Conformational study of the tandem repeat sequence in RNA polymerase II bycircular dichroism spectroscopy

The largest subunit of RNA polymerase II has an interesting C-terminal doma in, which consists of a multiple tandem repeat of a heptapeptide with the c onsensus sequence Ser-Pro-Thr-Ser-Pro-Ser-Tyr. However, the functional role of this sequence is unclear. One might assume that the conformation of the tandem repeat is very important for its function. The conformation of poly (Ser-Pro-Thr-Ser-Pro-Ser-Tyr) and H-Ser-Pro-Thr-Ser-Pro-Ser-Tyr-OH, corresp onding to the repeat and the repeating unit of the C-terminal domain, respe ctively, were investigated exhaustively by circular dichroism (CD). The CD spectrum of H-Ser-Pro-Thr-Ser-Pro-Ser-Tyr-OH indicated the presence of a tu rn structure in water, which was further stabilized in 2,2,2-trifluoroethan ol (TFE) and in acetonitrile. The CD spectra of the polyheptapeptide poly(S er-Pro-Thr-Ser-Pro-Ser-Tyr) suggested that the disordered conformation was predominant in water and that the rum structure was stabilized by increasin g the content of TFE or acetonitrile in the solvent. We suggest that the po lyheptapeptide forms not only a turn structure at the heptapeptide unit Ser -Pro-Thr-Ser-Pro-Ser-Tyr, but also a kind of super conformation induced by the periodicity of the sequence in TFE or acetonitrile.