Regulation of gene expression depends on the integrated function of a diverse array of regulatory proteins including sequence-specific transcription factors, co-activators, and chromosomal proteins. DNA-binding chromosomal proteins can modulate the affinity and specificity of transcription factors and recruit gene regulatory machinery to specific genes for tight control of gene expression. Despite their importance in gene regulation, the chromosomal proteins have been difficult to study at the molecular level because of their characteristic ability to bind to many different sequences with comparable affinities. Consequently, the current understanding of their structures and interaction with DNA lags substantially behind that of their sequence-specific counterparts. A long term goal of this research is to understand the functions of sequence-tolerant chromosomal proteins and their interactions with DNA, and other proteins at the level of molecular structure. HMG-D is a Drosophila melanogaster member of the HMG1 family of chromosomal High Mobility Group proteins, implicated in a diverse array of functions. The HMG-box is a DNA binding motif that transcription factors use to recognize DNA sequence. Although two structures of the transcription factor HMG-box proteins bound to DNA are known, no structures of chromosomal HMG-box-DNA complexes are known. Co-crystals of the complex of DNA and HMG-D diffract to 1.8Angstrom, and native data have been collected to 2.0Angstrom. Co-crystals of HMG-D with iodinated and brominated DNA have been made for phasing using MIR and MAD methods. This crystal structure and others with different DNA and HMG-protein sequences will reveal the molecular basis for sequence-tolerance of HMG-D, complementing ongoing thermodynamic studies, and answering specifically: (1) What is the interface of a non-sequence-specific protein-DNA complex like? (2) How differently do the non-sequence-specific and sequence-specific HMG-box proteins bind to DNA? (3) How does the HMG-box domain of HMG-D adapt to different DNA binding sites? Understanding the mode of binding and structural basis for sequence-tolerance of this family of chromosomal proteins may have implications for treatment of human disease. The non-sequence-specific HMG-domain proteins recognize cis-DDP lesions in vivo, and appear to be important in the function of a highly successful anti-tumor agent, cis-DDP. Structural studies with HMG-D will be valuable for understanding DNA recognition at a level of detail that will be helpful in the design of improved anti-tumor drugs.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM059456-05
Application #
6526225
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Lewis, Catherine D
Project Start
1998-08-01
Project End
2004-07-31
Budget Start
2002-08-01
Budget End
2004-07-31
Support Year
5
Fiscal Year
2002
Total Cost
$112,495
Indirect Cost
Name
University of Colorado Denver
Department
Pharmacology
Type
Schools of Medicine
DUNS #
065391526
City
Aurora
State
CO
Country
United States
Zip Code
80045
Pollock, David D; de Koning, A P Jason; Kim, Hyunmin et al. (2011) Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions. PLoS One 6:e26105
Churchill, Mair E A; Klass, Janet; Zoetewey, David L (2010) Structural analysis of HMGD-DNA complexes reveals influence of intercalation on sequence selectivity and DNA bending. J Mol Biol 403:88-102
Hill, Krista K; Roemer, Sarah C; Jones, David N M et al. (2009) A progesterone receptor co-activator (JDP2) mediates activity through interaction with residues in the carboxyl-terminal extension of the DNA binding domain. J Biol Chem 284:24415-24
Gangelhoff, Todd A; Mungalachetty, Purnima S; Nix, Jay C et al. (2009) Structural analysis and DNA binding of the HMG domains of the human mitochondrial transcription factor A. Nucleic Acids Res 37:3153-64
Roemer, Sarah C; Donham, Douglas C; Sherman, Lori et al. (2006) Structure of the progesterone receptor-deoxyribonucleic acid complex: novel interactions required for binding to half-site response elements. Mol Endocrinol 20:3042-52
Dragan, Anatoly I; Read, Christopher M; Makeyeva, Elena N et al. (2004) DNA binding and bending by HMG boxes: energetic determinants of specificity. J Mol Biol 343:371-93
Klass, Janet; Murphy 4th, Frank V; Fouts, Susan et al. (2003) The role of intercalating residues in chromosomal high-mobility-group protein DNA binding, bending and specificity. Nucleic Acids Res 31:2852-64
Thomas, Chad B; Scavetta, Robert D; Gumport, Richard I et al. (2003) Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding. J Biol Chem 278:26094-101
Dragan, Anatoly I; Klass, Janet; Read, Christopher et al. (2003) DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution. J Mol Biol 331:795-813
Watson, William T; Minogue, Timothy D; Val, Dale L et al. (2002) Structural basis and specificity of acyl-homoserine lactone signal production in bacterial quorum sensing. Mol Cell 9:685-94

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