Properties of Basic Amino‐Acid Residues

Abstract

The interaction of four basic polyamino acids, poly(L-lysine), poly(L-ornithine), poly(L-arginine) and poly(L-homoarginine) with nucleotides was investigated using equilibrium dialysis and circular dichroism. Polyhomoarginine was prepared by guanidization of polylysine. The interaction of 5'-GMP exhibited equal values for the binding cooperativity in all cases, indicating that nucleotidenucleotide interaction, i.e. the stacking tendency of the guanine base, was the origin of this affinity. The affinity parameters of 5'-GMP and other nucleotides directed towards the basic polypeptides, however, decrease in the series: polyarginine > polyhomoarginine > polyornithine > polylysine.This indicates that the ion bond between guanidinium and phosphate is stronger than that between ammonium and phosphate, and that decreasing the length of the poly(amino acid) side chains by one CH2 group results in an increase of affinity. The binding of 3'-GMP and 5'-GMP by polylysine and polyornithine induces a strong negative circular dichroism band in the absorption region of the base and in the case of polylysine also changes at shorter wavelength. Temperature-dependent measurements of these circular dichroic spectra revealed that polylysine fits best to and forms the most stable complexes with helical arrangements of bound GMP molecules.Protein-nucleic acid interactions include long-range electrostatic contributions which originate in the nucleic acid phosphates and the basic amino-acid residues of proteins, such as lysine and arginine. The ionic bond is thought not to exert much specificity. However, the chemical features of the side chains of the two basic amino acids are different enough such that one would except some specific influence on proteinnucleic acid recognition processes. Investigations in this field are chiefly those dealing with polymer-polymer interaction, for example studies of precipitation and melting of DNA * basic poly(amino acid) complexes and observations of spectral features mainly by circular dichroism (for review see [l]).There are also investigations on monomer-polymer interaction involving the binding of nucleotides by basic poly(amino acids), like polylysine and polyarginine [2-91. These offer some advantages over the polymer -polymer interaction mentioned above although they are dealing with some different aspects of the interaction. The former allows the direct determination of affinity data. In the present work comparative Part of this work was presented at the first European Biophysics Congress, Baden near Vienna, 1971. Abbreviation. CD, circular dichroic.experiments have been performed with poly(L-lysine), poly(L-ornithine), poly(L-arginine) and poly(L-homoarginine), using equilibrium dialysis and circular dichroism, in order to elucidate the influence of the nature of basic amino-acid side chains on the interaction with nucleotides. MATERIALS AND METHODSNucleotides were purchased from Boehringer Mannheim GmbH (Mannheim, Germany), poly(L-arginine) 0.5 HzS04, poly(L-lysine) HBr and poly(L-ornithine)...

Amino acids–nucleotides biomolecular recognition: from biological occurrence to affinity chromatography

“…Also, thermodynamic and kinetic analyses of biomolecular interactions reveal details of the energetic and dynamic features of molecular recognition processes, and complement structural analyses of the free and complexed conformations. One of the first studies involving determination of thermodynamic parameters of nucleotides and some amino acids was published in 1974 (Wagner and Arfmann, 1974). The equilibrium constants determined in this study by equilibrium dialysis and circular dichroism shows that Arg have the stronger affinities in the order:…”

RNA‐protein interactions in an unstructured context

“…have evaluated chromatographically the interaction propensities of amino acids and different pyridine derivatives in water . Finally, several groups have studied interactions between different nucleotides and polyamino acids, focusing typically on polylysine or polyarginine peptides . The scarcity of the experimental studies in this context can in part be attributed to the low solubility of bases and some side chains as well as the weak interaction strengths involved.…”

Further evidence for an allosteric model for ribonuclease

“…That nucleotides bind to amino acids has been clearly shown. For example, Wagner & Arfmann (1974) have demonstrated that large numbers of nucleotide molecules bind to poly(amino acids) such as polylysine and polyarginine. Since RNAase contains four arginine and ten lysine residues, all in positions well exposed to aqueous solvents (Richards & Wyckoff, 1971), weak binding sites may exist on RNAase for a large number of nucleotides, particularly since models based on the X-ray-diffraction data of Wyckoff et al (1967) for RNAase S show that 11 of these residues occur in a cluster centred around lysine-31.…”