i am working on two proteins each translated from two different genes belonging to same gene family. A closer look at the sequence tells me that the proteins differ in the number of charged residues. i wanted to investigate whether it has any functional differences amongst the two proteins. how should i proceed?
First, I would take a look if proteins have significant differences in biophysical properties. Second, if charged amino acid residues are in functional domains/motifs and/or affect folding. Also, if it still looks interesting, I would look for possible positive selection.
charged residues lie in the functional domains..how do i look fr differences in biophysical properties? are there tools available online? can u suggest a few?
Well, biophysics is mostly experimental - http://www.advantarlabs.com/superhero-services/biophysical-characterization
However, if there is structure solved for your protein, I would try modeling with Phyre2.0, http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index, to see if these residues affect secondary structure and, potentially, active center folding...
Sansrity,
Protein function can be predicted from its structure (see http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3213.html; http://raptorx.uchicago.edu/; https://www.predictprotein.org/)
but, it would be very common features and similar genes will not be separated in most of cases.
To show the functional/structural difference you must clone both of your genes, express them in E.coli (or different organism); extract, purify proteins, study kinetics of their activity on different substrates (if they are enzymes), binding to DNA/RNA/other proteins (if they are regulatory), conditions of denaturation (if they are structural). You also can crystalize your proteins alone or with substrate molecules and study their stricture. This is a very general schedule of work...