Chapter 10 - Protein and Nucleic Acid Complexes

Abstract

The chapter discusses complexes between deoxyribonucleic acids (DNAs) and proteins. Complexes between DNAs and proteins take two general forms: sequence specific, as would be expected for translational regulators, and nonsequence specific, as might be predicted for DNA-packaging proteins; such as the histones. Most of the complexes that have been studied by either X-ray or Nuclear Magnetic Resonance (NMR) methods involve B-DNA. In this form of DNA, the major groove of the duplex is large enough to accommodate protein secondary structure the size of an α helix. To be a regulator of DNA transcription, the protein motif must recognize specific nucleotide sequences. Such sequences are called “the recognition element.” The chapter discusses the structural data describing DNA. The chapter also mentions the interaction between DNA and site-specific proteins detailing the DNA binding motifs, and helix-turn-helix. Phage 434 repressor with regard to the DNA complex is then discussed, and a leucine zipper. Some of these structural observations are easily explained while others are not. The chapter concludes by stating that water molecules are observed to bind to specific sites on both DNA and protein. In fact, in some instances, they may form the link between nucleic acid and protein. Water, therefore, may play a significant role in complex formation, and therefore in the regulation process itself.