The Escherichia coil RNA polymerase oL-subunit binds through its carboxy-terminal domain (o~CTD) to a recognition element, the upstream (UP) element, in certain promoters. We used genetic and biochemical techniques to identify the residues in aCTD important for UP-element-dependent transcription and DNA binding. These residues occur in two regions of oLCTD, close to but distinct from, residues important for interactions with certain transcription activators. We used NMR spectroscopy to determine the secondary structure of ,vCTD. aCTD contains a nonstandard helix followed by four c~-helices. The two regions of ~CTD important for DNA binding correspond to the first a-helix and the loop between the third and fourth oL-helices. The o~CTD DNA-binding domain architecture is unlike any DNA-binding architecture identified to date, and we propose that aCTD has a novel mode of interaction with DNA. Our results suggest models for c~CTD-DNA and c~CTD-DNA-activator interactions during transcription initiation.

The Arg-Gly-Asp (RGD) sequence serves as the primary integrin recognition site in extracellular matrix proteins, and peptides containing this sequence can mimic the activities of the matrix proteins. Depending on the context of the RGD sequence, an RGD-containing peptide may bind to all of the RGD-directed integrins, to a few, or to only a single one. We have previously isolated from a phage-displayed peptide library a cyclic peptide that binds avidly to the alpha(v)beta3 and alpha(v)beta5 integrins but does not bind to other closely related integrins. This peptide, ACDCRGDCFCG, exists in two natural configurations depending on internal disulfide bonding. The peptide with the 1-4; 2-3 disulfide bond arrangement accounts for most of the alpha(v) integrin binding activity, whereas the 1-3; 2-4 peptide is about 10-fold less potent. Solution structure analysis by nuclear magnetic resonance reveals an entirely different presentation of the RGD motif in the two isomers of RGD-4C. These results provide new insight into the ligand recognition specificity of integrins.

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