Small molecules are used as inhibitors of protein action - as drugs. They most often do thisby blocking the active site within the protein. Potential drugs can be screenedcomputationally to determine if they are strongly bound to the protein.Figure 1 shows a possible conformation of a candidate drug molecule, 4-bromo-2-carboxymethylamide-pyrrole (abbreviation: BCMAP) at the active site of a protein(abbreviation: PR). Figure 2 shows the full protein structure whilst figure 3 shows a knowninhibitor of the protein at the site, overlayed with another calculated conformer of BCMAP.(c) Outline how you would investigate whether BCMAP would be an effective inhibitorfor the protein in competition with the molecules that the protein normally targets,and any solvent.Figure 1. 4-bromo-2-carboxymethylamide-pyrrole (BCMAP) (C, N, O, and Br atoms in yellow, blue,red, and brown, respectively) in the active site of the protein structure. Figure 2. Cartoon (ribbon) structure of the entire protein with a known inhibitor in position, asdetermined experimentally. Cations and water molecules in the protein structure are omitted forclarity. The links labelled can be cleaved chemically.lle1122CleavableLinksLeul120Tyr1167Asn1168Val1174Prol110Figure 3. An overlay of a known inhibitor (from Figure 2) and an example conformer of BCMAP. Dashedlines indicate hydrogens bonds and electrostatic interactions. The isolated cyan atoms are sodiumcations and the isolated red atoms the determined positions of the oxygen in a water molecule.

Inhibitors are the molecules that slow down or completely block the protein activity of molecules,…

Answered: (c) Outline how you would investigate…

Biochemistry

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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

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8L.Part I
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Find a method that uses some form of HPLC for the analysis of proteins. What was the stationary phase used? How does this kind of stationary phase separate the proteins? What kind of mobile phase was used? Was the method isocratic or was a gradient used? How were the proteins detected?
detail how cation exchange chromatography works and what you would use to elute your target protein. What protein information would you need to facilitate this approach? Would you need to do any protein engineering to utilize cation exchange chromatography, justify your answer?
The Graph below shows the binding curves of two proteins (A and B) for the same ligand (L). Use this Graph and determine the dissociation constant, K, for both proteins. Which protein (A or B) has a greater affinity for ligand L? Which of the two proteins would be more easily inhibited by an antagonist? 1.0 Y 0.5 2 A 4 6 B 8 [L] (μM) 10 12 14 16
When it comes to the sensitivity of the sensors, which one will be more preferred as a biosensor, the one with high sensitivity or with the low sensitivity ? Explain the reason with examples.
Please name the differences between competitive and noncompetitive inhibition.
VI. Although most biologically relevant sugars have the D-configuration, L-fucose is a commonly observed monosaccharide component in glycoproteins. Glycosylated antibodies (IgGs) observed in patients with active TB have more fucose than those found in patients with latent TB (Lu et. al., 2016). Latent TB occurs when a person has the TB bacteria, but bacterial proliferation is kept under control by the body's immune system; hence, the infected person is asymptomatic and not infectious. A person with latent TB will test positive for the tuberculin test or TB blood test. a) L-fucose is also known as 6-deoxy-L-galactose. Note that D-galactose is a C-4 epimer of D-glucose. Draw the Fisher projections for D-glucose, D-galactose and L-fucose. (Hints: D- and L-isomers are enantiomers. 6-deoxy means that the hydroxyl group at C-6 is removed leaving just the methyl group). D-galactose: D-glucose: L-fucose (6-deoxy-L-galactose): b) L-fucose can cyclize into a pyranose and form two anomers. Draw…
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2
2. “Most enzymes are gene-encoded proteins." Using this lens, explain: A) effects of increased temperature on the rate of enzymatic reactions, and B) effects of decreased temperature on enzymatic reactions, and C) importance of optimal pH and ionic strength on enzymatic reactions.

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(c) Outline how you would investigate whether BCMAP would be an effective inhibitor for the protein in competition with the molecules that the protein normally targets, and any solvent.