1E In terms of binding adenylate kinase, the Kd for ATP is ~50 M and the KI for GMP-PCP is ~50 nM. Explain how this may be possible in terms of molecular interactions. Name 4 different types of molecular interactions that may contribute to the increased binding affinity exhibited by GMP-PCP. Please help me in details
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1E
In terms of binding adenylate kinase, the Kd for ATP is ~50 M and the KI for GMP-PCP is ~50
nM. Explain how this may be possible in terms of molecular interactions. Name 4 different types
of molecular interactions that may contribute to the increased binding affinity exhibited by
GMP-PCP.
Please help me in details
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- 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 caseCrystal structures exist for three neurokinin-1 (NK1) ligand complexes with the following pdb codes (6hll, 6hlo,6hlp). State which is the highest quality crystal structure indicating the criteria you used to evaluate this.2. The two diagrams to the right il- lustrate plots of steady-state ki- 5FA 0.8 netic studies to characterize the in- nH = 3.5 0.6- teraction of heart muscle phos- phofructokinase-1 with a non-phy- siological, synthetic substrate fruc- tose-6-sulfate. Because the kcat is 0.4- 0.2- smaller than that for the natural 10 μΜ 20 μΜ 48 μΜ substrate, higher enzyme concen- trations could be used. The results show the influence of increasing 0.2 0.4 concentrations of ATP on the initial -0.6- > velocity of the enzyme catalyzed reaction in the presence of no -0.8 4 12 20 28 36 44 52 60 68 76 84 92 1.2 2.0 2.4 AMP (•), 10 µM AMP (•), 20 µM AMP (-), and 48 µM AMP (). [ΑΤPΙ (μM) log[ATP] (µM) (а) how ATP interacts with the enzyme in the case of no AMP (•). Write the reaction in words catalyzed by the enzyme for the alternative substrate, describe (b) with respect to the binding of AMP and ATP to the allosteric effector sites on the enzyme. Explain the physical significance of the displacement of the…
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- Small molecules are used as inhibitors of protein action - as drugs. They most often do this by blocking the active site within the protein. Potential drugs can be screened computationally 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 known inhibitor of the protein at the site, overlayed with another calculated conformer of BCMAP. (a) Explain what types of interactions, both intermolecular and intramolecular, that a molecular mechanics forcefield must be able to describe in order to be able to accurately determine the geometry of BCMAP in the protein. Identify which interactions will be the most important to describe accurately. Figure 1.4-bromo-2-carboxymethylamide-pyrrole (BCMAP) (C, N, O, and Br atoms in yellow, blue, red, and…3CLpro is a cysteine protease, which are among the most common proteases in biochemistry, however they are a structurally diverse family of enzymes especially in the organization of the active site amino acids. A group of scientists have reported a potential drug molecule based on a binding study using circular dichroism. They report that the molecule binds to the active site. Can the experiment support the claims, why or why not? Which techniques might be used to support this claim?An active site of a hypothetical serine protease with a peptide substrate bound is shown below: This serine protease has 3 specificity pockets (S1, S2, S1') as shown in the figure above. S1 pocket has a glutamic acid in the bottom, the S2 pocket is small and hydrophobic, and the S1' pocket is deep and hydrophobic. Based on this information you can conclude that R1 is most likely side chain of a. Asp b. Lys c. Lle d. Gly e. Phe