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Thermodynamic measurements of proteins indicate that the folding to the native state takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of proteins indicate that folding is guided through some sequence of contact bindings. We discuss the possibility of reconciling a two-state(More)
We propose a thermodynamic model that includes the non-specific binding of the lambda phage regulatory proteins CI and Cro. By fitting the model to experimental in vivo data on activities of the two promoters P(RM) and P(R) versus concentration, we estimate the free energy upon non-specific binding to be -4.1+/-0.9 kcal/mol for CI and -4.2+/-0.8 kcal/mol(More)
We investigate the sensitivity of the right operator in bacteriophage lambda. In particular, the system is probed in the three different regulatory protein concentration-regimes: 1), lysogen (CI dominates); 2), during induction (CI and Cro at comparable concentrations); and 3), after induction (Cro dominates). Systematic perturbations of the(More)
We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: (1) binding energy of folding relative to the orientational energy of bound water, (2) ratio of degrees of freedom between the folded and unfolded protein(More)
We estimate the Gibbs free energy for nonspecific binding (DeltaGNSB) to the Escherichia coli DNA for two regulatory proteins of the lambda phage, CI and Cro. By means of a statistical-mechanical approach, we calculate the cI and cro activities associated with the operator OR of an introduced lambda phage genome (prophage). In this statistical model we(More)
Thermodynamics related to hydrated water upon protein unfolding is studied over a broad temperature range (5-125 degrees C). The hydration effect arising from the apolar interior is modeled as an increased number of hydrogen bonds between water molecules compared with bulk water. The corresponding contribution from the polar interior is modeled as a(More)
We study a synthetic clay suspension of laponite at different particle and NaCl concentrations by measuring stationary shear viscosity and transient electrically induced birefringence (TEB). On one hand the viscosity data are consistent with the particles being spheres and the particles being associated with large amount bound water. On the other hand the(More)
We investigate the sensitivity of production rates (activities) of the regulatory proteins CI (repressor) and Cro at the right operator (OR) of bacteriophage lambda. The DNA binding energies of CI, Cro, and RNA polymerase are perturbed to check the uncertainty of the activity, due to the experimental error, by means of a computational scattering method(More)
Many small globular proteins are traditionally classified as thermodynamical two-state systems, i.e., the protein is either in the native, active state (folded) or in the denatured state (unfolded). We challenge this view and show that there may exist (protein) systems for which a van't Hoff analysis of experimental data cannot determine whether the system(More)
We investigate the transcriptional activity associated with the P(RM) promoter of lambda phage. The probability for formation of a transcriptionally active (open) RNA polymerase-DNA complex is calculated by means of an equilibrium statistical-mechanical model. In particular, we study two different models of the transcriptional activation mechanism when the(More)