Structure of Gene 5 Protein-Oligodeoxynucleotide Complexes as Determined by ¹H, ¹⁹F, and ³¹P Nuclear Magnetic Resonance

¹H nuclear magnetic resonance (NMR) spectra at 270 MHz of gene 5 protein from bacteriophage fd and its complexes with tetra- and octadeoxynucleotides show that ~12 of the 37 aromatic protons of the protein undergo upfield shifts upon nucleotide binding. In the complex with d(pT)₈, the upfield shifts of the aromatic protons average ~0.3 ppm, while in the d(pA)₈ complex the same resonances (assigned to tyrosyl protons) shift upfield ~0.8 ppm. These are interpreted as ring current shifts induced by stacking of the phenyl rings of three of the five tyrosyl residues with the bases of the nucleotides. ¹⁹F NMR of m-fluorotyrosyl gene 5 protein shows five separate resonances: two downfield from m-fluorotyrosine corresponding to “buried” tyrosyls and three near m-fluorotyrosine corresponding to “surface” tyrosyls. The latter (assigned to Tyr-26, -41, and -56, shown by chemical modification to be exposed to solvent) move upfield on nucleotide binding. The downfield ¹⁹F resonances are unaffected. Thus the aromatic protons shifted upfield on nucleotide binding appear to be those of Tyr-26, -41, and -56. In contrast to tetra-, octanucleotide ¹H nuclear magnetic resonance (NMR) spectra at 270 MHz of gene 5 protein from bacteriophage fd and its complexes with tetra- and octadeoxynucleotides show that ~12 of the 37 aromatic protons of the protein undergo upfield shifts upon nucleotide binding. In the complex with d(pT)₈, the upfield shifts of the aromatic protons average ~0.3 ppm, while in the d(pA)₈ complex the same resonances (assigned to tyrosyl protons) shift upfield ~0.8 ppm. These are interpreted as ring current shifts induced by stacking of the phenyl rings of three of the five tyrosyl residues with the bases of the nucleotides. ¹⁹F NMR of m-fluorotyrosyl gene 5 protein shows five separate resonances: two downfield from m-fluorotyrosine corresponding to “buried” tyrosyls and three near m-fluorotyrosine corresponding to “surface” tyrosyls. The latter (assigned to Tyr-26, -41, and -56, shown by chemical modification to be exposed to solvent) move upfield on nucleotide binding. The downfield ^l9F resonances are unaffected. Thus the aromatic protons shifted upfield on nucleotide binding appear to be those of Tyr-26, -41, and -56. In contrast to tetra-, octanucleotide binding to gene 5 protein induces large changes in the ¹H resonances of the -CH₃ groups of the Val, Leu, and lie side chains. These may reflect conformational changes induced by protein-protein interactions between two monomers bound to the octanucleotide. ¹H resonances of the _ϵ-CH₂ groups of the lysyl residues in the protein and the complexes with nucleotides are narrow with long T₂ values, suggesting considerable rotational motion. Thusϵ -NH₃⁺-phosphate interactions, if they occur, are on the surface of the complex and allow the _ϵ-CH₂ groups to retain considerable rotational freedom. ³¹P NMR of the bound nucleotides shows large decreases in T₁ for the 3′-5′ diesters, but little chemical shift suggesting no unusual distortion of the nucleotide backbone on binding to gene 5 protein. A three-dimensional model of a gene 5 protein-octanucleotide complex has been built based on predictions of the secondary structure from the amino acid sequence (87 AA) and tertiary folding dictated by known chemical and NMR features of the complex.