Molecular studies in protein/DNA recognition: Crystallographic trials of the retrovirus integrase protein and the crystal structure of the Escherichia coli response regulator NarL(C)/DNA complex

DNA structure and recognition is critical in all life stages. However, molecular rules describing sequence-dependent DNA structure or recognition by proteins have been elusive. The efforts of this dissertation have been toward understanding the molecular recognition of DNA through x-ray crystallographic studies. Although DNA is considered the stable transcript of life, the DNA of somatic cells has been shown to transmigrate, and the storage medium of DNA is an ancient, living, dynamic substance.; Two systems have been chosen to elucidate the recognition of DNA by proteins: the retroviral integrase protein and a bacterial signal transduction pathway transcription factor. (a) The feline immunodeficiency virus integrase protein binds DNA weakly, but yet readily performs the integration reaction essential to retroviral propagation. No diffraction quality crystals were obtained. (b) The NarL transcription factor does not bind DNA until activated by phosphorylation. The NarL C-terminal DNA-binding domain alone mimics the activated protein by site-specifically binding its DNA target. Crystals were grown of the DNA target site bound to the C-terminal domain. The crystal structure showed unusual patterns of recognition and allowed DNA recognition by related proteins to be predicted. Clearly, DNA recognition is the tender balance of steric, charged and dispersive forces between a set of pre-existent DNA conformations as they assume the deformations imposed by the protein surface.