               BACKBONE DIHEDRAL CONSTRAINTS

    Except for some sugar  puckering  and  the  'Chi'  angle
determining the orientation of the base part of a nucleotide
relative to its sugar moiety, the  conformation  of  an  RNA
molecule  is  primarily  determined  by  the  value  of  its
backbone  dihedral  (torsion)  angles.  For  each   internal
nucleotide these are designated as:

        'alpha' about the bond P-O5'
        'beta'    "    "    "  O5'-C5'
        'gamma'   "    "    "  C5'-C4'
        'delta'   "    "    "  C4'-C3'
        'epsilon' "    "    "  C3'-O3'
        'zeta'    "    "    "  O3'-P

For a 5' nucleotide the angle 'alpha' does  not  apply,  and
for a 3' nucleotide the angle 'zeta' does not apply.

    As an example, it is a  characteristic  feature  of  the
Hammerhead  RNA  molecule  that  it  contains  the conserved
segment CUGA in a conformation that is  virtually  identical
to that of the same segment in the yeast phenylalanine  tRNA
anticodon loop.  We thus have what appears to be a  backbone
dihedral  motif.   Our preliminary attempts to predict these
motifs starting from the secondary  structure  of  the  tRNA
anticodon  stem and its loop or from the secondary structure
of the Hammerhead RNA, have not  been  entirely  successful.
For  the  motif  to  show  up in reasonable computation time
apparently requires the stabilizing influence of a  hydrated
Magnesium ion strategically placed to interact with the CUGA
segment. Preference is therefore given to the equivalent but
more  practical  alternative  of  simply specifying dihedral
constraints that will insure realization of the motif  in  a
refinement subsequent to generating the initial 3D model.

    Like specifying  hydrogen  bonding  constraints,  adding
backbone  dihedral  constraints  to  the current 3D model is
interactively achieved via an item of the 3D  Edit  pulldown
menu, called Backbone Dihedral Constraints.  The constraints
can be entered manually, as a saved list, as a user motif or
as  a  sample  motif.  Sample motifs are those provided with
the progam.  User motifs are those provided by the user  and
which  are  stored  in  the  user's RNA_2D3D/Dihedral_Motifs
directory.  Typical entry of a motif into this directory  is
by  copying  it  from  a  PDB  file.  For instance, by first
calling in the sample transfer RNA file  6tna.pdb  (provided
in the sample PDB file directory) as Model A, and then using
the dihedral angle measuring utility  (an  item  of  the  3D
Utils  pulldown  menu)  to  list  the dihedral angles of the
segment CUGA (specified by pointing to its  first  and  last
bases),  subsequent  saving  of  this list provides the user
dihedral motif called 6tna.pdb.CUGA.

    Adding a  dihedral  constraint  requires  at  least  two
steps. The first is to select the desired constraint and the
second is to accept it.  When the desired  constraint(s)  is
in the form of a motif, another step is required to indicate
where in the molecule  the  motif  is  to  start.   This  is
achieved  by  specifying  the corresponding motif segment in
the molecule by picking its first base in the molecule.  For
instance, if the motif 6tna.pdb.CUGA is being added, picking
the base C in the molecule will tell the program  where  the
constraints are to be applied.

     Once a constraint has been added,  and  thus  become  a
part  of the molecule's current dihedral constraint list, it
can be viewed graphically by activating the "render  current
list"  item.   This item toggles on and off the rendering of
all the  current  dihedral  constraints  by  displaying  the
target  angle  and the current angle of each dihedral at the
midpoint of the bond  about  which  the  rotation  angle  is
defined.  The current angle is in parenthesis to distinguish
it from the target angle.

    Whatever the source of a specified dihedral constraints,
they  automatically will be incorporated into any subsequent
refinement procedure of the current 3D model being edited.

                          THE END





