International scientists have been racing to find a cure for the novel coronavirus with its genetic structure as a focal point, similar to how vaccines of pervious viruses have been developed. Even though much remains unknown about the virus, a team of researchers was able to release a fully accessible atomic model of the SARS-CoV-2 'spike,' or 'S,' protein.
All viruses attach and enter host cells within the body via protein structures. The spike, or S, the protein of coronavirus is what attaches to human cells and then multiply to spread a deadly infection.
Scientists from Seoul National University in South Korea, the University of Cambridge in the UK, and Lehigh University in the United States have collaborated to create an 'all-atom model of the S protein's full length that can be accessed online by anyone.' This is vital information for vaccine and protein-targeted antibiotic developments as the S protein plays a prominent role in cell entry.
The model-building online program is accessible on CHARMM-GUI's website where viewers can see the gene structure of the spike protein. Developed by Professor Wonpil Im, from Lehigh University's Department of Biological Sciences and Bioengineering Department, the program is a biomolecular systems simulator or a 'computational microscope.'
Full Access
The Chemistry at Harvard Macromolecular Mechanics (CHARMM) program is an online graphical user interface (GUI) with various programs, developed by Harvard professors. All programs are free and fully accessible by all viewers. Im's new research has already had more than one million global views.
Professor Im allows scientists to view COVID-19 proteins in a way that cannot be viewed otherwise and even includes several molecular levels. 'Our models are the first fully-glycosylated full-length SARS-CoV-2 spike (S) protein models that are available to other scientists,' he said.
'I was fortunate to collaborate with Dr. Chaok Seok from Seoul National University in Korea and Dr. Tristan Croll from the University of Cambridge in the U.K. Our team spent days and nights to build these models very carefully from the known cryo-EM structure portions. Modeling was very challenging because there were many regions where simple modeling failed to provide high-quality models.'
The design allows researchers to save time on building a molecular structure of the virus and focus more on finding a cure or ways of preventing infection. Im explains that studying viruses and vaccinations purely on experiments and human trials is quite challenging. A better way is when experiments are accompanied by molecular structure models.
Translocation
Currently, Professor Im is working on another genetic analysis called translocation, or when chromosomes rearrange as a result of mutation. Chromosome parts are exchanged between two non-identical chromosomes, resulting in new linkages.
He is looking specifically into the manner that bacteria respond to antibiotic drugs. Im is challenged by the concept of drug resistance that people have developed. He has queried over why there hasn't been a new type of antibiotic in the past 30 years, saying 'that's pretty scary.'
Modeling the two layers of bacteria membrane remains a specialized area of study that only a handful of scientists, including Im, is able to create. He and his team will be releasing their translocation research on CHARM-GUI and make it fully accessible as well.
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