Why "alanine" scanning?

Zophonias O. Jonsson zjons at vetbio.unizh.ch
Thu Oct 16 14:26:40 EST 1997


In article <625n3p$8a6 at panix.com>, iayork at panix.com (Ian A. York) wrote:

> My boss just asked me this, and I didn't have a very satisfactory answer: 
> Why, when doing alanine scanning, does one change to alanine instead of
> glycine?  I understand that alanine is sort of a generic, unexciting, Joe
> Amino Acid; but why isn't glycine just as bland, boring, and unexciting?
> 
> I mumbled about maybe having a sidechain made alanine a little more
> generic than glycine, but I couldn't come up with a clear justification.
> Anyone?

The idea is that glycine can allow too much flexibility so, at least
theoretically alanine is less likely to cause misfolding of the protein. 
In other words, glycine is actually too wild, not boring at all.  If I
quote loosely from James A. Wells (Methods in Enzymology (1991):202
pp390-410) the main reasons for choosing alanine are:

  It is the most common amino acid in proteins.
  It is found commonly in buried and exposed positions.
  It is found in all manner of secondary structures.
  It does not impose new hydrogen bonding, or lead to stearic problems.

Actually you may be better off mutating into something bulky in some
cases, it all depends on your situation.

Hope this makes some sense.

Zophonias

_____________________________________________________________________
Zophonias O. Jonsson
Institut fur Veterinarbiochemie               Tel: (41-1)-635-54-75
Universitat Zurich-Irchel                     Fax: (41-1)-635-68-16
Winterthurerstrasse 190
CH-8057 Zurich
Switzerland
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