Computational studies of influenza hemagglutinin
Hemagglutinin (HA) is a viral membrane protein responsible for the initial steps of the entry of influenza virus into the host cell. It mediates binding of the virus particle to the host cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies. The fusion of two membranes is thermodynamically favourable, but involves high activation barriers and proceeds through several intermediate states. This thesis focuses on the molecular details of the large conformational changes that take place in HA to catalyze the membrane fusion process. It describes how molecular dynamics simulations are used to determine key amino acid interactions during the HA rearrangements and the free energy that a single HA can deliver.