Go easy on proline
DUNTEN@XRAY.BMC.UU.SE
Wed, 22 Mar 1995 20:22:36 +0200 (MET)
As a Proline group member, I feel compelled to defend poor Proline. We read in
the course material that Pro causes problems for alpha-helices, as the
H-bonding is not so good when Pro occurs in a helix. What isn't mentioned, is
that crystal structures of proteins often show a well-defined water molecule
H-bonding to the Pro carbonyl-oxygen, satisfying one of the 'missing' H-bonds.
Furthermore, consider the driving force for helix formation. Is it H-bonding?
Doesn't seem likely, as a random coil structure will have the protein backbone
H-bond donors and acceptors satisfied by water molecules. The driving force
may be burial of hydrophobic surfaces, i.e. the beta CH2 (or CH3) substituent
of the side chains, and whatever may come after. Some such factor must explain
the differing propensities of the 20 amino acids to form helical secondary
structure. These ideas are explored further in the following 2 references:
Richards, FM & Richmond T (1978) Ciba Found. Symp. 60, pp. 23 - 45.
Blaber, M, Zhang, X-j & Matthews, BW (1993) Science 260, pp. 1637 - 1640.
Proline isn't so bad, really!! -Pete