Physical chemical studies of the structure and function of DNA binding (helix-destabilizing) proteins

Binding of proteins to DNA is fundamental to the mechanisms of replication, recombination and gene expression. The specific molecular features of DNA recognized by complementary features of the three-dimensional structure of the DNA binding proteins are under intensive investigation. Two large classes of DNA binding proteins have emerged. One class includes enzymes such as the RNA polymerases and restriction endonucleases and the nonenzymatic repressor proteins which recognize unique sequences present in only one or a few copies per genome. A second group is made up of non-sequence-specific DNA binding proteins which bind to DNA at high density and modulate subsequent enzymatic transformations of the DNA. Among the latter group are those proteins originally termed "unwinding proteins", which have in common a higher affinity for single-stranded than for double-stranded DNA and thus promote the melting of double-stranded DNA. They are better termed helix-destabilizing proteins to distinguish them from the enzymes which "unwind" the helix by making and breaking phosphodiester bonds. Because the helix-destabilizing proteins form complexes with all single-stranded DNA regardless of base sequence, the molecular details of complex formation have been much more accessible to direct physicochemical measurements. Structural conclusions derived with techniques which include chemical modification, ultraviolet spectroscopy, circular dichroism, NMR, and X-ray diffraction will be reviewed. The following proteins will be discussed in detail; the gene 32 protein of bacteriophage T4, the gene 5 protein from bacteriophage fd, and the helix-destabilizing protein from E. coli. The largest amount of specific structural information is available for the gene 5 protein and specific models for this protein and its complexes with DNA based on NMR and X-ray diffraction data are presented. A number of other helix-destabilizing proteins from both prokaryotes and eukaryotes have been described and a survey of these will be given. Some of the basic molecular features of DNA-protein interactions emerging from studies of the helix-destabilizing proteins are likely to be shared by the more highly specific binding proteins like the RNA polymerases and repressors. Properties of some of these more complex systems which suggest this will be discussed.