title: A 500-MHz proton nuclear magnetic resonance study of the structure and structural alterations of gene-5 protein-oligo(deoxyadenylic acid) complexes.
abstract: The complex of the gene-5 protein of bacteriophage M13 with octadeoxyadenylic acid [d(A)8] has been shown earlier to differ in various respects from the complex with polynucleotides [Alma, N. C. M., Harmsen, B. J. M., van Boom, J. H., van der Marel, G., & Hilbers, C. W. (1982) Eur. J. Biochem. 122, 319-326]. 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 oligonucleotide protein interactions. In the experiments also oligonucleotides deuterated at the adenyl C8 positions have been 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. It is concluded that 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 electron microscopic studies is used to propose a model for a possible orientation of the adenyl bases in the complex.
mesh_terms: D003090:Coliphages / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000378:metabolism*; D009841:Oligonucleotides / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D012097:Repressor Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D014764:Viral Proteins / Q000378:metabolism*
chemical_list: D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D012097:Repressor Proteins; D014157:Transcription Factors; D014764:Viral Proteins; C030570:oligodeoxyadenylic acid