Re: Primary, Secondry, Tertiary...

Daniel Dubois (ddubois@rsvs.ulaval.ca)
Thu, 26 Jan 1995 19:59:07 -0500

Hello to all of you, I'm a new one and let's say it's a try, OK? ;-)

BTW: Please be indulgent for my poor english writing, french is my primary
language

Here's my answer to:

>Dear All,
>
> 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.

I don't want to be insolent, since I'm just a student in the course,
but are you sure it's a good idea to include disulphide bonds in the primary
structure description? As far as I know, disulphide bridges stabilize the
three-dimentional structure of proteins (tertiary structure) and in some of
them these bridges hold together different polypeptide chains (says the A
and B chains of insulin after maturation, for exemple) wich might lead us to
quaternary structure. Is'nt the primary structure usualy mean the amino acid
sequence only?

>
> 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?

Please forgive me, but here againt I disagree...

Did'nt the hydrogene bonds pattern and the energy involve have been
use extensively, with the torsion angle distribution, for the determination
and differenciation of secondary structures? We might skip the beta-turn and
loops hydrogen bonds description since, I agree with you, it's still under
discussion, but for the alpha helix and the beta strand, I think it's well
describe and accepted, is'nt it? I might be important to mention that the
side chain are not involve in that stict hydrogen bond definition of theses
secondary structures and that ONLY main chain hydrogene bonding are
responsible for their formation.

>
> 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.

I think you're making a good point in mentioning the "time averaged"
aspect of a tertiary structure. We might had too the implication of the side
chain (for Van der Waals interactions, hydrogene bonding, electrostatic and
hydrophobics attraction or repulsion and disulphide bridges). Since we have
already describe secondary structure, should'nt we see tertiary structure as
a packing of secondary structure connected by undefined regions?

What about quaternary structure?

>
> 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
>|________________________________________________________________________
>

So that's all for me folks

Bonne journee et a la prochaine :-).
----------------------------------------------------------------------------
Daniel Y. Dubois Tel. 418 656-2131 #6273
Pav. Charles-Eugene Marchand Fax. 418 656-7176
Departement de Biochimie E-mail: ddubois@rsvs.ulaval.ca
Universite Laval
Ste-Foy, Quebec, Canada
G1K 7P4