The outer shell of a virus is called a capsid—it is there to surround and protect the genetic material of the virus, and it enables the virus to infect another cell. The capsid attaches to the cell and inserts the genetic material inside, allowing the virus essentially to take over and begin replication. This capsid shell is assembled with a series of protein interactions, the specific processes of which are still unknown. Questions such as what factors in these proteins are necessary for assembly, and whether there is any possibility of external control (such as blocking it from happening) are currently being studied.
Dr. Hagan has created a computational model of capsid assembly that he believes will help answer some of these questions. In his model, he can alter parameters and make the capsid more or less likely to form a complete, working structure. In this way, he can observe the dynamics of the protein interactions individually. The parameters he can play with include binding energy, angle tolerance, concentration, and time; a change in any of these will alter capsid formation. When the parameters are finely tuned, the proteins will interact, binding and unbinding, searching for the optimal connections. As these connections are found, the proteins begin to form a sphere—beginning with a ring of proteins of which each has two bonds, making it stable. This ring is the basis of the nucleus, and the rest of the capsid forms around it.
When the parameters are changed, the dynamics of the interactions change. More of the less-optimal connections, which would have been broken in the finely tuned model, will stay bound, and the capsid will contain multiple defects. These defects prevent the capsid from forming a closed structure. Therefore, very narrow parameters are needed for the viral capsid shell to assemble properly. Since the virus needs a properly assembled capsid to attach and infect a cell, this model could help to find ways to stop a virus from replicating.
