Stephen P. Edmondson
Research Associate Professor, Chemistry
Office: MSB 305
- Ph. D. in Biophysics, University of Texas at Dallas, 1983.
- Postdoc: Oregon State University and Los Alamos National Laboratory
- Research faculty:Vanderbilt University and Southern Illinois University
As part of a long range study on the structure and stability of thermophile proteins, I have determined the solution structure of a recombinant form of Sac7d, a DNA-binding protein from the extreme thermophile Sulfolobus acidocaldarius, which grows at temperatures up to 92°C. A high resolution structure was obtained from 2-dimensional NMR data using restrained molecular dynamics and a relaxation matrix refinement procedure. The precision of the structure is being assessed by a new Monte Carlo method that we have developed for this purpose. Work is currently in progress on the structure of the native Sac7d protein, which is 7°C more thermostable than the recombinant protein due to methylation of specific lysine residues. Several site-directed mutants of Sa7d have been prepared, and the stability of these proteins are being determined by differential scanning calorimetry and chemical denaturation.
Sac7d stabilizes the duplex form of DNA and increases the melting temperature of poly[d(AT)] by about 30°C. Binding isotherms measured by the quenching of tryptophan fluorescence demonstrate non cooperative binding with a binding constant of about 10^7 and a site size of about 4 base pairs. There is little change in protein structure upon complex formation; however, there is a significant conformational change in the DNA. Interestingly, binding titrations monitored by circular dichroism are sigmoidal, indicating that the conformational changes induced in the DNA upon protein binding are cooperative. A quantitative model, based on that of McGhee-Von Hippel, has been developed to explain the cooperative effects on DNA structure induced by the non cooperative binding of Sac7d.
As part of an effort in developing NMR methodology, computer software (FIRM, Full Iterative Relaxation Matrix) has been developed for calculating the NOE using a relaxation matrix procedure. When incorporated as part of a structural refinement protocol (e.g., restrained molecular dynamics), FIRM allows structure refinement to be based on NOE residuals rather than qualitative distance constraints. This procedure is now being used for structure refinements, and it forms the basis of the Monte Carlo method that we have developed for determining the precision of NMR structures.
Additional information is available on Biomolecular NMR at UAH.
You can also find out about my interests in astronomy.
- Calorimetric analyses of hyperthermophile proteins. Methods in Enzymology 334, 389-422 (2001). [link]
- DNA-binding proteins Sac7d and Sso7d from Sulfolobus. Methods in Enzymology 334, 129-145 (2001). [link]
- The acid-induced folded state of Sac7d is the native state. Protein Science 9, 1878-1888 (2000). [link]
- Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs. J. Mol. Biol. 27, 395-403 (2000). [link]
- The solution structure of the Sac7d/DNA complex: a small angle X-ray scattering study. Biochem. 38, 10247-10255 (1999). [link]
- Thermodynamic Stability of Archaeal Histones. Biochemistry 37, 10563-10572 (1998). [link]
- The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature 392, 202-205 (1998). [link]
- Linkage of Hydrogen Ion and Anion Binding to Protein Folding. J. Mol. Biol. 276, 203-224 (1998). [link]
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