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Template Structure
The next step involves generation of a template coordinate
set. This is required in all cases, except for the random
simulated annealing protocol. The template coordinate
set can be any conformation of the macromolecule with
good local geometry and no nonbonded contacts. It can
be generated by using most molecular modeling graphics
programs or, preferably, by using the X-PLOR protocol
described below. The purpose of the
template coordinate set is to provide distance
geometry information about the local geometry of
the macromolecule, to apply appropriate pseudoatom
corrections, and to provide a starting point for the
ab initio simulated annealing protocol. Furthermore,
template coordinates can be used to define large
rigid groups in distance geometry, e.g., if
certain portions of the protein structure are known
by other means or have been determined by other
methods.
The protocol below automatically generates a
template coordinate set. It initially
places the atoms of the macromolecule along the
-axis, with 
and 
set to random
numbers. The coordinates are then regularized using
simulated annealing. The protocol is
completely general, and it has been tested for both
proteins and nucleic acids.
Disulfide bonds and other covalent links between
sequentially distant residues may have to be
removed for successful completion of the template
generation. Generally, when too many covalent
links are present, the structure may get entangled
in a knot which will result in poor local geometry. Some experimentation
may be required to find out if certain covalent links
have to be removed; the goal is to obtain an energy
below 1000 kcal mole
for the final step of minimization.
This protocol has been successfully used with up to three disulfide
bridges. However, in the case of bovine pancreatic trypsin
inhibitor, removal of the disulfides was required.
Xplor-NIH 2024-09-13