Structure and dynamics of a tryptophanepeptide-polynucleotide complex

The binding of LysTrpLys to single stranded poly(A) was studied by measurements of fluorescence, UV-absorbance, electrodichroism and field jump relaxation. The van't Hoff enthalpy determined at constant degree of peptide protonation is -3.5 kcal/mol (delta S = 9 e.u.). The electrodichroism of bound tryptophane residues is negative; its absolute value decreases with increasing degree of binding theta. The magnitude of the dichroism at low theta indicates a preferential orientation of the tryptophane residues in the plane of the adenine bases, suggesting stacking of Trp with adenine bases. The overall degree of orientation decreases, however, to virtually zero at high theta. Relaxation measurements by low theta demonstrate the existence of two steps in the binding reaction of LysTrpLys to poly(A): a fast bimolecular step controlled by diffusion is followed by a slow intramolecular conversion with a forward rate of 1.5 x 10(5) s-1 and a backward rate of 2.7 x 10(3) s-1. The forward rate is close to that expected for an insertion reaction into stacked poly(A), yet the corresponding stability constant (approximately 55) is unexpectedly high.