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Originally published in Science Express on 12 June 2003
Science 27 June 2003:
Vol. 300. no. 5628, pp. 2097 - 2101
DOI: 10.1126/science.1084648
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Reports

Comprehensive Identification of Human bZIP Interactions with Coiled-Coil Arrays

John R. S. Newman* and Amy E. Keating{dagger}

In eukaryotes, the combinatorial association of sequence-specific DNA binding proteins is essential for transcription. We have used protein arrays to test 492 pairings of a nearly complete set of coiled-coil strands from human basic-region leucine zipper (bZIP) transcription factors. We find considerable partnering selectivity despite the bZIPs' homologous sequences. The interaction data are of high quality, as assessed by their reproducibility, reciprocity, and agreement with previous observations. Biophysical studies in solution support the relative binding strengths observed with the arrays. New associations provide insights into the circadian clock and the unfolded protein response.

Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.



* Present address: Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94143–2240, USA.

{dagger} To whom correspondence should be addressed. E-mail: keating{at}mit.edu

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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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