Comparison of calculated and experimental data.
the calculated stability value lg(cond(W)) is qualitatively proportional to the experimental value Kd
Verification of calculated and experimental data before conducting a large-scale computational process
An additional controlled parameter is the measure of change in the differential entropy (delta)H
The effect of the R188E is a direct effect on DNA binding by the TBPCORE
Figure 1. Wild-Type and Activated DNA Binding Mutant TBP Molecules Have Different TATA Box On Rates and Different DNA Binding Surfaces. Electrophoretic mobility retardation analyses of the rates of formation of the TBP-TATA box complex on the U6 promoter with (A) wild-type TBP and the (B) TBPR188E mutant TBP molecules.
A master binding reaction was prepared at 30C, and aliquots were removed at 1, 4, 9, 16, 25, 36, 49, 64, 81, and 100 min and immediately loaded onto the gel.
After incubation of a master binding reaction for 100 min at 30C, excess unlabeled DNA was added, and aliquots werremoved after an additional 1, 4, 9, 16, 25, 36, 49, 64, 81, and 100 min incubation at 30C and immediately loaded onto the gel. The graphs below the autoradiograms show the dissociation of TBP from the TBP-TATA box complexes over incubation time after addition of the competitor DNA. The unit of the vertical axis is arbitrary. Filled dots and open triangles represent the unbent TBPFL and bent TBPFL* complexes respectively.
Figure 2. The Bent, But Not the Unbent, Wild-Type TBP-TATA Box Complex Is Very Stable. Electrophoretic mobility retardation analysis of the dissociation rates of (A) TBPWT and (B) TBPR188E molecules from the TBP-TATA box complexes on the U6 promoter.
TBPR188E formed a TBPFL* complex rapidly beginning within 1 min of incubation and formation of the complex increased rapidly with timenot simpler.