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Re: modeling disulfide without template



Hi Tom,

I wonder why  it happens that an experimentally established disulfide bond is
not confirmed in several crystal structures. Maybe the crystallization
condition were not  oxidative to support disulfide bridge formation. In this 
modeling  case the template selection  step must be crucial: a structure with a
disulfide bridge, even if the structure itself is not the highest resolution
one available, should enjoy priority.

If you do not have such template at all and if you believe that for your
question  the physiologically meaningful situation is an oxidized Cys
connection, I would suggest to patch it from the beginning. You can ask for a
simultaneous, exhaustive MD/SA refinement. I believe it will be more accurate
when all the restraints used by Modeller will be taken into account all the way
during optimization (packing). To set the highest level of MD/SA optimization
include in your TOP file

SET MD_LEVEL='refine1'  

best wishes,

Andras



Tom Duncan wrote:
> 
> 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

-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras