Signatures of Protein-DNA Recognition in Free DNA Binding Sites

Journal Article · Thu Jan 01 04:00:00 EST 2009 · Journal of Molecular Biology

DOI:https://doi.org/10.1016/j.jmb.2009.01.007· OSTI ID:980452

Locasale, J; Napoli, A; Chen, S; Berman, H; Lawson, C

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.

• Research Organization: Brookhaven National Laboratory (BNL) National Synchrotron Light Source
• Sponsoring Organization: Doe - Office Of Science
• DOE Contract Number: AC02-98CH10886
• OSTI ID: 980452
• Report Number(s): BNL--93370-2010-JA
• Journal Information: Journal of Molecular Biology, Journal Name: Journal of Molecular Biology Vol. 386; ISSN JMOBAK; ISSN 0022-2836
• Country of Publication: United States
• Language: English

Related Subjects

36 MATERIALS SCIENCE
BENDING
CRYSTAL STRUCTURE
CRYSTALLIZATION
DATA
DNA
FINGERS
GEOMETRY
INFORMATION
INTERACTIONS
PROTEINS
SCREENING
ZINC
national synchrotron light source