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Re: [ccp4bb]: how to prepare a structure-based sequence alignment



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On Tue, 2 Jul 2002, fan zhang wrote:

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> Dear All,
>
> I'm very sorry it is not a question closely related to protein
> crystallography. Recently, I want to prepare a
> structure-based-sequence-alignment figure, but I don't know how to do it.
> In addition, how should I deal with those residues that are of similar
> physicochemical properties but are not of equal positions.

If you have structures of both (or more) proteins involved then just
superimpose them and align the structurally equivalent residues. Deciding when
to call two residues structurally equivalent can be a bit arbitrary. I
normally let O's lsq_refi sort out the equivalent bits. Maybe not perfect, but
no user-bias and a lot easier/faster then eyeballing the structures.

If you only have one structure and want to align other related sequences with
it you can help normal alignment programs, such as ClustalX, by providing it
with the location of secondary structure elements. You can also align
sequences to structure using threading, but the alignments are often not very
accurate. The THREADER program can align based on both physicochemical
positions and sequence homology. Maybe with proper weighting this is useful. I
would personally use standard sequence-only alignments and then analyse the
conserved features wrt the structure. Do conserved hydrophobic positions
correspond to hydrophobic core residues, does conservation of small residues
correspond to a cramped space etc. Based on such information you can often
spot errors in alignments of highly divergent sequences where sequence alone
cannot distinguish between alternate alignment possibilities.

> In addition, how should I deal with those residues that are of similar
> physicochemical properties but are not of equal positions.

I don't really understand what you get at here. If they don't occupy
structurally equivalent positions than you shouldn't normally align them even
if they have similar physicochemical properties. If the sequence-suggested
alignment is clearly at odds with the observed structural alignment then I
would suggest the sequence evidence has to be pretty strong to overrule the
structural information. I guess it is possible to have an insertion in a helix
leading to a shift of the subsequent residues. I only know this happening when
human beings make mutants, but maybe you can find examples in nature. In this
case you'll have to decide if the sequence alignment is supposed to show
evolutionary equivalence (the normal assumption) or structural equivalence.

Bart

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