500 MHz ¹H NMR study of the role of lysines and arginines in the binding of gene‐5 protein to oligoadenylic acids

Reductive Methylation of the Lysyl Residues in the fd Gene 5 DNA-Binding Protein: CD and13C NMR Results on the Modified Protein

“…Our identification of at least two (but no more than four) lysyl residues that may be involved in the gene 5 protein-DNA binding process is not in disagreement with previous work by Alma et al (21). In a 500 MHz 1 H NMR study of unmodified gene 5 protein, these authors resolved two proton triplets from lysyl t·CH 2 groups, the smaller triplet arising from one or two of the six lysyl residues.…”

“…This is the first time that four of the lysyl residues have been identified as being in unique environments. Previous 1 H NMR studies have led to the conclusion that a majority, and possibly five, of the six lysyl residues are equivalent and unaffected by DNA binding (13,21). While we cannot yet explicitly describe the environments of the four unique lysyl residues, the observed chemical shifts in our 13 C NMR spectrum of the methylated gene 5 protein are in the range previously observed for similarly modified lysozyme, concanavalin A, and ribonuclease A (30)(31)(32).…”

“…Coleman et al (13) reported from 270-MHz !H NMR data that the E-CH 2 lysyl protons did not undergo significant changes upon formation of complexes between gene 5 protein and d(pT) 8 or d(pA) 8 , although the o-CH 2 arginyl protons were affected. More recently, in a 500-MHz 1 H NMR study, Alma et al (21) investigated the resonances of E-CH 2 lysyl and o-CH 2 arginyl protons of gene 5 protein and changes that occur upon binding to d(A) 8 and d(Ahs-30 • These workers detected a triplet of E-CH 2 resonances from one or two lysyl residues that shifts downfield and broadens upon complex formation, in addition to a triplet of b-CH 2 resonances from two or three arginyl groups that is similarly affected upon complex formation. However, the majority of the lysyl residues (four or five) could not be distinguished from one another and appeared to retain considerable rotational freedom in the complexes.…”

Three-dimensional structure of the single-stranded DNA-binding protein encoded by gene V of the filamentous bacteriophage M13 and a model of its complex with single-stranded DNA

“…The binding of GVP to ssDNA has been studied with a wide variety of spectroscopic techniques [10][11][12][13][14][15][16]. From these analyses it has become apparent that ssDNA binding is primarily dictated by electrostatic interactions between the side chains of the basic amino acids in the DNA-binding domain (vide infra) and the phosphate groups of the polynucleotide backbone [10,13,17]. A few hydrophobic stacking interactions between the aromatic residues tyrosine and phenylalanine and bases of the polynucleotide chain have been noted as well [15][16][17][18][19][20][21].…”

“…From these analyses it has become apparent that ssDNA binding is primarily dictated by electrostatic interactions between the side chains of the basic amino acids in the DNA-binding domain (vide infra) and the phosphate groups of the polynucleotide backbone [10,13,17]. A few hydrophobic stacking interactions between the aromatic residues tyrosine and phenylalanine and bases of the polynucleotide chain have been noted as well [15][16][17][18][19][20][21]. It is attractive to speculate that these stacking interactions are responsible for the sequence preferences mentioned.…”