature the enzyme with detergent and heat. This is what happens when you prepare samples to run on SDS-PAGE with reducing agent in the sample buffer. The sample buffer contains SDS, which denatures the protein. Using SDS without reducing agent will not break disulfide bonds.
(3) If you really did mean H-bonds mediated by sulfate ions, then you can probably break them with a denaturing detergent such as SDS, or by adding a high concentration of NaCl, or by removing the sulfate by dialysis or gel filtration.
Do you heat denature your protein in the BME/DTT at 95-100C for 5 minutes before loading to the gel? If not then the SDS and DTT alone may not be sufficient to completely denature your protein even when run on SDS-PAGE.
Perhaps try heat denaturing your samples in the loading buffer prior to running the samples.
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