ALBERT

Notes: To better understand the structural basis of protein-DNA interactions, the conformational changes that accompany these interactions need to be described. In order to develop a methodological approach to this problem, Fourier transform infrared spectroscopy (FTIR) with derivative resolution enhancement has been used to identify conformational changes that occur when a 29-residue synthetic peptide binds nonspecifically to heterogenous cellular DNA in aqueous solution. The peptide sequence was chosen de novo, in order to rationally design a peptide model that would allow the relationship between DNA binding and the stability of protein secondary structure to be studied. Peptide at a concentration of 100-200 μM produces 50% saturation of heterogenous phage DNA sequences as well as of short synthetic oligonucleotides. FTIR spectra reveal significant changes in peptide and DNA upon binding. Second-derivative spectra resolve the amide I band of native peptide into components located at 1627 (β-strand), 1658 (α-helix), and 1681 (turn or β-strand) cm-1, with a distinct shoulder at 1647 cm-1 (disordered structure). Assignment of the 1681 cm-1 vibration to a turn conformation is supported by uv CD studies, which indicate significant amounts of turn structure in unbound peptide. Ultraviolet CD also confirms the existence of disordered and β-strand regions in the free peptide. Upon interacting with DNA the band at 1681 cm-1 (turn) is no longer seen; a new band appears at 1675 cm-1; the 1627 cm-1 band (β-strand) is considerably reduced in intensity; the position of the α-helical (1658 cm-1) component remains unchanged; the shoulder at 1647 cm-1 (disorder) disappears. The new vibration at 1675 cm-1 is characteristic of β-strand structures. The asymmetric stretch (vAS) of the DNA phosphates shifts from 1223 (unbound) to 1229 cm-1 (bound); the relative intensities of νAS and the PO2- symmetric stretch (vs) are altered upon peptide binding. The data is consistent with the following conclusions: (a)DNA binding changes the secondary structure of the peptide, (b) disordered region(s) are only observed in free peptide, i.e., DNA binding stabilizes and increases order in the peptide secondary structure, (c) turn(s) change into β-strand and/or α-helical conformations(s) when peptide binds to DNA, (d) a β-strand conformation that is characterized bya 1627 cm-1 vibration is present in free and bound peptide, (e) there is a particular β-strand vibration/conformation that is only present in the bound peptide, (f) an α-helical region exists in both free and bound peptide, (g) DNA remains in a B-family conformation upon peptide binding, and (h) DNA phosphates participate in peptide binding and/or subtle changes occur in the DNA conformation upon complex formation.