Analysis of protein structure always makes sense *in retrospect* - that is
after the sructure has been determined. Predictions, on the other hand,
aren't so easy...
In 1CRN (crambin), one could rationalize several reasons for the specific
beta-sheet formation. For example: disulfide pattern - your (B) arrangement
won't be possible in the context of the same S-S pattern as crambin actually
shows. Another point of view would be to consider that residues 1-4 and
their neighbors form a mini-core of the protein, maximizing the amount of
hydrophobic packing, which won't be as efficient as the alternative
arrangement. Other explainations abound, but all of them have one thing in
common - the structure is known, therefore such conclusions are reasonably
risk-free. In general, if you assume that the rest of crambin adopts the
'natural' sort of fold, then the fate of the beta-sheet is sealed, and is
determined by the rest of the protein. If you allow the rest of the protein
to adopt other conformations, then there is no good 'reason' why the beta
sheet adopts its natural shape. Unfortunately, this simply means that so far
we have no good ways to predict structure from sequence, because in reality
crambin folds properly into a structurally unique entity. When we develop a
more complete understanding (meaning predictive power) of why proteins fold
the way
they do, we will be able to really make claims why proteins fold one way and
not another.
Hope this helps.
A.G.E.
"Marc Parisien" <parisien at iro.umontreal.ca> wrote in message
news:3D78EF40.7E1F205C at iro.umontreal.ca...
> Hi All!
>> I was looking at the beta-sheet of the Cranbin protein (1CRN). This
> beta-sheet is composed of 2 strands (residues 1 to 4 and 32 to 35).
> H-bonds partners in the beta-sheets are 1 <-> 35 and 3 <-> 33, like:
>> A)
>> 1 <-> 35
> 2 34
> 3 <-> 33
> 4 32
>> Q. Is there any reasons why the h-bonding is such?
> Is there any counter to the possibility of having h-bonds partners 2
> <-> 34 and 4 <-> 32 instead of 1 <-> 35 and 3<-> 33, like:
>> B)
>> 1 35
> 2 <-> 34
> 3 33
> 4 <-> 32
>> this would inverse the side-chain orientation (the ones on top of the
> sheet will now be on the bottom and vice-versa) impacting on the
> surrounding side-chains, but if we look at only the sheet itself, is
> there a reason why would nature prefer setup A over setup B?
>>> Thanks for your time,
> Marc.
>
