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Literature summary for 3.4.17.23 extracted from

  • Chen, P.; Wang, J.; Xu, X.; Li, Y.; Zhu, Y.; Li, X.; Li, M.; Hao, P.
    Molecular dynamic simulation analysis of SARS-CoV-2 spike mutations and evaluation of ACE2 from pets and wild animals for infection risk (2022), Comput. Biol. Chem., 96, 107613 .
    View publication on PubMedView publication on EuropePMC
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Application

Application Comment Organism
medicine among 226000 SARSCoV-2 sequences, 1573 missense mutations are found in the spike gene, and 226 of them were within the receptor-binding domain region that directly interacts with human ACE2. Modeling shows that most of the 74 missense mutations in the receptor-binding domain region of the interaction interface have little impact on spike binding to ACE2, whereas several within the spike receptor-binding domain increase the binding affinity toward human ACE2 thus making the virus likely more contagious Homo sapiens
medicine among 226000 SARSCoV-2 sequences, 1573 missense mutations are found in the spike gene, and 226 of them were within the receptor-binding domain region that directly interacts with human ACE2. Modeling shows that most of the 74 missense mutations in the receptor-binding domain region of the interaction interface have little impact on spike binding to ACE2, whereas several within the spike receptor-binding domain increase the binding affinity toward human ACE2 thus making the virus likely more contagious Mus musculus
medicine among 226000 SARSCoV-2 sequences, 1573 missense mutations are found in the spike gene, and 226 of them were within the receptor-binding domain region that directly interacts with human ACE2. Modeling shows that most of the 74 missense mutations in the receptor-binding domain region of the interaction interface have little impact on spike binding to ACE2, whereas several within the spike receptor-binding domain increase the binding affinity toward human ACE2 thus making the virus likely more contagious Paguma larvata
medicine among 226000 SARSCoV-2 sequences, 1573 missense mutations are found in the spike gene, and 226 of them were within the receptor-binding domain region that directly interacts with human ACE2. Modeling shows that most of the 74 missense mutations in the receptor-binding domain region of the interaction interface have little impact on spike binding to ACE2, whereas several within the spike receptor-binding domain increase the binding affinity toward human ACE2 thus making the virus likely more contagious Manis javanica

Organism

Organism UniProt Comment Textmining
Homo sapiens Q9BYF1
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Manis javanica
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Mus musculus Q8R0I0
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Paguma larvata Q56NL1
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General Information

General Information Comment Organism
physiological function interaction between SARS-CoV-2 and ACE2. Most mouse ACE2 receptors (including rats and mice) show higher binding free energies than the human ACE2, indicating weaker binding to the SARS-CoV-2 spike. The mole ACE2 has a similar binding free energy to the human ACE2 due to their high sequence identity at the binding interface to the SARS-CoV-2 spike protein Mus musculus
physiological function interaction between SARS-CoV-2 and ACE2. The binding free energy of SARS-CoV-2 spike protein to the civet ACE2 is -5.11 kcal/mol, i.e. a lower binding affinity than human ACE2. Compared with the human ACE2 molecule, the civet ACE2 has a substitution from phenylalanine to serine at position 40 in the first helix at the N-terminal lobe region. This mutation breaks the pi-pi stacking interactions between the N-terminal helices, resulting in the side-chain rearrangement and loose helix-packing structures Paguma larvata
physiological function interaction between SARS-CoV-2 and ACE2. The binding free energy of SARS-CoV-2 spike protein to the human ACE2 is -60.64 kcal/mol on average. ACE2 residues Tyr41 and Tyr83 contribute most to the spike binding affinity for both SARS-CoV-2 and SARS-CoV. Residues Met82, Gly354, and Asp355 also have substantial contributions to the binding free energy between spike protein and ACE2 Homo sapiens
physiological function interaction between SARS-CoV-2 and ACE2. The binding free energy of SARS-CoV-2 spike protein to the pangolin ACE2 is -54.78 kcal/mol, i.e. a lower binding affinity than human ACE2. Compared with the human ACE2 molecule, the pangolin ACE2 has a substitution from Aso to Glu at position 38. This transformation has a significant impact on the hydrogen bond network in the left recognition region Manis javanica