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Evolution and Protein Folds

Simon Brocklehurst Bioc smb18 at mole.bio.cam.ac.uk
Fri Jun 24 11:33:14 EST 1994

ram at mbisgi.umd.edu (Ram Samudrala) writes:

>Suppose we have a gene duplication.  One copy of the gene stays
>mutationally put as there is selective pressure for the protein it
>produces.  The other copy is free to accumulate mutations and perhaps
>evolve to a new function.

   All kinds of things like this probably happened. Not just genes,
but sub-genes which code for folding motifs (modules etc), and smaller
bits of structure (e.g. helices etc).  It's just the enzymes involved
in nucleic acid synthesis making "mistakes". If theses "mistakes" lead
to favourable results at the protein level, the the changes stay.

>Now, all the books I've read talk about evolution in terms of protein
>function.  That is, there is selection as soon as the mutation gene
>produces a protein that has some function.  What I am interested in
>knowing is if there is any model that speaks of evolution in terms of
>protein structure.

 (Stuff deleted)

  What you wrote is generally accepted as being correct.  Quite a lot is 
known about what kind of amino acid substitutions are acceptable in particular
structural environments.  The most interesting analyses come from
looking at substitution patterns in aligned sequences of proteins with
known three-dimensional structure.

>If there is some preservation of protein structure between
>generations, how exactly is this accomplished?  

   Mutations are accepted at the level of the organism i.e.
if the mutation causes only problems for the organism, then
it (the organism) may not survive etc.

>I am also told that there is evidence of "genes" that produce proteins
>that misfold.  If this is true, how can be explained in terms of
>evolution/natural selection.  If you think this is false, why?

    I don't know about this.  But there is no reason why it couldn't
happen.  Surely it depends on what problems the lack of a particular
protein causes for the organism.

   All this stuff is in books, but take a look at the "learned journals",
like J. Mol. Biol., Protein Science etc which are full of this kind
of stuff.

|  ,_ o     Simon M. Brocklehurst,
| /  //\,   Cambridge Centre for Molecular Recognition,
|   \>> |   Department of Biochemistry, University of Cambridge,
|    \\,    Cambridge, UK.
|           E-mail: s.m.brocklehurst at bioc.cam.ac.uk

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