1: J Mol Biol. 2004 Aug 6;341(2):419-28. 

Modulation of DNA conformations through the formation of alternative high-order
HU-DNA complexes.

Sagi D, Friedman N, Vorgias C, Oppenheim AB, Stavans J.

Department of Physics of Complex Systems, The Weizmann Institute of Science,
Rehovot 76100, Israel.

HU is an abundant, highly conserved protein associated with the bacterial
chromosome. It belongs to a small class of proteins that includes the eukaryotic
proteins TBP, SRY, HMG-I and LEF-I, which bind to DNA non-specifically at the
minor groove. HU plays important roles as an accessory architectural factor in a
variety of bacterial cellular processes such as DNA compaction, replication,
transposition, recombination and gene regulation. In an attempt to unravel the
role this protein plays in shaping nucleoid structure, we have carried out
fluorescence resonance energy transfer measurements of HU-DNA oligonucleotide
complexes, both at the ensemble and single-pair levels. Our results provide
direct experimental evidence for concerted DNA bending by HU, and the abrogation
of this effect at HU to DNA ratios above about one HU dimer per 10-12 bp. These
findings support a model in which a number of HU molecules form an ordered
helical scaffold with DNA lying in the periphery. The abrogation of these
nucleosome-like structures for high HU to DNA ratios suggests a unique role for
HU in the dynamic modulation of bacterial nucleoid structure.

PMID: 15276833 [PubMed - indexed for MEDLINE]


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2: Biopolymers. 1999 Apr 15;49(5):341-53. 

Modeling DNA deformations induced by minor groove binding proteins.

Lebrun A, Lavery R.

Laboratoire de Biochimie Theorique, CNRS UPR 9080, Institut de Biologie
Physico-Chimique, Paris, France.

Molecular modeling is used to demonstrate that the major structural deformations
of DNA caused by four different minor groove binding proteins, TBP, SRY, LEF-1,
and PurR, can all be mimicked by stretching the double helix between two
3'-phosphate groups flanking the binding region. This deformation reproduces the
widening of the minor groove and the overall bending and unwinding of DNA caused
by protein binding. It also reproduces the principal kinks associated with
partially intercalated amino acid side chains, observed with such interactions.
In addition, when protein binding involves a local transition to an A-like
conformation, phosphate neutralization, via the formation of protein-DNA salt
bridges, appears to favor the resulting deformation.

PMID: 10101970 [PubMed - indexed for MEDLINE]


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3: Biochemistry. 1995 Sep 19;34(37):11998-2004. 

NMR spectroscopic analysis of the DNA conformation induced by the human testis
determining factor SRY.

Werner MH, Bianchi ME, Gronenborn AM, Clore GM.

Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and
Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520,
USA.

The conformation of an eight base pair DNA oligonucleotide duplex bound to the
human testis determining factor SRY and the orientation of the protein domain
within the complex have been analyzed by a variety of NMR methods which permit
the selective observation of protons attached to 12C nuclei in the presence of
uniformly enriched 13C/15N protein. Qualitative analysis of nuclear and rotating
frame Overhauser enhancement spectra at multiple mixing times indicates that the
conformation of the SRY-bound DNA is distinct from that of A- and B-DNA, in
agreement with the recent three-dimensional structure determination of the
complex [Werner, M. W., Huth, J. R., Gronenborn, A. M., & Clore, G. M. (1995)
Cell 81, 705-714]. Selective observation of intermolecular NOEs between protein
and DNA indicates that partial intercalation of a protein side chain occurs
between two adenine bases in the DNA octamer. The analysis of structural
features by NMR for this unusual DNA conformer and the orientation of the
protein domain on the DNA is discussed. The structural features of the DNA
complexed to SRY are remarkably similar, but not identical, to those of DNA
complexed to the TATA-binding protein (TBP).

PMID: 7547937 [PubMed - indexed for MEDLINE]


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