By Dr. Liji Thomas, MD Jul 21 2020
The pandemic of COVID-19 has spread rapidly and extensively, requiring urgent and intensive research to develop a vaccine as well as to design an antiviral preventive or therapeutic. These efforts require a complete understanding of viral structure.
Now, a new study by an international team of researchers and published on the preprint server bioRxiv * in July 2020 shows how this can be advanced at a greater speed by combining experimental results with homology models obtained by high-throughput pipelines. This will help produce new hypotheses that will show novel druggable targets for effective drug development.
The current study presents over 870 models of the structure of various proteins making up the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The sequencing and 3D data come from the latest entries in the protein database, which resemble any of the viral proteins by sequence. The researchers aligned the viral protein sequences to those of all 3D structures available in the PDB. They found that almost all the structures were those of viral proteins, but sometimes they were complexes of viral and host proteins. In a small number, they were of host proteins, indicating the virus was mimicking them.
These structures were then added to using prediction software to model the structure of over 32,700 proteins, and the whole set was then methodically explored to understand the features of these structures. They found only six proteins which showed evidence of binding to other proteins, structurally. These comprise two teams of three proteins each. Summary of all available 3D molecular structural knowledge for the viral proteome, as well as derived mimicry, hijacking, and protein interactions. Polyprotein 1a
This comprises non-structural protein (nsps) 1 to 10, with varying degrees of identity to the identified structures, from none, like nsp6, to nsp5, or 3CL-Pro, which was highly conserved and matched 2 CATH families, with 256 matching structures. Another region with multiple matches was the macrodomain region next to nsp2, and part of nsp3, with 144 matches.
Some were highly conserved, but others showed poor conservation. Polyprotein 1b
The five proteins from this region were all predicted to be highly ordered and to lack transmembrane helices. They include nsp 12 to nsp 16, with as few as four matches for nsp 14 and as many as 64 for nsp 13. Accessory Proteins and Capsid
The rest of the genome towards the 3’ end, encodes 12 proteins, which are assembled within the cell to form the nucleocapsid. None of these was found to bind to any related 3D structure. The structures with few matches include the ORF3a protein, the envelope protein, the ORF6 to ORF10, and ORF14. The Envelope Protein
This protein matched two structures from SARS-CoV, one a monomer and one an assembled pentameric protein of five identical units forming a transmembrane ion channel. Spike Protein
The researchers found 136 matches for this protein in 2 regions, one with 15 structures and matched to the C-terminal transmembrane helix, with four of the matches being with antibody complexes formed against MERS-CoV. The other had 121 matches, 34 almost full-length. These 34 formed a homodimer.
Of the 121, 68 were matched to antibody complexes and another two to complexes with inhibitory peptides. Others were complexed with human proteins, including the ACE2 receptor, with both ACE2 and other human proteins, and to other coronavirus antibodies.
Among all the capsid proteins, this was the only one that had matching structures but was bound to human proteins. The significance of this is that the capsid is mostly assembled within compartments inside the cell, and does not come into contact with host proteins or nucleic acid. There were still four unmatched regions in the region of the spike protein . The Nucleocapsid Protein
This N protein had 35 matches with known 3D structures, in two regions. One region at the N-terminal end contained structures mostly consisting of a single N protein monomer, but with some making up a dimer and one a tetramer. The other, near the C-terminus, had 13 matches, all dimeric structures. The Value of the Study
The study shows that very few instances of molecular mimicry by the virus of the host proteins were found. Hijacking or self-assembly was also rarely found. In fact, one graph was adequate to represent all such cases, indicating the lack of understanding of the virus’s structural proteins. Viral Proteins Team Up or Compete
The researchers suggest some interactions between the three proteins in each team.
Team 1 consists of nsp7, nsp8, and nsp12, all of which assemble to produce the viral protein complex in charge of RNA synthesis. Of these, nsp7 was found as a monomer in 2/15 matching structures available at present. Nsp8 was always complexed with nsp12 alone, nsp7 alone, or with both. However, nsp12 was found alone in 38 matching structures.
This finding agrees with older studies on SARS viruses, showing that nsp12 by itself acts as an RNA-dependent RNA polymerase, but shows immense enhancement when it interacts with nsp7 and nsp8. In short, team 1 is characterized by cooperative interactions. Related Stories
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