Protein similarity via hydropathy plots?

[Michael Coyne]

In article <1994Apr8.031825.14388 at alw.nih.gov>, bernard at elsie.nci.nih.gov
(Bernard Murray) wrote:

> Why not simply align the sequences in which you are interested?  By making
> these plots you are simply parameterising the amino acids and then using the
> values to generate something for easy (visual) comparison.  In doing this you
> bias the analysis by choosing that scale.  Is there a rational basis for
> picking hydrophobicity, as opposed to any of the other hundreds of scales
> available (eg. see Kidera et al. - J.Prot.Chem. 4, 23-55 [1985] for a
> comparison of a mere 198 parameters)?  Even Kyte & Doolittle (J. Mol. Biol.
> 157, 105-132 [1982] admit that "subjective adjustment" and "arbitrary
> assignment" were used in producing their (now widely used) hydrophobicity
> scale.

Well, the short answer is that the amino acid sequences show little
relatedness, the related nature of the proteins is based on genetic and
phenotypical evidence.  A simple alignment does not produce evidence of
relatedness.  These proteins (in particular, the product of the rfc genes)
are thought responsible for polymerizing the repeating sugar units of
lipopolysaccharide O-antigen side chains, thus, though each protein has a
similar function, they each work on a very different substrate (whatever
the repeating unit happens to be in the particular species and serotype). 
Thus, arguments showing relatedness have been based on things such as
hydropathy plots, my limited understanding of these alignments prompted my
question.

BTW, I have not seen the response from which you quoted.  Maybe there's a
pathway block.  Could you forward it to me via E-mail at
mjcoyne at warren.med.harvard.edu?  Thanks...

Mike