modeling disulfide without template

[Tom Duncan <duncant AT mail.upstate.edu>]

There are several good template structures for our target protein but,
although it is known that a disulfide can form between a specific pair
of cysteines in theses proteins (cysteines conserved in templates &
target), the known structures show these cyteines as 15-20 angstroms
apart. Nearby flexible loops or "hinge" regions can be identified. Would
it be reasonable to model the target directly with a disulfide patch, or
better to obtain an initial model based on the templates and then do
more thorough MD/SA cycles with a restricted region of the model and S-S
distance restraints before final refinement with the disulfide patch?

Thanks,

Tom Duncan
--
Thomas M Duncan
Research Associate Professor
Dept Biochemistry & Molecular Biology
Institute for Human Performance, Rm 4311
SUNY Upstate Medical University
750 E Adams St
Syracuse, NY 13210