The table, below, lists three sets of values for the parameters in the Concerted Model (MWC model) for protein-ligand binding by three different trimeric proteins. The proteins can exist in either of two conformations (call them T and R). The parameters are as defined in class: K1 = [RO]/[TO], and Kar and Kar are the Kg for ligand binding to the Tand R conformations, respectively. protein A protein B protein C 0.005 0.01 0.02 Кат 125 0.25 10 10 KAR Consider the two graphs given below. Which set of parameters goes with which of the graphs? (Two different parameter sets go with the two graphs, one for each graph. The other parameter set does not go with a graph.) Explain how you decided, for both graphs. 1.0 2 1.0 1 0.8 0.8 Y 0.6 Y 06 0.4 0.4 0.2 0.2 0.0 140 160 00 40 60 80 100 120 2. 20 LL uM

The table, below, lists three sets of values for the parameters in the Concerted Model (MWC model) for protein-ligand binding by three different trimeric proteins. The proteins can exist in either of two conformations (call them T and R). The parameters are as defined in class: K1 = [RO]/[TO], and Kar and Kar are the Kg for ligand binding to the Tand R conformations, respectively. protein A protein B protein C 0.005 0.01 0.02 Кат 125 0.25 10 10 KAR Consider the two graphs given below. Which set of parameters goes with which of the graphs? (Two different parameter sets go with the two graphs, one for each graph. The other parameter set does not go with a graph.) Explain how you decided, for both graphs. 1.0 2 1.0 1 0.8 0.8 Y 0.6 Y 06 0.4 0.4 0.2 0.2 0.0 140 160 00 40 60 80 100 120 2. 20 LL uM

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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Similar questions

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?
12 mM of protein A is combined with 6 mM of ligand X in water. After the protein-ligand complex binding reaches equilibrium, you measure that the free ligand concentration is 3 mM and the concentration of protein-ligand complex is 3 mM. What is the Kd for protein A? Although they would be in mM, do not include units in your answer, only the number as a whole integer.
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.
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?
a) What is the KDD for this myoglobin variant? b) What is the predicted fractional saturation for the last box in the table? (please show your work so I can better understand) c) What is unexpected about the binding curve above? (5 words or less) d) What must be structurally different about this new variant relative to other known Myoglobin variants to generate this graph?
Koshland, Nemethy and Filmer, proposed a model for the binding of a ligand to a dimeric protein, where the following interaction constants were introduced: KTT: KRT, KRR. Give the relationships between these constants as well as Kb1 and Kb2 during no cooperativity, positive homotropic cooperativity and negative homotropic cooperativity.
Three different ligands, Ligand Q, Ligand T, and Ligand W, bind to the same protein but with different affinity: The association constant (Ka) for the binding of Ligand Q to the protein is 0.033 nM-1. The fractional saturation (Y) of the protein is 0.20 when the concentration of Ligand T is 1.25 nM. The fractional saturation (Y) of the protein is 0.80 when the concentration of Ligand W is 72 nM. Given this information, Calculate Kd for the binding of each ligand to this protein. Which ligand binds with greatest affinity? Which ligand binds with the lowest affinity?
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?
While each G-protein subunit has a distinctly characteristic C-terminal sequence that binds certain GPCRs better than others, the GPCRs that prefer the same G-protein subunit do not share a conserved sequence motif, even in the regions that form the binding pocket for the C-terminal domain of the G-protein a subunit. Given this fact, what must be similar about the binding pockets of these GPCRs in order to achieve specificity?
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.
A recent genome sequencing project for the bacterium Burkholderia mallei has identified a new protein with high similarity to the lysylphosphatidylglycerol flippase enzyme. A short section of the new protein sequence is shown below. TVEVNAPGDVQKALSELQQINDGRLDIRI (a) Are any reverse turns likely to be present? Explain your answer. (b) Are any beta-strands likely to be present? Explain your answer. (c) Are any alpha helices likely to be present? Explain your answer. (d) Is any supersecondary structure likely to be present? Explain your answer. (e) Identify two residues that are likely to be buried in the core of the folded protein. Explain your answer. (f) Identify two residues that are likely to be hydrogen bonded to each other. Explain your answer.
When protein X is subjected to dimethylsuberimidate and SDS electrophoresis a 50 kDa band is seen; when the protein X is subjected to SDS electrophoresis without DMS, two bands of 20 kDa and 10 kDa are seen. How many different oligomeric structures of the native protein X are possible, being consistent with these observed results? one two three none of the above which is the answrr? and explain