left2right=right2left? (protein aminoacid sequences)

Emir Khatipov khatipovNO at NOuchicago.edu
Mon Sep 16 16:07:52 EST 2002


No they would not fold identically. If you compare e.g. sequence ABC
consisting of L-isoforms of aminoacids and sequence CBA consisting of
R-isoforms of aminoacids, they will form mirror images of each other. You
should read about protein structure, chirality, torsional angles,
Ramachandran plots, etc.

You can imagine the following weak but commonly used analogy: polypeptide
looks like a x-mass tree, with the branches (side chains) pointing down and
the N-terminus on the top. If you cut the trunk of the tree so that each one
segment has one branch on it, and put the bottom one on top, etc. down to
the top segment to be put at the bottom, you will not have the same
structure, because now the resulting tree has branches pointing in the wrong
direction (towards the top segment). You cannot turn around the segments to
correct this problem, because that would be equivalent to exchanging carboxy
and amino groups in the aminoacid, which is not possible, because it would
also mean exchanging phi and psi angles, i.e. producing mirror images of
aminoacids.

One more thing, even if you synthesize in a test tube 2 proteins L-A...L-Z
and R-Z...R-A, there is no guarantee they will fold into mirror image
structures, because in nature folding of many proteins is assisted by
complex of factors (chaperones, etc.) that are adapted to polypeptides
consisting of L-isoforms of aminoacids. Correct folding of such proteins
into exact mirror images would be possible only if one is folded in the
"left-hand" (L) world, and another in the "right-hand" world (R) (that has
not been yet discovered :-)).

I hope I did not make things seem even more complicated for you then they
were. Well, in fact this stuff is quite complicated.
Emir


"Adrian Laugarvatn" <AdrnLgrvtn at gazeta.pl> wrote in message
news:Xns928ACF634ED1CAdrnLgrvtnGazeta at 193.42.231.152...
> Is the sense of aminoacid sequence important for protein folding? If You
> have 2  sequences that look identical when the first one is scanned from
> left to right and the second to the oposite then will the 2 proteins fold
> into the identical 3D-structure either?
> --
> Adrian
>
> --
> Serwis Usenet w portalu Gazeta.pl -> http://www.gazeta.pl/usenet/





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