After some discussion, it seems that a thread on the subject
of definitions of primary, secondary and tertiary structure may
be appropriate. These terms are the sort of thing everyone
knows (or thinks they know) how to define. But it may actually be
that there is no consensus. So the question is, can we come up with
some definitions that everyone is happy with? I think there's a
possibility that all sorts of interesting things could come up here
along the way (maybe to do with molecular forces, free energy etc).
So I'll start the ball rolling just with some quick definitions that I
think I'm happy with at the moment.
Primary Structure:
A description of the entire covalent structure of a polypeptide chain.
So this should include all disulphide bonds as well as what is
effectively a knowledge of the amino acid residue sequence.
Secondary Structure:
Consecutive repeats of resides possessing similar main-chain
conformations.
Some might people like to include something about hydrogen bonds
here, but I think this can cause more problems than it solves.
Anyone disagree?
Tertiary Structure:
Effectively the overall fold of a polypeptide chain. We could
say it's a time-averaged model of the relative positions in
three-dimensions of all the atoms in a polypeptide chain, but
I'm sure someone can come up with something better than this.
Well I think that's enough from me. Anyone think that these
definitions are useful/useless/dangerously misleading/something else
in helping people to understand protein structure and function
(NB if anyone says "tedious" in the something else category -
there will be trouble ;-)).
-- Simon
_________________________________________________________________________
|
| ,_ o Simon M. Brocklehurst,
| / //\, Oxford Centre for Molecular Sciences,
| \>> | Department of Biochemistry, University of Oxford,
| \\, Oxford, UK.
| E-mail: smb@bioch.ox.ac.uk
|________________________________________________________________________