Dear Mahesh -
I can't comment on the energy changes for the protein, but I can say
that the changes you've highlighted are not really due to alterations of
the protein, but rather inconsistency in assignment of secondary
structure. If you look closely at the areas you've highlighted, you
will see that the C-alpha backbone as depicted in this cartoon rendering
is still making a helix even in the structures where it is not drawn as
an alpha-helix.
This typically means that some residues have just fallen below whatever
threshold the rendering program uses to define secondary structure (like
position on a Ramachandran plot) in one structure, and the same residues
are just above the threshold in the other structure. This is not a
significant change. Indeed, different programs may render the same
structure differently.
I hope that clears up some confusion.
All the best,
Matt
On 10/18/13 2:52 PM, Mahesh Lingaraju wrote:
Hello experts
Attached is an image showing different crystal structures of the same
protein in diffrent states (mutant vs substrate bound vs unliganded)
and highlighted are little changes in secondary structure. I was
wondering how real such small changes are and if they are real could
they be enough to perturb the energy potential of the protein
significantly.
I apologize if this is a naive question as this is clearly not my area
of expertise.
Thanks for your input
Mahesh
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374
