affinity of a protein-protein or protein-ligand interaction can be described by theDissociation Constant, Kd (written below). Consider a protein P and its inhibitor,I.I inhibits P's activity when bound to it:koff _ [A][B]Dissociation Constant: Ka=koN[AB]QuestionWhen [I] is 10-7 M, 99% of P's activity is inhibited. What is the Kd of this Protein-Inhibitor interaction?

Protein can function as enzymes, signal molecule, ligand, receptor, etc. Its function can be…

Answered: When [I] is 10-7 M, 99% of P's activity…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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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.
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.)
For the investigation of positive homotropic cooperativity within protein-ligand binding interactions, Hill proposed a reaction as well as a graphic approach. Give the Hill equation as well as a Hill graph and explain the use/meaning of the graph
Two proteins, A and B, bind to the same ligand, L, with the binding curvesshown below. What is the dissociation constant, Kd , for each protein? Which protein (A or B) has a greater affinity for ligand L?
the number of low affinity binding sites occupied by a ligand at 100% saturation is greater than the number of high affinity binding sites occupied by a ligand at 100% saturation true or false?
For the binding of a ligand to a protein, what is the relationship between the Ka (association constant), the Kd (dissociation constant), and the affinity of the protein for the ligand?
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.
Which of the following must be true based on the data below for ligand L binding to protein A and to protein B? Choice 1 of 4:Protein A binds at least 2 molecules of ligand L. Choice 2 of 4:The Kd for ligand binding to B is approximately 4 micromolar. Choice 3 of 4:When exposed to ligand L, protein A reaches maximal binding faster than does protein B. Choice 4 of 4:Protein B must adopt at least 2 different conformations with different binding affinities.
Amino acids at the interaction site ( F,I and L) and its G protein partner (P, L, Y) are very conserved.If the amino acids are swapped between the protein and GPCR is binding expected to be as tight?
high and low affinity binding sites require the same amount of ligand to achieve saturation true or false?
Denatured protein is in a low energy state. What sort of explanation can you use to rationalize that statement? Hint: consider Gibbs free energy.
Calculate θ for a certain protein-ligand pair when the ligand concentration = 1 M and the Kd = 1 X 10-15 M.

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When [I] is 10-7 M, 99% of P's activity is inhibited. What is the Kd of this Protein- Inhibitor interaction?