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Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich interaction domain (ARID) binds DNA: A nitrogen-15 relaxation study

Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1570, USA

(RECEIVED October 1, 2004; FINAL REVISION December 7, 2004; ACCEPTED January 7, 2005)

AT-rich interaction domains (ARIDs) are found in a large number of eukaryotic transcription factors that regulate cell proliferation, differentiation, and development. Previously we elucidated how ARIDs recognize DNA by determining the solution structure of the Drosophila melanogaster Dead ringer protein in both its DNA-free and -bound states. In order to quantitatively determine how ARIDs alter their mobility to recognize DNA, we have measured the relaxation parameters of the backbone nitrogen-15 nuclei of Dead ringer in its free and bound forms, and interpreted these data using the model-free approach. We show that Dead ringer undergoes significant changes in its mobility upon binding, with residues in the loop connecting helices H5 and H6 becoming immobilized in the major groove and contacts to the minor groove slowing down the motion of residues at the C terminus. A DNA-induced rotation and displacement of the N-terminal subdomain of the protein increases the mobility of helix H1 located distal to the DNA interface and may partially negate the entropic cost of immobilizing interfacial residues. Elevated motions on the micro- to millisecond timescale in the N-terminal domain prior to DNA binding appear to foreshadow the DNA-induced conformation change.

Keywords: AT-rich interaction domain; ARID; protein–DNA interaction; NMR; backbone dynamics; ¹⁵N-relaxation; Dead ringer protein

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041154405.

Reprint requests to: Robert T. Clubb, Department of Chemistry and Biochemistry, University of California, Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095-1570, USA; e-mail: rclubb{at}mbi.ucla.edu; fax: (310) 206-4749.

¹ Present address: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0510, USA.

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