fractional occupancy
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What is the fractional occupancy of a protein binding site when the ligand concentration (L) =1mM and the ligand equilibrium binding constant at the binding site K10= 10microM.
- 0.01
B.0.1
C.0.91
D.0.99
- none of the listed values
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- A one-to-one protein (P)-ligand (L) complexation (P + L PL) has a dissociation equilibrium constant (Kd) value of 100 nM at 25°C, and the Kd remains the same at 37°C. 1) What is AS of binding at 25°C? Assume ACp of the binding is 0 over the temperature range. AS = 1.34E2 kJ/(mol*K) (note the unit!!) (sig. fig =3) 2) What is the concentration of the PL complex formed at equilibrium when you mix 0.20 uM (microM) of Protein and 1.0 uM of Ligand together at 37°C? PL at equilibrium = 8.1E-1 uM (note the unit!!) (sig. fig =2)A protein-ligand binding reaction is run. At equilibrium, half the protein is ligand bound, the unboundligand concentration is 0.657 nM. Calculate the koff value for this reaction. Assume the kon value is typical ofprotein-ligand interactions.A tetrapeptide, glutamate-glycine-alanine-lysine, is prepared at at concentration of 1 mM (0.001 M) and is measured in the standard setup (pathlength of 1 cm). What is the approximate absorbance of this peptide at 280 nm? Hint: if the peptide contained a single tryptophan, the answer would be about 10. 10 280 1 0
- Which of the following situations would produce a Hill plot with nH < 1.0? Explain your reasoning in each case.(a) The protein has multiple subunits, each with a single ligand-binding site. Binding of ligand to one site decreases the binding affinity of other sites for the ligand.(b) The protein is a single polypeptide with two ligand-binding sites, each having a different affinity for the ligand.(c) The protein is a single polypeptide with a single ligand-binding site. As purified, the protein preparation is heterogeneous, containing some protein molecules that are partially denatured and thus have a lower binding affinity for the ligand.Give the general Adiar equation for the binding of a ligand to a dimeric protein. Explain further what your understanding is of the terms "no-, positive-, and negative cooperativity” and graphically present the relationship between Ȳ and [S] for each of these cases. Also, give the relationship between the constants Kb1 and Kb2 in each case.Based on the Hill Plot below, this protein-ligand interaction displays log Y 1-Y 5 2.5 0 -2.5 -2.5 nH1 2.5 Binding that obeys the Law of Mass Action Negative cooperativity 5
- An experiment was carried out to measure the reaction rate of hydrolysis of acetylcholme (substrate) with serum enzymes (Eadie, 1949). In the experiment, two experiments were conducted, namely experiment 1 without using a prostigmine inhibitor and experiment 2 using a prostigmine inhibitor at 1.5 x 10^-7 mol/l. the data obtained are: a. Is prostigmine competitive or noncompetitive inhibitor? b. determine the value of km and rmax for the two experiments, compareThe following data describe binding of ligand A to a protein, using both Scatchard plots and Hills plots, tell as much as you can about the binding reaction. [A](M) 1X10-6 5 X10-6 1 X10-5 5 x 10-5 1 X 10-4 5 x 10-4 1x 10-3 5X10-3 ṽ 0.101 0.381 0.591 1.116 1.409 1.813 1.899 1.955..A family of proteins known as cupredoxins contain a single redoxactive Cu ion coordinated by a Cys, a Met, and two His residues. The reduction potentials of cupredoxins range from about 0.15 V to 0.68 V. What does this information reveal about the role of the protein component of the cupredoxins?
- The equilibrium constant for the hydrolysis of the peptide alanylglycine (Gly-Ala in the reaction from Part B) by a peptidase is K = 9.0 × 10² at 310 K. Calculate AG for this reaction. Express the Gibbs free energy to three significant figures. AG = Submit ΠΑΠΙ ΑΣΦ Request Answer ? kJ/mol Keq [Gly] [Ala] [Gly-Ala]Consider the dissociation reaction for a protein-ligand complex: P•L P + L A. Sketch a binding curve (fractional saturation θ vs. ligand concentration [L]) for this protein-ligand complex (ligand A). Show where on that curve you could obtain the dissociation equilibrium constant Kd for the reaction. B. Now sketch on the same axes a θ vs. [L] plot for a different ligand (B) that binds more weakly than the first ligand. C. Does the weaker binding ligand have a higher, or lower, Kd than the tighter binding ligand? D. Sketch a binding curve for a cooperatively bound ligand with K0.5 higher than that of Kd for A or B. (Note: for cooperative binding, each protein molecule would have to have more than 1 binding site for the ligand; K0.5 is the experimentally determined ligand concentration that gives θ = 0.5.)The hexapeptide Ala-Met-Leu-Lys-Phe-Asp is digested in the same tube with both Cyanogen Bromide and Trypsin at the same time at pH=7. Draw the structure of the product(s) that would bind to a cation exchange column. (Relevant pKa values are 2.2, 3.9, 9.5 and 10.5. Assume pKa values for any newly generated a-amino and a-carboxyl groups are 9.5 and 2.2 respectively)