UC San Diego

The influenza A virus surface hemagglutinin (HA) plays the critical role in governing the viral adaptation of a human host by switching binding specificity from long [alpha]-2, 3 to long α-2, 6 sialylated glycans receptors. The relationship between HA receptor binding domain (RBD) mutation and HA-glycan binding specificity, however, is not well understood due to varying experimental results. The human 1918 pandemic virus, A/South Carolina/1/18 (SC18) and its D190E/D225G avian-type mutant (AV18*) serves as an excellent paradigm for mutagenesis investigation of the molecular mechanisms of the double mutation, which has been qualitative and limited to visual inspection of superimposed crystal structures. In this study, a computational approach that integrates explicit molecular dynamics (MD) simulations, statistical glycan conformational clustering analysis, molecular mechanics- Generalized Born surface area (MM-GBSA) residue based pairwise energy decomposition and molecular mechanics- Poisson-Boltzmann Surface Area (MM-PBSA) binding free energy calculation was developed. Using this approach, key HA-glycan residue interactions and relative overall binding free energies of SC18, AV18*, a 2009 swine-origin like S145K/A227E double mutant (CA18*), and CA04 bound to physiological [alpha]-2, 3 and [alpha]-2, 6 sialylated glycans receptors at atomic level have been identified. The structural and energetic data reveal the markedly distinct binding patterns of SC18 and AV18*, the deterministic role of residue 190 in anchoring sialic acid and the auxiliary role of residue 225 coupled with [alpha] -2, 3/[alpha]-2, 6 linkage. Furthermore, destabilization of D190 by A227E and increased importance of the 130-loop in the RBD causes an increase of overall [alpha]-2, 3/ [alpha]-2, 6 binding in CA18* and swine-origin A/ California/04/2009 (CA04)