BIOL 3410 Cell Biology Fall 2021 Section 3.
Assignment 1 (57 points)
This assignment is based on the paper published by Lan et al. (2020), which is available in the Assignment 1 folder on D2L. You will need to refer to that paper as you complete this assignment.
Lan et al. (2020) set out to determine the crystal structure of the SARS-CoV-2 spike protein in complex with the ACE2 protein as a way to better understand the molecular interactions between these two structures, and to set the groundwork for developing neutralizing antibodies against SARS-CoV-2. Figure 1 of the paper shows a diagram of the viral spike protein.
- Did the authors express the entire ACE2 and SARS-CoV-2 spike proteins in order to generate their crystal? (1 point)
- The Authors used a 6-His tag to help purify the proteins of interest prior to crystallization. What is this and how does it work? (Yes, you’ll have to look this up). (2 points)
- What do the acronyms ACE2, RBD, and RBM mean? (3 points)
- Figures 1(b) and 1(c) show ribbon diagrams of the ACE2 and SARS-CoV-2 spike protein structures in a binding complex with each other. What is the main secondary structural motif seen in the ACE2 protein? (2 points).
- What types of secondary structure are seen in the SARS-CoV-2 RBD model? (2 points).
- What is the arrangement (parallel or antiparallel) of the secondary structural element in the core of the SARS-CoV-2 spike protein? (1 point).
- The SARS-CoV-2 RBD protein is stabilized by four covalent interactions between amino acid side chains. What amino acid is involved in these interactions and what is this bond usually referred to as? (2 points)
- How long is the beta3 strand of the SARS-Co-V2 RBD protein (region T…R)? (1 point)
- How many of the beta3 strand amino acid side chains are theoretically capable of hydrogen bonding? (3 points)
- If all hydrogen bonding amino acids in the beta3 region were replaced with alanine, would you expect the structure to be more or less stable? Explain your answer. (4 points).
- Which end (N terminus or C terminus) of the ACE2 protein does the CARS-CoV-2 RBM interact with? (1 point).
- Does the ACE2 structure feature any covalent bonds between amino acid side chains and if so, what is their likely purpose? (3 points).
Figure 2 shows a detailed image and alignment of the interacting regions of SARS-CoV-2 and ACE2.
- There is an interaction between Lys417 of SARS-CoV-2 and Asp30 of ACE2. Draw a diagram of how these two amino acid side chains might interact at physiological pH. What type of interaction is this? (4 points)
- The paper compares the interaction of ACE2 with the RBDs of SARS-CoV-2 and the related corona virus SARS-CoV. Based on the data published, are these interactions identical and what does this mean when understanding the relatedness of these two corona viruses? (4 points).
Table 1 summarizes the amino acid interactions between SARS-CoV-2 and ACE2.
- Draw a diagram demonstrating how Gly502 of SARS-CoV-2 could hydrogen bond with Lys353 of ACE2. Is this an interaction between the two amino acid side chains, and if not, why not? (4 points).
- During the original SARS outbreak in 2003, a series of neutralizing monoclonal antibodies were developed that could bind to the SARS-CoV spike protein and help fight viral infection. Unfortunately, these previously characterized antibodies do not bind to SARS-CoV-2. Why is this so, considering the striking similarity between the two viral strains? (3 points).
- If you were in charge of a SARS-CoV-2 antibody development program at the CDC, how might you set about finding neutralizing antibodies that specifically bound to this current corona virus (note that there’s more than one way to do this – show me your creative thinking). (6 points).
Go to the following website: https://www.rcsb.org/3d-view/6M0J. Play around with the image. It should look familiar.
- What is the normal function of ACE2? (yes, you’ll have to look this up). (2 points).
- What do you notice about the tertiary structure of ACE2? (2 points).
- Insert a time-stamped screenshot of the ACE2 protein to illustrate your answer to question 20 (2 points)
- Why do you think this particular protein shape might facilitate its normal function? (3 points).
- What quaternary components are in the ACE2 protein that might help it to function? (2 points).