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Hi everyone, I have a crystal structure for an enzyme (1M80) that is
missing a loop, residues 311-319. I also have a structure of a homologue
in which this loop is not missing, and I was hoping to use this as a template
to model the missing loop. I’ve been using: http://www.salilab.org/modeller/wiki/Missing
residues as a guide. Briefly, I generate an initial model of
the loop in 1M80 by filling in the sequence of the missing residues and aligning
with the sequence in 1M80, inserting gaps for missing residues. This
model is then used (with the inifile parameter under the automodel class),
along with an alignment of the filled in 1M80 sequence with the homologous
structure, to actually homology model the loop. As I don’t want the
rest of the protein to move, in both of these steps, I’m modifying
select_atoms to include only the residues in the loop. The resulting model looks pretty good in terms of the
conformation of the loop. What I notice, however, is that the geometry is
a little bad where the loop reconnects with the rest of the protein. For
example, the peptide bond between residues 310-311 and 319-320 is about 1.55
angstroms (ideal being ~1.33). I’ve tried “optimizing out”
this issue with approaches like: a.library_schedule=autosched.slow a.max_var_iterations=500 a.md_level=refine.very_slow a.repeat_optimization=5 …and even increasing repeat_optimization to 25
cycles. This doesn’t seem to help. Also, expanding the
residues included in the optimization (from 311-319 to 310-320, for example)
just moves the bad geometry to the boundary of that new window. Any ideas on what I’m doing wrong? Or how to fix
the geometry within modeller? Thanks for the help! Omar Davulcu |