Exploring the Effect of SARS-CoV-2 Spike Protein Mutations on Viral Infectivity and Transmission
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SARS-CoV-2 is a virus that has caused the biggest global pandemic in recent history, beginning in 2020. COVID-19, the disease caused by this virus, has infected millions of people around the world.
Coronaviruses are a large family of viruses that are present in humans and a number of animals, including camels, goats, cats, and bats. They are named for the crown-like spikes on their surfaces. Human coronaviruses come in a number of forms, including those that cause common upper-respiratory-tract infections.
Like MERS-CoV and SARS-CoV, the SARS-CoV-2 virus is a beta coronavirus. The roots of all three viruses can be traced back to bats. The sequences from patients in the United States are identical to those from China, implying that this virus emerged recently from an animal reservoir. However, the virus's precise cause has yet to be discovered.
SARS-CoV-2 variants are circulating all over the world. In the fall of 2020, several new variants appeared, including:
A. D614G Mutation
B. The United Kingdom variant (UK)
C. The South African variant
Scientists are trying to learn more about these variants in order to better understand how quickly they can spread and how effective currently approved vaccines are against them.
This tutorial aims to provide molecular representations and animations to visualize and explore some of the spike protein mutations linked to high infectivity and transmission of the SARS-CoV- 2- virus.
The spike protein is located on the viral membrane of the SARS-COV-2 virus. The spike protein recognizes and binds to the ACE2 receptors of the host cell. The binding of the ACE2 receptors allows for the virus to infect the host.
How many subunits are present in the SARS-COV-2 Spike protein?
One Subunit
Two Subunits
Three Subunits
Four Subunits
There are a number of point mutations that occur in the spike protein that affect the infectivity and transmission of the virus. One of the main subunits of the SARS-COV-2 virus has the mutation D614G, which is one the main mutations that will be discussed in this tutorial. The other mutations are present in the subunit from the United Kingdom and the South African variant. One of the mutations present in both the United Kingdom and the South African variant is the N501Y mutation. The South African mutation also includes mutations K417N and E484K. The United Kingdom mutation includes the deletion of the amino acids at position 69 and 70.
What is a point mutation?
How would point mutations, insertions or deletions affect virus- host interactions? Discuss three potential outcomes.
The open and closed conformations of the spike proteins change to be more open with these mutations. The open conformation is required for angiotensin-converting enzyme 2 (ACE2) binding because the ACE2 binding site is partially shielded in the closed conformation (Fernández, 2020). SARS-CoV-2 enters via the ACE2 receptor by interacting with the glycoprotein spikes (Behl, 2020).
The aspartic acid in position 614 in essence acts as a latch that secures the two protomers together. A single amino acid change from aspartic acid to glycine (D614G) causes the spike protein to assume the open conformation more readily . This amino acid change disrupts the latch like interprotomer contact causing the protein to shift towards an open conformation (Fernández, 2020).
What is the strongest atomic bond?
Covalent
Ionic
Hydrogen
The various conformations of the latch are shown above. The unmutated closed conformation latch is shown with a flashing green to yellow hydrogen bond between the aspartate (shown with a flashing magenta color) at position 614 and the threonine at 859. The mutation D614G can be seen with a thin flashing cyan bond between the glycine at 614 and the threonine at 859. This represents the inability for a hydrogen bond to form as the distance is too great for one to form after the mutation. The open conformation of the mutated latch depicts how a hydrogen bond also cannot form due to the threonine 859 changing conformation to not be accessible for bonding with the aspartate at 859.
The ability of an antibody to interact with the receptor-binding domain (RBD) has a great deal to do with infectivity in general. Even after the mutation changes the latch confirmation, D614G is still potently neutralized by antibodies that target the receptor-binding domain. When tested, the monoclonal antibodies demonstrated similar neutralization potency against D614G as they did against D614. Overall, the D614G and D614 variants are considered equally sensitive to neutralization by human monoclonal antibodies targeting the S protein RBD (Fernández, 2020). However, D614G affinity for ACE2 is less than that of D614 because the D614 receptor-binding domain is more concealed.
