Folding <-> Binding

Background papers for Spolar and Record Discussion

The primary paper (Spolar, R. S. and Record, M. T., Jr., 1994, "Coupling of local folding to site-specific binding of proteins to DNA." Science 263, 777-84), to be discussed 3/4/96, presents a framework for interpreting heat capacity changes upon protein-DNA binding and for assessing the contribution of linking folding and binding. We will look into the background, some newer experimental results on protein-DNA calorimetry, and one or two structural examples.

Background Area (paper)
Calorimetry on lambda cI repressor-operator (Merabet and Ackers, 1995)
Calorimetry on the Trp repressor (Ladbury et al., 1994)
Record's earlier work on the h-phobic effect in protein-DNA interaction (Ha et al., 1989)
Pitfalls in interpretation of DeltaCpdeg. (Ferrari and Lohman, 1994)
Application to TBP, including kinetics (Petri et al., 1995)
General overview of calorimetry of macromolecules (Plum and Breslauer, 1995)
Application to kinetics of conformational change (Roe et al., 1985)
Structure of glucocorticoid receptor-DNA complex (Luisi et al., 1991)
Structural backbround on Trp repressor (Sigler, 1992)

Ferrari, M. E. and Lohman, T. M. (1994). "Apparent Heat Capacity Change Accompanying a Nonspecific Protein-DNA Interaction. Escherichia coli SSB Tetramer Binding to Oligodeoxynucleotides." Biochemistry 33, 12896-12910.

Ha, J.-H., Spolar, R. S., and Record, M. T., Jr. (1989). "Role of the Hydrophobic Effect in Stability of Site-specific Protein-DNA Complexes." J. Mol. Biol. 209, 801-816.

Ladbury, J. E., Wright, J. G., Sturtevant, J. M., and Sigler, P. B. (1994). "A Thermodynamic Study of the trp Repressor-Operator Interaction." J. Mol. Biol. 238, 669-681.

Luisi, B. F., Xu, W. X., Otwinkowski, Z., Freedman, L. P., Yamamoto, K. R., and Sigler, P. B. (1991). "Crystallographic Analysis of the Interaction of the Glucocorticoid Receptor with DNA." Nature 352, 497-505.

Merabet, E. and Ackers, G. K. (1995). "Calorimetric Analysis of lambda cI Repressor Binding to DNA Operator Sites." Biochemistry 34, 8554-8563.

Petri, V., Hsieh, M., and Brenowitz, M. (1995). "Thermodynamic and Kinetic Characterization of the Binding of the TATA Binding Protein to the Adenovirus E4 Promoter." Biochemistry 34, 9977-9984.

Plum, G. E. and Breslauer, K. J. (1995). "Calorimetry of proteins and nucleic acids." Curr. Opinion Struct. Biol. 5, 682-690.

Roe, J.-H., Burgess, R. R., and Record, M. T., Jr. (1985). "Temperature Dependence of the Rate Constants of the Escherichia coli RNA Polymerase-lambdaPR Promoter Interaction: Assignment of the kinetic steps corresponding to protein conformational change and DNA opening." J. Mol. Biol. 184, 441-453.

Sigler, P. B. (1992). "The Molecular Mechanism of trp Repression." In Transcriptional Regulation. Ed. McKnight, S. L. and Yamamoto, K. R. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. Vol. 1, pp. 475-499. (see me if you can't find it in the library)