Omicron ja delta variantti sekä wt Wuhan sars-2 CoV vertailtuna rakenteellisilta ominaisuuksiltaan

Sars-2 viruksesta saatiin  viime vuonna hyviä luetteloita sen interaktiotaipumuksista ihmisen proteomin kanssa. Yli 320 proteiinia ihmiseltä lueteltiin niissä taulukoissa. Nyt alan etsiä, minkälaisia interaktioita tekee  omikron, koska se on  hieman eriävä  entisistä varianteista, mutta ei vielä ole varsinaisia taulukoita saatavilla. Sen sijaan löydän artikkelin, jossa vertaillaan alkuperäistä wild type virusta  deltan ja omikronin kanssa.  Otan sitaatin näistä mielenkiintoisista ja olennaisista havainnoista.

 https://www.biorxiv.org/content/10.1101/2021.12.02.470946v1.full

Omicron and Delta Variant of SARS-CoV-2: A Comparative Computational Study of Spike protein

View ORCID ProfileSuresh Kumar, Thiviya S. Thambiraja, View ORCID ProfileKalimuthu Karuppanan, View ORCID ProfileGunasekaran Subramaniam

doi: https://doi.org/10.1101/2021.12.02.470946

Now published in Journal of Medical Virology doi: 10.1002/jmv.27526

(Sitaatti  tiivistelmöstä) 

 We used computational studies to examine the Delta and Omicron variants in this work and found that the Omicron variant had a higher affinity for human ACE2 than the Delta variant due to a significant number of mutations in the SARS-CoV-2 receptor binding domain, indicating a higher potential for transmission. Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2. In comparison to the Delta variant, both the entire spike protein and the RBD in Omicron include a high proportion of hydrophobic amino acids such as leucine and phenylalanine. These amino acids are located within the protein’s core and are required for structural stability. Omicron has a higher percentage of alpha-helix structure than the Delta variant in both whole spike protein and RBD, indicating that it has a more stable structure. We observed a disorder-order transition in the Omicron variant between spike protein RBD regions 468-473, and it may be significant in the influence of disordered residues/regions on spike protein stability and binding to ACE2. A future study might investigate the epidemiological and biological consequences of the Omicron variant.

 (Koska artikkeli selventää monia  proteiinin luonnehtimiseen käytettyjä menetelmiä ja variabeleita , otan sitaatteja tuloksista myös). 

( Sitaatti)

 From a previous study, it is observed that RBD T470-T478 loop and Y505 as viral determinants for specific recognition of SARS-CoV-2 RBD by ACE2 ²⁸. T478 is a common mutation seen in Delta and Omicron variants (Figure 2). RBD has the potential to be developed into an efficient and safe subunit vaccine against SARS-CoV-2 due to its ability to produce very robust nAb responses. Numerous mutations in the spike protein’s receptor-binding region in Omicron compared to the Delta variant (Figure 3) suggests that the Omicron variant may be immunologically resistant to antibody-mediated protection (Table 1).

 

 (Sitaatti)

Analysis of physicochemical parameter

The Wuhan-Hu-1 (wild type), delta, and omicron variant sequences were analysed using the ExPASy ProtParam online tool. ProtParam calculates the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, anticipated half-life, instability index, aliphatic index, and grand average of hydropathicity (GRAVY).

(Huom. tässä tulee mielenkiintoisia tuloksia !!)