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Biophys J, August 2001, p. 1195-1204, Vol. 81, No. 2

Substrate Binding to DNA Photolyase Studied by Electron Paramagnetic Resonance Spectroscopy

Stefan Weber,* Gerald Richter,dagger Erik Schleicher,dagger Adelbert Bacher,dagger Klaus Möbius,* and Christopher W. M. Kay*

 *Institute of Experimental Physics, Free University Berlin, 14195 Berlin, Germany and  dagger Institute of Organic Chemistry and Biochemistry, Technical University Munich, 85747 Garching, Germany

Structural changes in Escherichia coli DNA photolyase induced by binding of a (cis,syn)-cyclobutane pyrimidine dimer (CPD) are studied by continuous-wave electron paramagnetic resonance and electron-nuclear double resonance spectroscopies, using the flavin adenine dinucleotide (FAD) cofactor in its neutral radical form as a naturally occurring electron spin probe. The electron paramagnetic resonance/electron-nuclear double resonance spectral changes are consistent with a large distance (>= 0.6 nm) between the CPD lesion and the 7,8-dimethyl isoalloxazine ring of FAD, as was predicted by recent model calculations on photolyase enzyme-substrate complexes. Small shifts of the isotropic proton hyperfine coupling constants within the FAD's isoalloxazine moiety can be understood in terms of the cofactor binding site becoming more nonpolar because of the displacement of water molecules upon CPD docking to the enzyme. Molecular orbital calculations of hyperfine couplings using density functional theory, in conjunction with an isodensity polarized continuum model, are presented to rationalize these shifts in terms of the changed polarity of the medium surrounding the FAD cofactor.

Biophys J, August 2001, p. 1195-1204, Vol. 81, No. 2
© 2001 by the Biophysical Society   0006-3495/01/08/1195/10  $2.00


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