Computer aided study of the interaction of thyroid hormone receptor with DNA

Interaction of the first zinc finger from human thyroid hormone receptor (finger) with hexanucleotide duplex d(AGGTCA).d(TGACCT) from thyroid regulatory element has been studied by molecular mechanics simulation technique. The structure of the finger as well as its complex with DNA is optimized using constrain of tetrahedral coordination of the zinc ion to Cys sulphurs. The finger is stabilized by series of H--bonds (5 in backbone, 2 in side chains and 2 between backbone and side chains). The complex is stabilized by H-bonds between side chains of Tyr 11, His 12, Tyr 13 and Arg 14 with G2, G3 and G8. DNA is in B form. H--bonding network within DNA is preserved. Opposite strand P-P and Cl'-Cl' distances are changed slightly. There is a systematic change in the backbone torsional angles and sugar pucker. Also, there is an evidence of protein-induced conformational change in DNA.