These react with PITC and produce artifact peaks that co-elute with amino acid residues. However, if obscuring certain residues by artifact peaks is not a problem for you, some contamination with urea, guanidine, tris, etc. Non-volatile buffers will usually interfere and cause lag due to their buffering effect during the Edman sequencing reaction.
Again, this may not be a problem if a very long sequence run is not necessary. It is not the molarity of the matrix components that matters as much as the amount that we must load. Five uls of mM salt is usually harmless whereas ul of a more dilute salt may cause a problem. The PVDF is then placed directly into the sequencer.
These membranes are coated with a material to assist in Western blotting and will severely clog our sequencer! Blotting protocols are available at the lab. Although in SDS-PAGE theory, protein is saturated with SDS and the pI of the protein should not matter, we recommend that a membrane also be placed on the cathode side of the transblot sandwich in case the pI of the protein is near or greater than the pH of the blotting buffer.
We recommend that two sheets be aligned back-to-back on the anode side of the sandwich if PVDF-P is being used.
Glycine blotting buffer has a pH of about 8. We prefer to cut the protein band out of the membrane ourselves so that the contrast of band to background can be seen and concentration estimated.
However, if you want to cut out the bands yourself, cover the whole membrane with Saran Wrap and photocopy the membrane before you excise the protein bands. In either case, deliver it H2O rinsed and dry. We can only load about 0. If you wish to ensure that enough sample is present and minimize any possible protein modifications, blot with tris glycine buffer and stain with ponceau red.
If you can see the sample with ponceau red, you have more than enough to sequence and the moderate pH of the tris-gly buffer will minimize modifications.
Minimum needed is pmoles. Gel slice sample preparation Note: most internal sequencing Edman work for protein ID and mapping has been replaced by mass spectrometry which is cheaper and faster to accomplish. This is especially true as the MW of the protein to be digested increases.
Larger proteins are generally more difficult to electroelute and transfer from gel. One simply runs the gel, stains with CBB, destains, excises the protein band and a control band and submits them for analysis. The percentage gel used and the way you stain and destain are important so follow the gel slice preparation instructions below. The protein to gel ratio density is very important so keep protein density as high as possible. Getting sequence from achieved gels is also possible but you will need somewhat more protein.
Also, the sample should be reduced e. Heat at 60 C. This unfolds the protein and allows better digestion. We need at least pmoles to perform the in-gel digest and would prefer more if possible. With a 50 pmole sample we can use robust 2 mm diameter chromatography but at the 25 pmole level we must use 1 mm chromatography which requires extensive equilibration and at least an extra day of HPLC time. Ken Williams and Kathy Stone Gel slice preparation sumary:. A summary of the Ken Williams and Kathy Stone in-gel digest protocol from reference 1. Recommend gel thickness 0. The final density of the protein in the stained gel should be at least 0.
Thicker gels are OK if high density is maintained. Keep protein sample as concentrated as possible without compromising separation. Effort should be made to limit the amount of Coomassie Blue staining to what is necessary only. If the entire gel still has CBB background, continue destaining until the background is nearly clear. Regardless of the amount of staining, the gel must be exposed to stain and destain for a total of at least three hours and have several destain changes to ensure adequate removal of SDS i.
Overnight destaining is OK. Measure and record on the request form the dimensions of the sample band LxHxW. Place in a 1.
Measure and record the dimensions of the control band. Please call MIT Biopolymers lab. Ken Williams and Kathy Stone Gel slice preparation references:. Techniques in Prot. VI p , John W. Crabb, ed. Rasmussen, J. Van Damme, G.
Bauw, M. Puype, B. Gesser, J. Vandekerckhove, "Protein-Electroblotting and Microsequencing in.
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Verlag, Basel, pp. ISBN and Matsudaira, ed. Solution phase digests:. Solution phase digests always work best. The protein is in the liquid phase so enzymes in addition to trypsin and achromobacter lyticus lys-C can work well. The protein is denatured more thoroughly so more peptides are generated.
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Yields are higher too. We sometimes find that in-gel or membrane proteins which failed to digest initially due to i. If you are sample limited and we cannot detect the protein by UV, you may have to radio-label some material and determine if it elutes in the pilot run by counting column fractions.
We do have experience with in-situ PVDF and glass fiber filter GFF CnBr digestion, but use it only as a last-ditch effort to gain sequence from samples which have been run on the sequencer that are suspected to be N-terminally blocked. These in-situ CnBr digests rarely yield a good sequence because many methionines are usually present in a protein. It does, however, indicate how much protein was loaded and confirm blockage as opposed to lack of sample as the cause of the sequence failure.
Advise if you want our CnBr protocols to use in your lab. We like membrane digests because they produce fewer background chromatography peaks than in-gel digests. You may prefer in-gel digests if your protein is large or likely to have trouble transfering to the membrane from the gel.
Protein Sequencing Protocols
We use the Fernandez et al. The contents of a gel are onto a membrane, the membrane stained, destained and the appropriate bands cut out and digested in a buffer incorporating hydrogenated triton X RTX or an alternative detergent. Staining is not necessary in these cases. We ask for at least pmol of protein for an in-situ digest on NC or PVDF and 25 pmol for a solution digest but prefer at least double these amounts if possible. You won't have to worry about wasting sample because the N-terminus was blocked.
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You will also get several fractions suitable for sequencing and thus have backup peptides in the event of instrument malfunction. Highly glycosylated samples are usually resistant to enzymatic cleavage and may produce few if any peptides. Post-translationally modified residues often appear as blank cycles on the sequencer.
Related Protein Sequencing Protocols
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