Methods, Acknowledgements, References

Methods: Atomic Coordinate Files.

The 19 base-pair DNA segment in 1D66.PDB was chosen because the helix is nearly straight. The protein and water were deleted from the PDB file which speeded up the rotation frames/second in Chime by about 6-fold. The end base pairs were remarked-out so as to produce 3' hydroxyl's and 5' phosphates on the ends, leaving 17 base pairs in 1D66-PWZ.PDB. Of course all hydrogens are missing since the atomic coordinates in 1D66.PDB were determined by X-ray diffraction, which cannot resolve hydrogen atoms.

The AT and GC base pairs are residues A27 T12 and C33 G6 taken from 1D66.PDB. The free program WebLab (which like Chime is also derived in part from RasMol's source code) from Molecular Simulations Inc. was used to extract each base pair into a separate atomic coordinate file. WebLab allows atom-by-atom mouse picking as well as selecting by named residue. Each base pair was saved in a MOL file because this, unlike WebLab's PDB-saving, preserved double bond information. Some manual correction of bond orders was required. WebLab was then used to add hydrogen atoms (a few inappropriately added were removed). In the case of the GC, the hydrogens involved in hydrogen bonding were not well oriented towards their bonded oxygens/nitrogens, so WebLab's bond torsion capability was used to position these hydrogens in a more favorable orientation. Both real (from H to N/O) and simplified hydrogen bonds (from N to N/O) were added manually to the bond list.

Acknowledgements. Thanks to MDLI for donating Chime to the world. Thanks to Tim Maffett at MDLI for making script-enhanced Chime available during its development. Thanks to Roger Sayle who pioneered the molecular structure rendering methods in RasMol, and whose source code was used in the development of Chime. Thanks to GlaxoWellcome for supporting Roger Sayle's work on RasMol and its continued donation to the world. Thanks to the Brookhaven National Laboratory Protein Data Bank for making PDB files readily available. Professor Anne Simon suggested the page on ends and antiparallelism.

References. The structure in 1D66.PDB was determined by:

R. Marmorstein, M. Carey, M. Ptashne, and S.C. Harrison, DNA recognition by Gal4: Structure of a protein/DNA complex. Nature 356:408, 1992.

This page is maintained by Eric Martz.