Genetics - A. V. Syvolob 2008

The Nature of Genetic Material
DNA Structure
Protein-Nucleic Acid Interactions

In living systems, DNA constantly interacts with A wide variety of Proteins. The surface of DNA features phosphate residues and exocyclic groups of nitrogenous bases located within its grooves. It is precisely these groups that engage in contact with amino acid side chains and peptide groups on the protein surface. All proteins that interact with DNA can be divided into two categories: those that bind to DNA of any sequence, and those that specifically recognize a particular base-pair sequence. Proteins that perform such recognition typically also interact nonspecifically with any other DNA sequence.

Several Examples of The Structure of protein-nucleic acid complexes are shown in Fig. 1.7. The H3-H4 histone dimer (Fig. 1.7, a) engages in nonspecific electrostatic (ionic) interactions with DNA phosphates, playing a key role in DNA packaging within the Cell Nucleus, as will be discussed below. Other proteins depicted in Fig. 1.7 act as regulators of Gene activity by specifically recognizing certain sequence regions.

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Fig. 1.7. Examples of protein-nucleic acid complexes: H3-H4 histone dimer (a); leucine zipper (b); catabolite activator protein (c); zinc finger protein (d). Images were generated using PyMOL (http://www.pymol.org/) utilizing structures from the Protein Data Bank with accession codes 1AOI, 1NWQ, 1CGP, 1ZAA.

The primary condition for establishing contacts between DNA and a protein is the mutual adaptation of the interacting structures through corresponding conformational adjustments: via specific structural rearrangements (sometimes minor, sometimes quite substantial) of The Double Helix, the chemical groups of the DNA are "brought into position" to contact the chemical groups of the protein. In other words, efficient recognition requires a specific conformation of the double helix and/or certain alterations in this conformation. Both are ultimately determined by the base-pair sequence.



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