not just sequence dictates 3D?

Artem Evdokimov AEVDOKIMOZ at cinci.rr.com
Sat Sep 21 12:26:38 EST 2002


> Are there some PRECISE databases listing how conformation changes for
> particular protein item/identity/sequence and, AS WELL, pH, temperature,
> and other factors?

No. There are experimental ways to determine such effects in particular
cases, but AFAIK no one has compiled anything of the sort you ask for.

> As far as the protein databank entries as I know (sorry
> for ignorance) usually for each protein item entry only one 3D-strucure is
> presented. If this is not correct, please, provide me with some link (or,
> wishfully, with ad hoc explanation)!

Well, proteins can be presented in the PDB many times, look at all the
structures of lysozyme, or any kind of pharmaceutically important protein
which has been crystallized with (sometimes hundreds) multiple ligands.
Moreover, some PDB files contain more than one copy of the molecule inside,
because there are multiple copies in the asymmetric unit. NMR structures are
routinely presented as ensembles of 20+ conformational states.

> In general, what protein database gives the richest information on
relation:
> sequence->fold ??? Could You please give me the url?

Aside from experimental databases such as PDB and derivatives of PDB
generalized over superclasses of sequences (kinases, for instance, or GPCRs)
there aren't any comprehensive sequence-structure ones. Sequence-structure
relatinship is a *the* problem of computational structural biology.

A.G.E.





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