Office: Material Sciences Building Room 311
Many DNA-binding proteins distort the structure of DNA, often with significant changes in the twist and bend angles of the duplex. Distortions in the binding site and beyond are necessary for DNA packaging, as well as the regulation and expression of many genes of medical relevance. Although about 500 structures of protein-DNA complexes have been determined, our understanding of the interplay between the energetics of binding and distortion is very much in its infancy. This limitation stems from a number of factors, not the least of which is ambiguities derived from protein instability since accurate descriptions of the energetics of binding require data collection over a temperature range that is inaccessible with many complexes. In addition, ideally it should be possible to not only measure distortion, but also manipulate and control it so that the energetics of distortion can be directly related to structural changes. We use a novel approach to this problem by developing and characterizing two model systems that are well-suited for measuring the energetics of DNA binding and distortion. These are obtained from the hyperthermophile Sulfolobus and are similar to proteins with direct biomedical relevance which have proven to be difficult to characterize energetically. The first protein, Sac7d, is a small chromodomain protein similar to the DNA-binding domain of HIV-1 integrase. Sac7d binds to the minor groove of DNA and induces one of the largest known kinks in DNA with intercalation of two amino acid side chains. NMR, fluorescence resonance energy transfer (FRET), and calorimetry (ITC and DSC) are being used to quantitatively characterize the role of protein residues and DNA sequence in defining the structure of the complex and the energetics of distorting DNA. The second protein, Sso10a, is a dimer of winged helices that is being used to test the generality of the conclusions drawn from Sac7d. This is the the first calorimetric study of DNA binding by a winged helix, a fold important in many human transcription factors. This is a basic research project which will provide a description of the energetics of DNA interactions and distortions that are important in many disease-related protein-DNA complexes. The results will enhance our ability to rationally control protein-DNA binding interactions in pharmacology and therapeutics.
Peters, W.B., Edmondson, S.P., and Shriver, J.W. "Effect of Mutation of the Sac7d Intercalating Residues on the Temperture Dependence of DNA Distortion and Binding Thermodynamics" Biochemistry 44, 4794-804 (2005).
M. Kahsai, S.P. Edmondson, and J.W. Shriver (2005) "Solution Structure, Stability, and Flexibility of Sso10a", Biochemistry 44, 2822-2832.
J. Bedell, S. Edmondson, and J.W. Shriver (2005) "The Role of a Surface Tryptophan in Defining the Structure, Stability, and DNA Binding of the Hyperthermophile Protein Sac7d" Biochemistry 44, 915-25.
W.P. Peters, S.P. Edmondson, and J.W. Shriver (2004) "Thermodynamics of DNA Binding by the Hyperthermophile Chromatin Protein Sac7d" J. Mol. Biol. 343, 339-360.
Stephen Edmondson and John W. Shriver (2004) "DNA-Binding Proteins Sac7d and Sso7d from Sulfolobus" Methods in Enzymology 334, 129-145.
P. Edmondson, M. Kahsai, R. Gupta, and J.W. Shriver. (2004) "Characterization of Sac10a, a Hyperthermophile DNA Binding Protein from Sulfolobus acidocaldarius" SBiochemistry 43, 13026-36.
L. Chen, L.-R. Chen, W. Zhou, Y. Wang, M. Kahsai, A.T. Clark, S.P. Edmondson, Z.J. Liu, J.P. Rose, B.-C. Wang, E.J. Meehan, J.W. Shriver (2004) "The Hyperthermophile Protein Sso10a is a Dimer of Winged Helix DNA-Binding Domains Linked by an Antiparallel Coiled Coil Rod" J. Mol. Biol. 341, 73-91.
A.T. Clark, B.S. McCrary, S.P. Edmondson, and J.W. Shriver (2004) "Thermodynamics of Core Hydrophobicity and Packing in the Hyperthermophile Proteins Sac7d and Sso7d" Biochemistry 43, 2840-53.