Homodimer Structure Calculation Using CYANA

Dimer Structure Calculation by CYANA

CYANA2.1 can handle handle structure calculation:

Symmetric Dimers

Two new types of restraints have been introduced that improve the treatment of symmetric dimer structures. Identity restraints are harmonic potentials on the difference between corresponding torsion angles in the two molecules. They help to ensure identical structures of the two monomers. Symmetry restraints are harmonic potentials on the difference symmetry-related interatomic distances and can help to maintain the symmetry of the homodimeric structure. Various other problems relating to symmetric dimers have been resolved.

• Automatic run

1. 1. Define your sequence as two molecules with a linker.
      MET 11 ALA 12 GLU 13 VAL 14 GLU 15 ... GLU 106 PL 107 LL2 108 ... LL2 208 LL2 209 LP 210 MET 211 ALA 212 GLU 213 VAL 214 GLU 215 ... GLU 306
      Here, PL is the residue linking the protein to the linker, LL2 is residue of the linker, LP is the residue linking the linker to protein. The residues PL, LL2 and LP have zero vanderwaals radius.
      Note: The number of linker residues should be larger enough to find the correct demer interface.
      
      
   2. Duplicate the shifts in the protlist ( so that the seconde molecule also has assignments). e.g.
      155 119.362 0.000 N 11 156 8.323 0.004 HN 11 157 56.722 0.000 CA 11 158 4.318 0.005 HA 11 159 31.426 0.000 CB 11 160 2.010 0.000 HB2 11 161 2.137 0.000 HB3 11 ... 1818 119.362 0.000 N 211 1819 8.323 0.004 HN 211 1820 56.722 0.000 CA 211 1821 4.318 0.005 HA 211 1822 31.426 0.000 CB 211 1823 2.010 0.000 HB2 211 1824 2.137 0.000 HB3 211
      
      
   3. Define the ranges of the monomers in your CYANA macro init.cya . e.g.
      name:=hr2106-cyana cyanalib read seq $name.seq rmsdrange:=12..104,212..304 molecules define 11..106 211..306
      
   4. Run the CYANA noeassign macro as usual. Addtional manual distance constraints (intra- or inter- molecular) or dihdral can be applied as usual and will help the structure converge.
      
      

• Manual run

Similar to the automatic run, modify the seq file, prot list, init.cya, and run the CYANA manual CALC macro as usual.

-- Main.GaohuaLiu - 31 Jan 2008