Part 1. Using the data provided on the table below answer questions 1 Protein Li
ID: 211154 • Letter: P
Question
Part 1. Using the data provided on the table below answer questions 1 Protein Ligand Binding reaction conditions Mg is present Mgis not present Kd (M) NU1 NU1 NU1 NU5 NU5 NU5 5 X 10 2.2 X 10 9.0 X 10 6 X 10 3.9 X 10 4 X 10 Ompl Ompl Omplp R89A Ompl Ompl Omplp R89A In the table above R89A means that an arginine amino acid (single letter code R) is normally at position 89 in the amino acid sequence but is replaced by an alanine amino acid (single letter code A). This change was a result of a change in the DNA gene sequence for Omplp such that this new amino acid is put into the protein at that position instead of the "normal" amino acid that was originally in that position. la. Which protein ligand combination shows the highest affinity? Explain your choice Mg is present Mgis present Mg is not Mg is present ent lb. Which protein ligand combination shows the lowest affinity? Explain your choice lc. If you had 1.5 uM of the NU5 ligand with 0.03 uM of the Omplp protein present and with Mg present, what fraction of your ligand binding sites would be occupied? ld. What are the two most likely explanations you would provide to explain the difference in Kd values observed between Omplp with Mg + present and with Mg not present with the NU1 ligand? 1e. What are the two most likely explanations you would provide to explain the difference in Kd values observed between Omplp with Mg present and Omplp R89A with Mg present with the NU5 ligand?Explanation / Answer
1a) Omp1p + NU5 has highest affinity as it has the lowest Kd.
1b) Omp1pR89A + NU1 has lowest affinity as has the highest Kd.
1c) fraction of binding site occupied = [conc. of ligand]/ [conc. Of ligand]+Kd
In this case, the answer is 5/7
1d) the protein and ligand show less affinity in presence of Magnesium ion the probable reasons may be The ion has more affinity towards the protein thus acting as an inhibitor.
1e) out of the two Omp1p + NU5 has more Kd than the other ligand protein group mentioned in the question. Reason is the former has less affinity towards the thus more Kd as compared to later.
Also, it may be possible