Information from electron microscope images and protein databases has been used to develop a detailed 3D model of SARS-CoV-2, which can be readily updated as new data becomes available. The modeling tool has potential for visualizing components in other biological organisms, ranging from 10 to 100 nanometers in size.
“Our 3D model demonstrates the current state-of-the-art structure of SARS-CoV-2 at the atomistic level and reveals details of the virus that were previously impossible to see, like how we think nucleocapsid proteins form a rope-like structure inside it,” says KAUST research scientist Ondřej Strnad. “The approach we used to develop the model could steer biological research into new, promising directions for fighting the spread of COVID-19, as it could help scientists rapidly incorporate newly discovered information into the model and thus provide an up-to-date structure of the virus,” he says.
The modeling system is intuitive and easy to use. It takes information from readily discernible structures in a small number of electron microscope images of an organism. For SARS-CoV-2, this involved information on the shape and size of the virus’s membrane and on the protein structures attached to it.
Scientists can then incorporate information into the model about other proteins within the cell from existing databases. This included information on SARS-CoV-2’s single RNA strand and the nucleocapsid proteins protecting it. Finally, a set of rules is created that defines how each of the components is oriented and interacts with the others. “The system uses the provided information to predict the overall shape of the cell and generate a 3D model,” explains Strnad.
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