Many uncharacterized proteins were found in genome annotation. These proteins are crucial to be known as it could be a protein with noble functions. However, not many strategies have been developed in order to tackle these vast amounts of uncharacterized proteins.
i dnt know much about this thing. but crystal lattice formation may be a good option. to characterize a protein molecule or to identify the amino acid sequence in a protein molecule is it possible to run a NMR spectrometry???
It depends on the genome you are studying, and the time/money you are willing to spend. Obtaining knock-out mutants or doing siRNA knock downs and examining the phenotpype of the resulting cells/organisms is one possibility.
If you know the sequence of the genome, then you can identify the protein nature by using genome sequence alignment tools like BLAST2, MegaBLAST and MUMmer
Hi, what type of protein you are talking about? The gene you annotate does not need to be functional. Take an example of fungus there are many gene clusters encoding unknown molecule. These gene cluster are silent under laboratory condition but recently many strategy are being used to activate these silent cluster leading to produce newer molecule.One eg is the use of chromatin modifying chemicals like sodium butyrate (inhibits histone deacetylation).
This is a tough question. Bioinformatics can find proteins homologous to the "Uncharacterized protein". STRING and IBIS programs can be used to find proteins which interact or bind the "Uncharacterized protein". Once you get good clues about the possible function of this "Uncharacterized protein"., one can do the knockout experiments suggested by Alejandro. This approach will be much faster than cloning, and expressing the "Uncharacterized protein".
Hi Venil, I agree that you can use bioinformatics means to get some idea about the protein coded by the gene you have annoted but creating knock out may not be helpful always as I mentioned above.In that case you can you have to clone and express the gene or else if there is orthologs in other system then try cross complement with your gene of inetrest in that system.
Yes Pranav, But once you remove the epigenetic silencing (as you did), the gene should be expressed and the knockdown should work. If the "Uncharacterized protein" has many isoforms, or is a part of a large gene family...then, the knockdown experiment may fail . .Otherwise, it should work.
I agree with Alejandro Martin. generating knock-outs could be very helpful if you have a way to analyze the mutants and potential intermediates or phenotypes.
I think the first step is to define so-called "noble function". Generally, from nutrition aspect, amino acids composition or antioxidant properties of hydrolyzed products would be focused. While from functional aspect, solubility, emulsifying property, foaming property, gelation property, or film property would be focused. Depends on which aspect you care about, a lot of choices for this question.
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