Hi all
I
wrote last time but got only one feedback. I know some of you guys must
have this experience that how to delete loops from the protein. Please
help me with suggestions.
I
am working with a human protein which have around 20% sequence identity
with the other proteins of the same family. Structure of some of the
proteins from this family have been solved. All the solved structures
have around 20% identity with my protein. I am trying to crystallize the protein but it looks like very hard to get crystal.
I have tried different N and C terminally truncated constructs for
crystallization but no crystal. My feeling is that probably there is
some flexible loops with in the protein which limiting the crystallization.
So
I want to delete the loops with in the protein (not to truncate in the terminal, I already have done this). I am not asking suggestion about how to
delete the loop rather how to decide where the loop is. I am not sure how much it will be helpful to get a homology model of such a protein having low sequence identity. Is there any
strategy to decide where the loop could be? Does anybody know any
established/ rational method to do that.
Waiting for your suggestions
Obayed Ullah