Entering edit mode
10.9 years ago
Pappu
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2.1k
I am trying to find out why proteins from a few species are more stable than human proteins by analysing the DNA and protein sequences. I am wondering what kind of statistical analysis to be performed rather than basic amino acid compositional analysis and secondary structure prediction. I calculated the log odds substitution matrix from the concatenating the alignments of orthologs. Does it make sense?
Did you try to calculate synonymous and non-synonymous substitution rates (Ka and Ks) for human and other species genes? The Ka/Ks ratio will give you an idea about selective pressure acting on a protein-coding gene. It might be the case, that Ka/Ks ratio for your human genes might be significantly higher, meaning that this group might be under different selective constraints. I highly recommend this software: http://www.ncbi.nlm.nih.gov/pubmed/17531802.
You should keep in mind that there are proteins (i.e. Heat-Shock proteins) that associate with other proteins in order stabilize their confirmation, for instance during stress. So in other words the sequence of the protein in question may not be the root of the change in the stability. Some other proteins (or other molecules) may have evolved to change the stability of the protein of interest.
I am saying that in vitro the proteins are more stable without any HSPs.