HMG-D complexed to a bulge DNA: An NMR model

An NMR model is presented for the structure of HMG-D, one of the Drosophila counterparts of mammalian HMG 1/2 proteins, bound to a particular distorte d DNA structure, a dA(2) DNA bulge. The complex is in fast to intermediate exchange on the NMR chemical shift time scale and suffers substantial lineb roadening for the majority of interfacial resonances. This essentially prec ludes determination of a high-resolution structure for the interface based on NMR data alone. However, by introducing a small number of additional con straints based on chemical shift and linewidth footprinting combined with a nalogies to known structures, an ensemble of model structures was generated using a computational strategy equivalent to that for a conventional NMR s tructure determination, We find that the base pair adjacent to the dA(2) bu lge is not formed and that the protein recognizes this feature in forming t he complex; intermolecular NOE enhancements are observed from the sidechain of Thr 33 to all four nucleotides of the DNA sequence step adjacent to the bulge. Our results form the first experimental demonstration that when bin ding to deformed DNA, non-sequence-specific HMG proteins recognize the junc tion between duplex and nonduplex DNA, Similarities and differences of the present structural model relative to other HMG-DNA complex structures are d iscussed.