Secondary structure prediction of adenylate kinase by circular dichroism spectroscopy of synthetic peptides

Abstract

The synthesis of 13 segments of porcine adenylate kinase (AK 1) consisting each of 15 residues and covering the whole sequence of AK 1 is reported. The peptides were obtained by multiple peptide synthesis applying Fmoc/tert. butyl strategy. For the conformational analysis by circular dichroism spectroscopy different mixtures of phosphate buffer (pH 7), trifluoroethanol and methanol were used. Ten peptides showed alpha-helical conformation in all solvents except of pure buffer. The conformation of these peptides correlated well with the secondary structure obtained by homology modelling and even more striking with the X-ray structure of adenylate kinase, which was published recently. In contrast, three peptides, which were suggested to adopt no helical conformation did not show any content of alpha-helicity in any of the solvents that we investigated. One peptide, which contains a beta-sheet according to the X-ray analysis revealed a high content of beta-conformation by CD in buffer and in mixtures with trifluoroethanol. The two other peptides revealed mainly random coil in all solvents which we investigated. Therefore, we conclude that synthetic peptides are suitable tools to investigate the secondary structure of protein segments and that this conformation is frequently preserved in the intact protein.