Re: [modeller_usage] Modeling of a C-terminal segment
To: Bo Yang <>
Subject: Re: [modeller_usage] Modeling of a C-terminal segment
From: Modeller Caretaker <>
Date: Fri, 28 Sep 2007 12:24:27 -0700
Cc:
Bo Yang wrote:
I have a question of modelling the C-terminal region of my target. The
protein matches with the crystal structure templates except the
C-terminal region (named as C-tail here). I did BLAST search using this
segment to against the proteins with known structures at Protein Data
Band. It returns a match with a short region of an antibody at 56%
sequence identity with the inclusion of 4 gaps. The function of my
target protein has nothing to do with antibody. I am not sure if it is
reasonable to use the BLAST match results as templates to model the
conformation of the C-tail.
I have thought to model this C-tail region using the “Loop Model” in
Modeller. There are some concerns here. First, the C-tail contains 24
amino acids. Will this be too long for the loop-model in Modeller? If
the length is not the problem, how reliable are the conformations of the
segment? Second, the segment is at the C-terminal of the protein. For my
understanding, the “Loop Model” in Modeller requires the N’ and C’
terminus of the segment to be fixed. The position of the last residues
of the segment will have significant influence on the “Loop”
conformation. Which one is more reasonable, to model this segment based
on the sequence homology, or use a loop modelling algorithm?
You will have a lot of trouble modeling this with the loop modeling
procedure. 24 residues is far too long, even for a loop with both ends
fixed (15 is about the limit). With a non-fixed C terminus, the space to
sample is just too large - the loop will be free to explore too much
space. If you have some other information about the loop (e.g.
interactions with other protein residues or ligands) then that might
help to reduce the search space. Otherwise, it is probably best to
remove these C terminal residues from your model.