Structural studies of a synthetic peptide derived from the carboxyl‐terminal domain of RNA polymerase II

The conformation of the repeating heptapeptide unit of the carboxyl‐terminal domain of RNA Polymerase II, Y¹S²P³T⁴S⁵P⁶S⁷ has been examined using nuclear magnetic resonance spectroscopy and circular dichroism. Nuclear Overhauser effects and CD spectra for the synthetic 56‐residue peptide H₂N‐(S²P³T⁴S⁵P⁶S⁷Y^l)₈‐COOH in water indicate that the peptide is largely unordered. A small population of folded molecules is observed to contain β‐turns located at Ser²‐Pro³‐Thr⁴‐Ser⁵ (SPTS) and Ser⁵‐Pro⁶‐Ser⁷‐Tyr¹ (SPSY). CD and NMR results in 90% TFE also indicate an equilibrium population of structures, but the fraction of turns is higher. Similarities of nuclear Overhauser effects in water and in 90% TFE suggest that the structures in TFE are biologically relevant. Based on these observations, the average structure of a single conformer of the heptapeptide repeat in 90% TFE was obtained by a distance geometry‐simulated annealing method, using distance restraints extracted from nuclear Overhauser data. NMR spectra of the 56‐mer show signals corresponding to only one repeat indicating that each repeat is in an identical environment. Thus it is possible to obtain an average structure of the heptapeptide repeat from NOE data on the 56‐mer. Twenty‐seven final structures were calculated and the root mean square deviations between the 27 structure and the mean coordinates was 1.52 Å for the backbone and 2.2 Å for all nonhydrogen atoms. The heptapeptide repeat consists of two overlapping β‐turns which are potentially stabilized by hydrogen bonds. The hydroxyl side chains of Ser², Ser⁵, Thr⁴, and Ser⁷ all appear to be equally exposed for potential phosphorylation. The tyrosyl side chain of each repeat is folded inwards to the backbone and can potentially hydrogen bond to the carbonyl oxygen of the tyrosine in the preceding repeat. Iteration of the average structure of the heptapeptide repeat results in a model of the carboxyl‐terminal domain with a regular but unusual secondary structure consisting of a series of staggered β‐turns. © 1995 Wiley‐Liss, Inc.