Problems

Introduction

1)a. What should authors try to accomplish with the introduction to this research paper?

b. Do the authors make a case for why this is an important study?

c. The authors are looking at a specific domain of a larger protein. Give two reasons for the focus on the selected domain. 

d. What are the overall goals of this study?

e. Briefly describe (or list) the primary techniques the authors used and the basic information they gained or hoped to gain from that technique. 

Results

2) Define the meaning of the following terms.

  • Far-UV (with respect to CD)
  • Ellipticities
  • Cm
  • Tm
  • GuHCl
  • Red-shift

3) The authors produced a model by protein fold recoginition. Why did they not produce a model based on sequence homology?

4) Answer the following questions regarding Figure 3a.

a. What type of spectrum is shown in the figure?
b. What part of the protein is reponsible for the observed signal (spectrum).
c. What information about the protein is gained from the analysis? (See table 2)
d. What other analysis did the authors use to estimate secondary stucture content of the protein? *

5) Answer the following questions regarding figure 4.

a. The authors state in the experimental section that "the typical two-state transition (N U) was presumed ..."
Do the results from the equilibrium unfolding experiments support this presumption?

b. For figure 4a. What is the fluorophor in this study? Is it intrinsic or extrinsic? Using figure 4a describe the effect of unfolding in GuHCl on the fluorescence spectrum of the protein (represent the change with a rough sketch of the fluorscence spectrum at 3 or 4 GuHCl concentrations). From your previous experience with fluorescence spectroscopy and protein folding provide a brief explanation for the observed changes.

c. What other information was derived from the plots in figure 4? (See table 1)

6) Answer the following questions regarding figure 2.

a. Using figures 2a and 2b, describe the effect of increasing temperature on the observed fluorescence spectrum of the protein.

b. The authors noted a slight difference in the observed changes in thermal vs chemical denaturation. What was the observed difference and what is the explanation for the difference?

Discussion/Critique

7) What experimental results were explicited used to support the proposed structural model?

8) What experimental results were not well-connected (at least explicitely in the discussion) to the proposed structural model?

9) List 3-4 other parameters that the authors could have used to support the validity of their molecular model.

10) The authors state the following at the end of the instroduction. "Among these 14 residues, the 10 residues from Lys344 to Phe501 are positioned in the ACE-2 binding fragment and the last three residues are located in the major immunodominant site." How did the authors use this observation to support the validity of theor model?

 


* The accession number for the spike glycprotein is Q6T7Y1. Using the ProtScale tools on expasy analyze regions of the Sb1 domain for secondary structure propensity to confirm the results shown in Fig 7.

For instance, you might want to select residues 300 - 350 for analysis. You may use the Chou/Fasman or Deleage/Roux scales.

http://www.uniprot.org/uniprot/Q6T7Y1