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These features could be potential targets for drug development, Aksimentiev said. The simulations did reveal common structural features and defects, particularly at the edges and corners of the capsid, where its shape has the greatest influence on the DNA inside. "This opens another dimension to looking at infectivity and whether these differences among viruses account for variability in their ability to infect." "These differences show that the concept of individuality is not exclusive to animals and plants but extends down to viruses, the most primitive form of gene-replicating structures," Aksimentiev said. We know the genetic sequence, but what was not known was the structure of the packaged genetic material inside."Ĭredit: University of Illinois at Urbana-Champaign We also know the structure of the capsid from experiments. "We know from experiments that the capsid has a portal, and there is a motor protein there that pushes the DNA in. It has been well-studied experimentally, so the Illinois group would be able to compare its simulations to what has been found previously, said Aksimentiev, who also is affiliated with the Beckman Institute of Advanced Science and Technology at Illinois. While the structures of many hollow capsids have been described, the structure of a full capsid and the genetic material inside it has remained elusive.įor this first look at a complete packaged viral genome, the researchers focused on HK97, a virus that infects bacteria. Viruses keep their genetic material-either DNA or RNA-packaged in a hollow particle called a capsid.
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"Knowledge of the internal structures gives us more targets for drugs, which tend to focus on receptors on the surface or replication proteins." We know what's inside in terms of components, but we don't know how they're arranged," said study leader Aleksei Aksimentiev, an Illinois professor of physics. "To fight a virus, we want to know everything there is to know about it. DOI: 10.1038/s41580-4Ī computational model of the more than 26 million atoms in a DNA-packed viral capsid expands our understanding of virus structure and DNA dynamics, insights that could provide new research avenues and drug targets, University of Illinois Urbana-Champaign researchers report in the journal Nature. Each streamline is colored by the local nematic order with white corresponding to zero order, and blue corresponding to the maximum order observed in the system. h, Streamlines of the nematic director field of select capsids reveal a distinct pattern for each genome. g, Example of a packaged genome featuring a baseball seam interface between early-packaged (blue) and late-packaged (red) DNA. f, Toroidal order of the packaged genome. The local nematic order (6 nm neighborhood), and the Frank–Oseen nematic energy calculated from the nematic director field. d, Quantification of switchback loops during packaging, including the absolute number of loops detected, the average loop length (note that loops may overlap) and the amount of the packaged DNA in at least one switchback loop. The DNA is colored by the instantaneous bend energy from 0 kcal mol −1 (red) to 1.5 kcal mol −1 (blue). The first switchback loop (cyan) is extruded by the packaging motor until growth of the loop stalls and the nascently packaged DNA buckles, forming a second loop (green). The three genome configurations depict the formation of two switchback loops (in cyan and green). Inset depicts a switchback loop with a highly curved center and two arms that remain within 6 nm. c, Switchback-loop formation during packaging. b, Internal pressure and energy during packaging and equilibration (Equil.) simulations.
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among eight independent packaging simulations (replicas) for each curve. Solid lines here and throughout the figure depict ensemble averages shaded regions depict the s.e.m. Bottom, the plots illustrate simulations of the packaging process (left) driven by the portal potential (inset) and of spontaneous ejection (right). a, Top, packaging of the HK97 genome at 4 bp per 2 bead resolution.