The overall aim is to investigate the molecular basis of protein-DNA interactions through the high resolution crystal structural analysis of a number of sequence-general DNA-binding proteins and their complexes with DNA. In particular, chromosomal proteins from archaeabacteria (Sulfolobus) and bacteria (E. coli) complexed to double-stranded DNA and bacteriophage single-stranded DNA binding proteins complexed to ssDNA will be the major focus.
Specific Aim I. Double-stranded DNA-binding proteins. (A) Sac7d and Sso7d are two dsDNA-binding proteins that play the important role of stabilizing dsDNA in hyperthermophile archabacteria. Dr. Wang has obtained high quality crystals of Sac7d and Sso7d bound to DNA (resolution between 1.3 Angstrom to 1.9 Angstrom). He will study: (1) the novel DNA-binding mode of Sac7d/Sso7d through the structural analysis of the protein-DNA complexes, (2) the conformational modulation of DNA at the kink site, (3) the conformational modulation of proteins using site-directed mutants of Sac7d/Ddo7d. (B) HU protein from E. coli is a bacterial chromatin protein that forms a """"""""nucleosome-like"""""""" structure. Dr. Wang has obtained diffraction-quality crystals of HU protein bound to a DNA octanucleotide. He proposes to solve the structure of this HU-DNA complex to its highest resolution possible. Comparison of chromosomal proteins from archaea (Sac7d, HMfb), bacterial (HU) and eucaryotic (histones) kingdoms will be useful in the understanding of the evolution of chromatin organization.
Specific Aim II. Single-stranded DNA-binding proteins are important in the life cycle of many cells. Dr. Wang has determined the 1.6 Angstrom resolution structure of the M13 bacteriophage gene V protein (GVP) and proposed a model for its superheical protein-DNA complex. He will determine the crystal structure of the M13 GVP complexed with DNA hexamers which will allow a direct visualization of the protein-DNA interaction. In addition, the GVP from another I2-2 phage (108 a.a) will be analyzed at better than 2.0 Angstrom resolution. The above protein-DNA systems will be studied by cryo x-ray crystallography and their structures correlated with biological functions. Other biophysical techniques will also be employed when needed. These studies will greatly improve our understanding on the biological functions of those sequence-general DNA-binding proteins.
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