Y [S] Fig. 12.2 Graph of Y against [S], at fixed protein concentration, where the binding shows positive homotropic cooperativity.
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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 caseV-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?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.His-Met-Asp-Tyr-Phe-Ser Calculate an approximate pI (isoelectric point) for this peptide. Please use the pKa's listed within Table 3-1 of Lehninger. Show and/or explain all your work; you must be very clear about WHY you use particular pKa's in your calculation.
- 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.A protein gives a single band on SDS gel electrophoresis, as shown in lanes 1 and 2 below. There is little if any effect from addingAt a pH of 10, would you expect this peptide to be retained for a longer time within an anion exchange column or a cation exchange column? His-Met-Asp-Tyr-Phe-Ser
- Crystal structures of neurokinin-1 with pdb codes 6hll, 6hlo, 6hlp. Which is the highest quality crystal structure?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.)peptide Lys-Glu-Trp answer the following questions: Draw the structure of this peptide when all the ionizable groups are fully protonated. How many ionizable groups does this peptide have? Label the pKa for each of the ionizable groups in the structure above. Draw the appropriate titration curve for this peptide on graph paper starting at pH 0 and ending at pH 14. Label the x-axis, y-axis and the pKa Determine the overall net charge of this peptide at each full equivalent point (including 0) where the ionizable group is 100% deprotonated. Determine the pI for this peptide. Determine the average overall net charge of a mixture of this peptide in a solution where pH=8.5.