LESSONS FROM THE HIGH-RESOLUTION CRYSTALLOGRAPHY OF PROTEIN-DNA COMPLEXES. Stephen C. Harrison, HHMI and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA

Proteins recognize specific DNA sequences and DNA conformations. Crystal structures of protein/DNA complexes, particularly those of transcription factors bound to specific regulatory sites, have yielded high-resolution images of protein/DNA interfaces. End-on stacking of DNA fragments often dominates molecular packing in crystals of protein/DNA complexes, so that variation of the lengths and terminal sequences of synthetic DNA fragments facilitates crystallization. Use of halogenated bases rationalizes the search for isomorphous derivatives. Local recognition of short DNA sequences often involves small, distinct, DNA-binding domains of larger proteins. There are a number of stereotypical recognition motifs, frequently with an [[alpha]]-helix that lies in the DNA major groove. Side chains (e.g., from this "recognition helix") have extensive non-covalent interactions with the edges of bases; van der Waals complementarity is as important as hydrogen bonding. There is no recognition "code", but there are noteworthy regularities. Positioning contacts to sugar-phosphate backbone are important for presenting a recognition motif to DNA bases. Extended specificity, for recognition of longer sequences, can involve homo- or hetero-dimerization, concatenation of domains in a longer polypeptide, and heterologous interactions with other proteins. All these points will be illustrated with specific structures.