Dna Binding Proteins
DNA binding proteins are central to the regulation and execution of essential cellular processes such as replication, transcription, translation and repair. Once proteins combine with DNA there can be a number of consequences. Sometimes they merely block other processes such as transcription, a classic example being the lac repressor of the bacterium Escherichia coli. In other cases they act as enzymes such as RNA polymerase, which makes RNA using DNA as a template. DNA binding proteins can also recruit other proteins to build up functional complexes, for example the transcription factor (TFII) which builds up the transcription initiation complex.
There are essentially two kinds of protein-DNA interactions: non-specific, meaning that the protein binds anywhere along the DNA and sequence specific. Histones, proteins that are important for the packaging of DNA and maintaining chromosome structure in higher, eukaryotic, organisms, are examples of proteins that bind non-specifically. Proteins that recognize specific DNA sequences include those that repress or induce the transcription of particular genes. The interactions of these proteins with DNA occur by the precise association of amino acid side chains with the bases and/or the sugar phosphate backbone of the DNA. Specificity is achieved when the side chains recognize contact points at which associations can be made with the bases through electrostatic charges and hydrophobic interactions. The major groove, because of its larger size is an important protein binding site, although the family of eukaryotic high mobility group (HMG) proteins, which include a number of transcription factors, are known to bind in the minor groove.
The specific base sequences at which protein molecules bind to the DNA are frequently palindromic which means they read the same forwards and backwards (the word "refer" is a palindromic sequence of letters). Because of this, proteins interacting with DNA are often dimers, meaning that the protein units are composed of two identical polypeptide chains. Each polypeptide combines with identical sequences on one of the two DNA strands. DNA binding proteins usually contain domains interacting with their specific DNA base sequences, which can have very characteristic structures. One example is the helix-turn-helix domain found in repressor proteins. Repressors control gene expression by binding to DNA sequences at or near the gene so as to prevent its transcription. The helix-turn-helix domain contains segments of about 20 amino acid residues arranged as two protein spirals, or a-helical regions, separated by a short flexible amino acid run such that the helices cross at an angle of 120 °. The second helix usually inserts into the major groove in the DNA helix. Proteins with a helix-turn-helix motif are found in most organisms and examples include the repressor from the bacterial virus (bacteriophage) Lambda, and the lac and trp repressors from the bacterium Escherichia coli.
Whereas prokaryotic organisms commonly have repressors with the helix-turn-helix structure, eukaryotic organisms employ a wider range of structural motifs to bind DNA. For example, the zinc-finger motif, found in the transcription factor IIIA (TCFIIIA) has a characteristic DNA binding domain consisting of 30 amino acids repeated nine times along the length of the protein. The repeating domains form loops and each loop contains a zinc atom bound tetrahedrally between pairs of the amino acids cysteine and histidine. Another common motif found in DNA binding proteins, though it is not in itself the DNA binding motif, is known as the leucine zipper and was first identified in the C/enhancer binding protein (C/EBP) from liver cell extracts. This unique domain is known to mediate the dimerization of DNA binding proteins. This dimerization domain lies towards one end of the protein known as the C-terminus. In this region leucine recurs every seventh amino acid over a stretch of 35 amino acids. The region is twisted to form a helix and the leucines align on one face of the helix. As the leucine molecule has a hydrophobic (water repelling) side chain, this alignment creates a hydrophobic surface. The opposite surface contains charged amino acids making it more hydrophilic (water loving). The leucine rich surfaces of two monomers are more strongly attracted to each other than to their aqueous surroundings and bind together, with the leucine side chains slotting together like the teeth of a zipper and holding the dimer together. The actual DNA binding region is found adjacent to the leucine zipper in each of the two constituent monomers. This region is rich in positively charged amino acids, which bind to the negatively charged backbone of the DNA.
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