The D614G has now become the wild type mutation in the population due to the high infectivity that occurs in the mutation. The D614G mutation occurs in the S1 and S2 subunits of the spike protein. The aspartic acid at position 614 in the non mutated strand makes a hydrogen bond in between the threonine at position 859. The nitrogen on the aspartic acid also forms a hydrogen bond with the position 647. The glycine mutation can not form a hydrogen bond with the threonine at position 859, however a hydrogen bond will not form which allows for more space in between position 614 and 859 than seen with the aspartic acid. This also leads to the mutant strand to have higher infectivity. The bond between 647 and 614 would strengthen with the mutation because the glycine is better oriented to the amino acid in position 647. The strengthening of the bond between 647 and 614 stabilizes the protein in the open conformation allowing easier binding to the cell receptors.
In the mutation D614G, an aspartic acid was changed to a glycine. Based on the chemical properties of these amino acids, how would this mutation affect biochemical interactions with amino acids present near position 614? Explain.
The aspartate at position 614 can be seen by a flashing magenta to light pink coloration in the animation. This is an important amino acid in the active site and plays a role in infectivity.
Mutation with 859 bond onlyAfter the mutation from an aspartate to a glycine as seen above, the distance between 614 and 859 lengthens which can be seen by the green bond.
What amino acid could you add at position 614 to mimic the properties of aspartic acid?
Lysine
Asparagine
Glutamic Acid
Alanine
Valine
The mutation causes a longer distance to form between the aspartate at 614 and the glycine at 859 while the distance between the glycine at 614 and the alanine at 647 shortens. It goes from a bond length 2.7 angstrom in the wildtype between D614 and T859 to 8.1 angstrom following the mutation to glycine. This is too long for a hydrogen bond to form. The measured bond length between D614 and A647 is 3.5 angstrom in the wild type, but shortens to 2.8 angstrom in the mutant. This means a stronger hydrogen bond forms.
The mutations E484K and K417N are both present in the South African variant. The positions 484 and 417 are in the receptor-binding domain (RBD) region of the spike protein. The mutations increase the affinity of the ACEs receptors which cause the higher infectivity with this mutation.
Mutations 417 and 484The glutamic acid at position 484 on chain A and the lysine at position 484 on the other chains are shown with a flashing cyan color change while the aspartate at position 417 are shown with magenta.
The deletion of position 69 and 70 in the spike protein is seen in the United Kingdom variant. The deletion of the amino acids at position 69 and 70 are located in the S1 subunit, and the deletion causes an allosteric shift in the conformation of the S1 subunit. (Xie, 2021) This conformation change causes a blockage of antibody interactions.
The Deletion of 69 and 70Histidine 69 and valine 70 are shown above. When the positions 69 and 70 are deleted then there is a conformational change.
The mutation N501Y is an emerging mutation that is present in both the United Kingdom and South African variants. The N501Y is a mutation located in the receptor-binding domain (RBD) that is the region of the spike protein that is responsible for recognizing and binding to the human cell. The mutation N501Y is specifically in the receptor-binding motif (RBM), which plays an important role for maintaining structural stability in the RBD. The mutation N501Y has a higher affinity for the ACEs receptors, however the exact bond relationship for why this happens is still unknown. (Ahmed, 2021)
Mutation 501The tyrosine at position 501 is highlighted by alternating color change from a light yellow to a magenta color.
Ahmed, Wesam, et al. 'Stable Interaction Of The UK B.1.1.7 Lineage SARS-CoV-2 S1 Spike N501Y Mutant With ACE2 Revealed By Molecular Dynamics Simulation.' BioRxiv, Cold Spring Harbor Laboratory, 1 Jan. 2021, www.biorxiv.org/content/10.1101/2021.01.07.425307v1.
Behl, Tapan, et al. 'The Dual Impact of ACE2 in COVID-19 and Ironical Actions in Geriatrics and Pediatrics with Possible Therapeutic Solutions.' Life Sciences, Elsevier Inc., 15 Sept. 2020, www.ncbi.nlm.nih.gov/pmc/articles/PMC7347488/.
Fernández, Ariel. (2020). Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. ACS Medicinal Chemistry Letters 11( 9):1667–1670.
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