title: Binding of cationic (+4) alanine- and glycine-containing oligopeptides to double-stranded DNA: thermodynamic analysis of effects of coulombic interactions and alpha-helix induction.
abstract: Coulombic interactions and coupled conformational changes make important contributions to stability and specificity of many protein-nucleic acid complexes. As models of these phenomena in simpler systems, we have investigated the binding to mononucleosomal (160 base-pair) calf thymus DNA of a high charge density (compact) 5-residue (+4) oligopeptide (with 4 lysines and 1 tryptophan) and of four lower charge density (extended) 17-residue (+4) oligopeptides (each with 4 lysines, 10-12 alanines, 0-2 glycines, and 1 tryptophan). The fractional helicity (f(h)) of each oligopeptide before and after DNA binding was determined using circular dichroism. At low univalent cation concentration ([M+] = 6.4 mM), binding to DNA increases f(h) significantly for all but one of the extended oligopeptides. Oligopeptide-DNA binding constants (K(obs)) and apparent binding site sizes (n) were quantified using the noncooperative McGhee-von Hippel isotherm to fit tryptophan fluorescence quenching data. For each of the oligopeptides studied, n is found to be approximately equal to four, the number of lysine charges. In the range 6.4 mM < or = [M+] < or = 21.5 mM, power dependences of K(obs) on [M+] (SK(obs) = d log K(obs)/d log[M+]) for all 17-residue (+4) oligopeptides are similar with an average value of -3.7 +/- 0.4, which is indistinguishable (outside uncertainty) from the value obtained here for the compact (+4) oligopeptide and from values reported elsewhere for another compact tetralysine and for spermine (+4). Our results are consistent with the conclusion that the nonspecific binding to DNA of all these tetravalent ligands is driven primarily by coulombic interactions. At any [M+] investigated, values of K(obs) for the four extended (+4) oligopeptides differ by less than an order of magnitude, but all are 1-2 orders of magnitude less than values of K(obs) for two compact (+4) oligopeptides and for spermine. The differences in K(obs) for oligopeptide-DNA complexes, which all have similar n and similar SK(obs) indicate that when an extended oligopeptide binds to DNA it becomes more compact as a result of conformational changes, such as the additional alpha-helix formation detected by circular dichroism.
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, 53706, USA.
authors.forename: S
authors.initials: S
authors.lastname: Padmanabhan
authors.forename: W
authors.initials: W
authors.lastname: Zhang
authors.forename: M W
authors.initials: MW
authors.lastname: Capp
authors.forename: C F
authors.initials: CF
authors.lastname: Anderson
authors.forename: M T
authors.initials: MT
authors.lastname: Record
mesh_terms: D000409:Alanine / Q000378:metabolism*; D000595:Amino Acid Sequence; D002942:Circular Dichroism; D004247:DNA / Q000378:metabolism*; D005998:Glycine / Q000378:metabolism*; D007700:Kinetics; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; D004247:DNA; D000409:Alanine; D005998:Glycine