Briefly discuss the reason behind the differences in the graphs below. Y[S]Fig. 12.2 - Graph of Y against [S], at fixed protein concentration, where the bindingshows positive homotropic cooperativity. Y[S]Fig. 12.1- Graph of fractional saturation (Y) against ligand concentration ([S],at fixed concentration of a protein having a single binding-site for S.

Allosteric regulation is a mode of regulation of an enzyme or other protein. Allosteric activators…

Answered: Y [S] Fig. 12.2 Graph of Y against [S],…

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter32: The Reception And Transmission Of Extracellular Information

Section: Chapter Questions

Problem 11P

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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.
Crystal structures exist for three neurokinin-1 (NK1) ligand complexes with the following pdb codes (6hll, 6hlo, 6hlp) For each of the three crystal structures identify four amino acids in the NK1 binding site that contact the ligand indicating both the residue type in three letter code and the residue number. One of the chose amino acids should form a hydrogen binding interaction to the ligand, state which functional group the amino acid utilises in each case
V-M-Y-F-E-N: This is the single-letter amino acid abbreviation for a peptide. What is the net charge of this peptide at pH 7.0? An enzyme called a protein tyrosine kinase can attach phosphates to the hydroxyl groups of tyrosine (Y). What is the net charge of the peptide at pH 7.0 after it has been phosphorylated by a tyrosine kinase? What is the likely source of phosphate used by the kinase for this reaction?
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?
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One round of Edman degradation of the peptide: H2N- Gly-Arg-Lys- Phe-Asp- COOH which of the following structures would result when add cyanogen bromide ? A) H2N-Gly-Arg-COOH + H2N–Lys-Phe- Asp-COOH B) H2N-Arg-Lys-Phe-Asp-C0OH+ Gly C) H2N- Gly-Arg-Lys-Phe-Asp- COOH D) H2N-Gly-Arg-Lys-Phe-COOH + Asp E) H2N-Gly-Arg-Lys-COOH + H2N-Phe-Asp-COOH
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Crystal structures of neurokinin-1 with pdb codes 6hll, 6hlo, 6hlp. Which is the highest quality crystal structure?
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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.)
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Y [S] Fig. 12.2 Graph of Y against [S], at fixed protein concentration, where the binding shows positive homotropic cooperativity.