Interactions between Nucleic Acids and Proteins

The dynamic interaction between nucleic acids and proteins is another central theme of Part III. With the important exception of a few catalytic RNA molecules (discussed in Chapters 26 and 27), the processes that make up the pathways of cellular information flow are catalyzed and regulated by proteins. An understanding of these enzymes and other proteins can have practical as well as intellectual rewards, because they form the basis of recombinant DNA technology (introduced in Chapter 9). 

Interactions between nucleic acids and proteins are also hard to elucidate because of the difficulty involved in determining the individual contribution of each substance protein bands are usually masked by the strong absorbance bands of nucleic acids. 

The field of nucleic acid-protein interactions has become increasingly active in the last few years, and it is thus difficult to be up-to-date here. This discussion will focus on the structural factors that determine the interactions between nucleic acids and proteins. [An excellent account of DNA-protein interactions has been written by von Hippel and McGhee (1).]... 

In all these events, the hydrogen-bonded Watson-Crick base pair is operative and is responsible for DNA reduplication, transcription, and translation. Since mispairing can occur, all these processes are checked for fidelity by several enzymes which can correct for errors [6521. At this and all other levels of DNA reduplication and protein biosynthesis, intermolecular hydrogen bonds between nucleic acids and between nucleic acids and proteins are responsible for recognition, interaction, and, finally, for information transfer. 

Matsui et al. [235,236] have recently used zeolites with a higher Si/Al ratio (i.e., Na-BEA) for the purification of nucleic acids and proteins due to the electrostatic and hydrophobic interactions between biopolymers and zeolites. In addition, the activity and structure of the proteins are preserved even under denaturing conditions, thus emerging as promising materials for biochemical and biotechnological applications. 

These interactions are frequently ionic in character. The coulombic forces of interaction between macroions and lower molecular weight ionic species are central to the life processes of the cell. For example, intermolecular interactions of nucleic acids with proteins and small ions, of proteins with anionic lipids and surfactants and with the ionic substrates of enzyme catalyzed reactions, and of ionic polysaccharides with a variety of inorganic cations are all improtant natural processes. Intramolecular coulombic interactions are also important for determining the shape and stability of biopolymer structures, the biological function of which frequently depends intimately on the conformational features of the molecule. 

The AMBER, CHARMM, and GROMOS force fields have been developed consistently for nucleic acids and proteins, and modeling the interactions between those two types of macromolecules is possible. Other force fields, such as flex and Veal-Wilson, are more specifically designed... 

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