Weak and Strong Bonds Determine A la crom alectilai Structure

FIGURE 5-22 Structure of the TBP-TATA bo* complex. "Jhe backbone of T8P ts shown in purple at the top of the figure; the DMA helix belnw is shown in gray and rOsf=. (INikolov D.B, Chen H„ Halay ED., Usheva AA, Misstate K, Lee O.K., Roeder R.G.. and Burley SK. (995. Noture 377 i !9.) Image prepared with MolScnpt, BobSaipt, and Raster 30. Extended DMA on either 5ide of image modeled by leemor ioshuaTor.

can be considered the beginning of a potential (and almost always nonspecific) binding site. Thus in E. coli, which has -5 X 10" bp in its circular genome, there would be -5 X 1011 nonspecific binding sites. So, although the ratio of specific to nonspecific DNA binding affinity is high (lOMold), the ratio of nonspeofic-to-specific sites is even higher (5 x iO(I-foid). This comparison explains why the eel) would have to contain multiple copies of the repressor protein to ensure continued occupancy of the specific regulatory DNA-binding site. Under these conditions, most of the repressor protein molecules will be bound to nonspecific sites.

Nonspecific protein-DNA interactions are not just an unavoidable consequence of proteins using the charge of the DNA backbone in DNA recognition. These interactions are believed to speed up the rate at which a given regulatory protein finds its appropriate target. Nonspecifically-bound proteins are constrained, by their charge interaction, to diffuse linearly along DNA, rather than simply hopping on and off the DNA. This diffusion allows a DNA-binding protein to sample sites at random in their "search" for a specific binding site. By being restricted to linear movements, proteins will reach their targets faster than if ihey were free to diffuse throughout the cell.

A small subset of DNA-binding proteins do not merely diffuse on DNA, but instead, actively track along the DNA. These proteins use directional movement on DNA to perform key functions during DNA replication, repair, and recombination (see Chapters 8, 9, and 10). Because this movement is directional, it requires energy. Thus, these proteins hydrolyze ATP to direct changes in their binding to DNA.

Diverse Strategies for Protein Recognition of RNA

As introduced above, RNA is structurally more diverse than DNA. RNA-binding proteins have various roles in RNA function, from stabilizing the RNA to enzymatically processing the RNA. The structures of several RNA-binding proteins bound to their target molecules reveal various strategies for protein-RNA recognition-

Allostery: Regulation of a Protein '$ Function by Changing Its Shape 87

Some RNA-binding proteins interact specifically with double-slranded RNA. In these cases, the proteins recognize features that distinguish the RNA from the DNA double helix. For example, the presence of the 2'-hydroxy 1 group is clearly a distinguishing feature of RNA, as is the fact that RNA forms predominantly an A-form helix (see Chapter 6), which has both deeper and narrower grooves than the B-fnrm fielix. In contrast to the DNA-binding proteins discussed above, these proteins do not engage the nucleic acid by inserting a helical regions into the RNA grooves.

Many important RNA-binding proteins bind to RNA molecules that are not in a regular helical conformation. Included are proteins that interact with messenger RNA molecules during transcription and RNA processing. Likewise, machineries that splice and translate RNA contain subunits consisting of RNA comptexed with protein. The ribonuclear protein (RNP) motif is one of the most common protein sequence motifs that is dedicated to making specific RNA contacts. This 80 residue domain has a mixed a-p. fold (Figure 5-23). It binds to stem-loop structures in RNA, as illustrated by the complex of the spliceosomal protein UlA (see Chapter 13) with U1 snRNA (see Figure 5-23). Clearly the shape of the RNA binding surface is specific for this structural motif in RNA.


The binding of either small or large molecules (ligands) to a protein can cause a substantial change in the conformation of that protein. Such ligand-induced conformational changes can have a variety of

FIGURE 5-2 J Structure of spliceosomal protein-RNA complex: UlA binds hairpin II of U1 snRNA. The protein is shown in gray; the U t snRNA is shown in gteen. (Oubndge C, Ito N., Evans PR, teo CH-, and Nagai K. I9y4. Nature 572 432.) Image prepared with MolScnpt, BobScript, and Raster 3D.

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