The bioactive conformation of lead compound I was confirmed when a crystal structure wasr.obtained showing I bound to its target (an enzyme).Ala-312inHis-42Val-307CIAsp-305Phe-47H.Ser-254I bound to target proteinUsing the information shown above, draw the structure of an analog that you predict will exhibit improvedbinding to the target. Explain how you arrived at this proposed analog structure.

The amino acids present in the active sites of an enzyme are responsible for the specificity of the…

Answered: The bioactive conformation of lead…

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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What is the dissociation equilibrium constant of a protein if the concentration of free ligand is 3.0um when the fraction of bound sites is 0.6
A decapeptide was analyzed and the following information obtained. Determine the primary structure of the peptide. Edman's Degradation: PTH-Ala Trypsin produces 3 peptides of the following composition: 1. Gly, His 2. Ala, Leu, Lys, Val 3. Arg (2), Phe, Pro Chymotrypsin produces 2 peptides of the following composition: 1. Ala, Leu, Lys, Phe, Val 2. Arg (2), Gly, His, Pro Elastase produces 1 amino acids and 3 peptides 1. Ala 2. Leu, Val 3. Arg (2), Lys, Phe, Pro, Gly, His Arg Gly His Leu Phe Pro Val
(b) The values of kinetic parameters for a variety of synthetic ester and peptide substrates ofa- chymotrypsin are compared for the reaction scheme below where ES is the Michaelis complex, ES' E+S Substrate K₁ N-Ac-Trp–OC₂H5 N-Ac-Phe-OC2H5 N-Ac-Leu-OC2H5 N-Ac-Phe-CONH2 N-Ac-Tyr-p-nitro-anilide ES K₂ 3.5 13.0 3.2 1.7 K-₁ is the acylenzyme, P₁ is the first product to be released, P2 is the second product, k2 is the acylation rate constant, k3 is the deacylation rate constant, and kcat = k2 k3/( k2 + k³). In the table below, N- Ac = N-acetyl; -CONH₂ = carboxamide; -OC₂H5 = ethyl ester; p-nitroanilide = −NH-C6H4-NO2 simulating a peptide group. ES' K2 (S-¹) K3 (S-1) 0.84 2.2 0.19 P₁ K3 0.073 H → E+ P2 Kcat (S-1) 0.82 1.9 0.18 0.070 0.038 KM (MM) 0.08 1.3 4.2 24.0 0.35 1 Kcat/ KM (mM-¹ s¯¹) 10.3 1.5 0.04 0.003 0.11 The value of kcat for N-Ac-Phe-OC2H5 is two-fold greater than that for the L-tryptophanyl analog and more than 10-fold greater than the value of kcat for the ester substrate…
What's the simple rule to predict ligand binding sites for Rossmann Fold
A protein has been sequenced after cleavage of disulfide bonds. The protein is known to contain 3 Cys residues, located as shown here. Only one of the Cys has a free —SH group, and the other two are involved in an —S—S— bond. The only methionine and the only aromatic amino acid (Phe) in this protein are in the positions indicated. Cleavage of the intact protein (i.e., withdisulfide bonds intact) by either cyanogen bromide or chymotrypsin does not break the protein into two peptides. Where is the —S—S— bond (i.e., AB, BC, or AC)?
Please don't provide handwritten solution
A peptide with an amino acid sequence and molecular mass (1028.5193 Da) is given below HVMTLNLGEΚ Determine the maximum number of positive charges of this peptide. а. b. Determine the possible m/z ratio of this peptide at different charge states.
A range of substituted biphenyls have been evaluated as antagonists of the GPCR neurokinin-1 (NK1) , a target for the treatment of cancer chemotherapy endured nausea and vomiting. With reference to table 1, discuss the structure activity relationships related to the nature of the substituent R1 and linker group L. In your answer, aim not just to identify trends, but to give possible explanations to them. Include as much detail as possible.
The aromatic side chain of Trp residues in proteins and peptides can be chemically modified by two photochemical reactions using ultraviolet light (hv) at 20°C (Figure 1). hv CCI3CO₂H (10 mm), Buffer A (pH 8.0) O HO HN HN- O A. Acidic NH ww O B. Basic O c. Hydrophobic O D. Polar neutral OB. Indole NH ww Figure 1 Photochemical reactions of Trp side chain with CHCl3 and CCI₂CO₂H O A. Imidazole Each substitution on Trp replaces one hydrogen atom attached to a carbon somewhere on the indole ring. Photochemical modification percentages of various Trp residues in carbonic anhydrase at 20°C are shown in Table 1. Table 1 Photochemically Modified in Carbonic Anhydrase Reactant Buffer W4 W15 W96 W122 W190 W207 W243 51% 0% 44% A 37% 0% 0% CHCI 3 0% CHCI₂ B 0% 0% 0% 0% 0% 0% 55% CCI,CO₂H A 72% 66% 0% 100% 100% 0% 75% O c. Pyrimidine OD. Pyrrole hv W15 and W96, which are in the interior of carbonic anhydrase, are 21% and 29% modified respectively by 10 mM CHCl3 in Buffer A at 75°C, a temperature…
One of the reasons for oxidizing the disulfide bonds in RNase A before removing the urea in the Anfinsen experiment was to demonstrate that ... Urea promotes disulfide bond exchange O Incorrectly-folded proteins lose their enzymatic activity. Urea prevents disulfide bond formation. Urea forms thio-esters with reduced cysteines at pH 8.2 Disulfide bonds are required for enzyme activity.
What is the first thing that must occur in order for the catalysis of the peptide bond to begin. What is a specificity pocket? What are the preferences of chymotrypsin due to its specificity pocket?

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