Homology modelling could provide approximate structures of proteins encoded by the SARS-CoV-2 genome
Structure is often the first point of reference for biologists wishing to understand the mode of action or mechanism of a biological phenomenon given that binding between biomolecules often dictate course of biological phenomenon. Biomolecules do not randomly bind each other, rather, there are specific rules encoded in three-dimensional space that dictate whether one biomolecule or protein would bind to another. Such rules are determined typically by experimental structural biology approaches such as X-ray crystallography or cryo-electron microscopy. But, not all protein structures could be determined in good time such as the case during this SARS-CoV-2 pandemic where efforts in structural biology are geared towards elucidating the structures of spike protein and RNA-dependent RNA polymerase. In the absence of experimental structures, structural homology modelling may be able to offer a helping hand in delivering approximate structures useful for understanding the mechanism of action of particular protein encoded in the virus genome. Not exact, but useful, structural homology modelling by the online Phyre2 server may be used to obtain the homology structures of all the proteins encoded by the genome of SARS-CoV-2 downloaded from GenBank. Overall, experimental structures take time to obtain typically due to inadequate sample preparation. In the time of the current SARS-CoV-2 pandemic, structural homology modelling could step into the fold to provide approximate structures of less often studied proteins encoded by the virus genome, that, may offer a hitherto not understood path to understanding disease pathogenesis mechanism perpetuated by the coronavirus.
