A 500MHz proton nuclear magnetic resonance study of the structure and structural alterations of gene-5 protein-oligodeoxyadenylic acid complexes

Abstract

The complex of the gene-5 protein of phage M13 with octadeoxyadenylic acid [d(A)8] was shown earlier to differ in various respects from the complex with polynucleotides. In this paper the gene-5 protein-d(A)8 complex is compared with the complex formation between the gene-5 protein and a mixture of longer oligonucleotides, i.e., d(A)25-30. Nuclear Overhauser experiments have been performed on both systems to obtain structural information regarding the oligonuleotide protein interactions. In the experiments also oligonucleotides deuterated at the adenyl C8 positions were used in order to distinguish between the adenyl H2 and H8 resonances. Combination of the experiments shows that the nucleotides in the complexes are situated in such a way that the adenyl H8 and the sugar H1'' protons are near the protein surface while the adenyl H2 protons are relatively far removed from all other protons, indicating that this side of the base is pointing away from the protein surface. Structurally different complexes can be obtained for the d(A)25-30 system. The complex with d(A)25-30 undergoes a structural transition when going from excess oligonucleotide to excess gene-5 protein. This transition is identified with the transition between the oligonucleotide and the polynucleotide binding mode. The information derived from the present NMR experiments combined with known data from X-ray diffraction and EM studies is used to propose a model for a possible orientation of the adenyl bases in the complex.