Is There a Dynamic DNA-Protein Interface in the Transcription Factor IIIA-5 S rRNA Gene Complex?

Others (Foster, M. P., Wuttke, D. S., Radhakrishnan, I., Case, D. A., Gottesfeld, J. M., and Wright, P. E. (1997) Nat. Struct. Biol. 4, 605–608; Wuttke, D. S., Foster, M. P., Case, D. A., Gottesfeld, J. M., and Wright, P. E. (1997) J. Mol. Biol. 273, 183–206) have proposed that several amino acid side chains exhibit considerable conformational mobility at the DNA-protein interface in the transcription factor IIIA·5 S rRNA gene complex and that the rapid movements of these side chains permit them to make fluctuating contacts with adjacent bp in the DNA target site. This “dynamic interface” model makes biochemical predictions concerning the consequences of truncating specific amino acid side chains and the effects of these truncations on sequence selectivity in DNA binding. The model also makes predictions concerning the effects of DNA sequence context on the apparent energetic contributions to binding made by individual bp. We have tested these predictions, and our results are inconsistent with any significant energetic role being played by the contact of multiple bp by conformationally mobile amino acid side chains. They do, however, show that some individual amino acids affect the recognition of multiple bp through mechanisms other than direct interaction.