Biochemistry: Concepts and Connections
1st Edition
ISBN: 9780321839923
Author: Dean R. Appling, Spencer J. Anthony-Cahill, Christopher K. Mathews
Publisher: PEARSON
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Chapter 6, Problem 11P
Theoretical and experimental measurements show that in many cases, the contributions of ionic and hydrogen-bonding interactions to ΔH for protein folding are close to zero. Provide an explanation for this result. (Hint: Consider the environment in which protein folding occurs.)
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affinity of a protein-protein or protein-ligand interaction can be described by the
Dissociation 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]
Question
When [I] is 10-7 M, 99% of P's activity is inhibited. What is the Kd of this Protein-
Inhibitor interaction?
Theoretical and experimental measurements show that in many cases, thecontributions of ionic and hydrogen-bonding interactions to ΔH for proteinfolding are close to zero. Provide an explanation for this result.
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.)
Chapter 6 Solutions
Biochemistry: Concepts and Connections
Ch. 6 - Prob. 1PCh. 6 - Bovine pancreatic trypsin inhibitor (BPTI; Figure...Ch. 6 - A schematic structure of the subunit of...Ch. 6 - In the protein adenylate kinase, the C-terminal...Ch. 6 - Give two reasons to explain why a proline residue...Ch. 6 - Consider a small protein containing 101 amino acid...Ch. 6 - a. Based on a more conservative answer to Problem...Ch. 6 - The following sequence is part of a globular...Ch. 6 - a. A protein is found to be a tetramer of...Ch. 6 - Under physiological conditions, the protein...
Ch. 6 - Theoretical and experimental measurements show...Ch. 6 - The peptide hormone vasopressin is used in the...Ch. 6 - A protein gives under conditions of buffer...Ch. 6 - A protein gives a single band on SDS get...Ch. 6 - It has been postulated that the normal...Ch. 6 - Prob. 16PCh. 6 - Do you expect a Pro Gly mutation in a...Ch. 6 - Rank the following in terms of predicted rates...
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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)arrow_forwardGive 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.arrow_forwardA 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.arrow_forward
- Predict the direction of migration for the following amino acids in solutions of the specified pH. Write Isoelectric, if no migration occurs: Lys at pH=12 (pk values: 2.2; 9.2; 10.8) Glu at pH= 2.0 (pk values: 2.1; 9.5; 4.1) Leu at pH= 6.0 (pk vaues: 2.3; 9.7)arrow_forwardA peptide has the sequence: Glu–His–Trp–Ser–Gly–Leu–Arg–Pro–Gly1. What would be the net charge of the molecule at pH a) 3, b) 8, and c) 11? (Use pKa values. Do not calculate the value per se, but instead estimate considering only fully protonated, or deprotonated states. Then estimate the pI for this peptide. Show full, clear and complete procedurearrow_forwardWhich intermolecular forces are important in acetic acid, CH3 –(C=0)-oh? A particular amino acid contains a- CHNH3+ group. Is this amino acid more likely to be found on the inside or the outside of the folded protein? Briefly explain. The addition of ethanol, CH3CHOH, t an aqueous solution lowers the surface tension of the solution. Predict whether adding ethanol to an aqueous protein solution will tend to stabilize or unfold the protein. Briefly explain.arrow_forward
- Protein concentration can readily be determined using the Beer-Lambert law: A = e l c where A = absorbance e = molar absorption coefficient (M-1cm-1) l = light path length (cm) c = concentration (M) If the molar absorption coefficient at 280 nm for yeast ADH is 48860 M-1cm-1 and a 10 mL solution of the protein has an absorbance at 280 nm of 0.4 (as measured by a spectrometer with pathlength 1 cm), then what is the concentration of the protein solution (in μM)? i.e. concentration = ______ μM If the molecular weight of the protein is 36849, what is its concentration in mg/mL? i.e. concentration = _______ mg/mL For each part of the question, show your calculations to arrive at your answers.arrow_forwardThe major difference between a protein molecule in its native state and in its denatured state lies in the number of conformations avail- able. To a first approximation, the native, folded state can be thought to have one conformation. The unfolded state can be estimated to have three possible orientations about each bond between residues. (a) For a protein of 100 residues, estimate the entropy change per mole upon denaturation. (b) What must be the enthalpy change accompanying denaturation to allow the protein to be half-denatured at 50 °C? (c) Will the fraction denatured increase or decrease with increasing temperature?arrow_forward12 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.arrow_forward
- . The process of a protein folding from an inactive unfolded structure to the active folded structure can be represented by the following equation: unfolded protein = folded protein The values of AH and AS° for the folding of the protein lysozyme are: AH = -280 kJ/mol AS = -790 J/mol · K (a) Calculate the value of AG for the folding of lysozyme at 25 °C. (b) At what temperature would you expect the unfolding of lysozyme to become favorable?arrow_forwardWhich 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.arrow_forwardThe major difference between a protein molecule in its native state and inits denatured state lies in the number of conformations available. To a firstapproximation, the native, folded state can be thought to have one conformation. The unfolded state can be estimated to have three possible orientations about each bond between residues.(a) For a protein of 100 residues, estimate the entropy change per moleupon denaturation.(b) What must be the enthalpy change accompanying denaturation to allow the protein to be half-denatured at 50 °C?(c) Will the fraction denatured increase or decrease with increasingtemperature?arrow_forward
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