Signatures of Protein-DNA Recognition in Free DNA Binding Sites

JOURNAL OF MOLECULAR BIOLOGY

卷:386

Article

Locasale, Jason W.^1,2  Napoli, Andrew A.¹  Chen, Shengfeng¹  Berman, Helen M.¹  Lawson, Catherine L.¹ 

[1] Rutgers State Univ, Dept Chem & Chem Biol, Piscataway, NJ 08854 USA

[2] Harvard Univ, Sch Med, Dept Syst Biol, Boston, MA 02115 USA

关键词: DNA structure;    transcription factors;    indirect readout;    protein-DNA interactions;    gene regulation;   

DOI  :  10.1016/j.jmb.2009.01.007

来源: Elsevier

【 摘 要 】

One obstacle to achieving complete understanding of the principles underlying sequence-dependent recognition of DNA is the paucity of structural data for DNA recognition sequences in their free (unbound) state. Here, we carried out crystallization screening of 50 DNA duplexes containing cognate protein binding sites and obtained new crystal structures of free DNA binding sites for three distinct modes of DNA recognition: anti-parallel strands (MetR), helix-turn-helix motif + hinge helices (PurR), and zinc fingers (Zif268). Structural changes between free and protein-bound DNA are manifested differently in each case. The new DNA structures reveal that distinctive sequence-dependent DNA geometry dominates recognition by MetR, protein-induced bending of DNA dictates recognition by PurR, and deformability of DNA along the A-B continuum is important in recognition by Zif268. Together, our findings show that crystal structures of free DNA binding sites provide new information about the nature of protein-DNA interactions and thus lend insights towards a structural code for DNA recognition. (C) 2009 Elsevier Ltd. All rights reserved.

【 授权许可】

Free