Thermodynamics of Single-Stranded RNA Binding to Oligolysines Containing Tryptophan

The equilibrium binding to the synthetic RNA poly(U) of a series of oligolysines containing one, two, or three tryptophans has been examined as a function of pH, monovalent salt concentration (MX), temperature, and Mg²⁺. Oligopeptides containing lysine (K) and tryptophan (W) of the type KWK_P-NH₂and KWK_p-C0₂(p = 1-8), as well as peptides containing additional tryptophans or glycines, were studied by monitoring the quenching of the peptide tryptophan fluorescence upon binding poly(U). Equilibrium association constants, K_obsand the thermodynamic quantities ΔG°_obs, Δ°_obs, and ΔG°_obsdescribing peptide-poly(U) binding were measured as well as their dependences on monovalent salt concentration, temperature, and pH. In all cases, K_obsdecreases significantly with increasing monovalent salt concentration, with (∂ log K_obs/∂ log [K⁺]) =-0.74 (±0.04)z, independent of temperature and salt concentration, where z is the net positive charge on the peptide. The origin of these salt effects is entropic, consistent with the release of counterions from the poly(U) upon formation of the complex. Upon extrapolation to 1 M K⁺, the value of ΔG°_obsis observed to be near zero for all oligolysines binding to poly(U), supporting the conclusion that these complexes are stabilized at lower salt concentrations due to the increase in entropy accompanying the release of monovalent counterions from the poly(U). Only the net peptide charge appears to influence the thermodynamics of these interactions, since no effects of peptide charge distribution were observed. The binding of poly(U) to the monotryptophan peptides displays interesting behavior as a function of the peptide charge. The extent of tryptophan fluorescence quenching, Q_max, is dependent upon the peptide charge for z ≤ +4, and the value of Q_maxcorrelates with z-dependent changes in ΔS°_obsand ΔS°_obs(l M K⁺), whereas for z ≥ +4, Q_max, Δ°_obs, and ΔS°_obs(l M K⁺) are constant. The correlation between Q_maxand ΔH°_obsand ΔS^obs(l M K⁺) suggests a context (peptide charge)-dependence of the interaction of the peptide tryptophan with poly (U). However the interaction of the peptide tryptophan does not contribute substantially to AG°obs for any of the peptides, independent of z, due to enthalpy-entropy compensations. Each of the tryptophans in multiple Trp-containing peptides appear to bind to poly(U) independently, with ΔH°_Trp=-2.9 ± 0.7, although ΔG°_TRPis near zero due to enthalpy-entropy compensations. These studies provide important comparative information for the interpretation of the thermodynamics of protein-ss nucleic acid interactions.