Influenza hemagglutinin (HA) is the most abundant surface antigen of the virus. Since there are 18 subtypes of HA with different antigenicity, there is a strong need to develop broadly neutralizing antibodies targeting multiple subtypes. In collaboration with the Wu Lab at the University of Illinois, Resource researchers reconstructed the structure of the complex between HA and a broadly neutralizing antibody on the viral membrane and simulated it with NAMD. The simulation results revealed membrane interactions for the antibody, which were then confirmed by mutagenesis experiments. The results are made recently available as a cover article in Structure and provide a foundation for rational design of more effective antibodies.

NAMD 3.1 (available in the Nightly Builds directory) now supports trajectory output for atom selections with different frequencies. This feature helps users save significant storage space by retaining high-frequency outputs only for regions of greatest interest and reduce the writing frequency for the rest of the system. The user can set different writing frequencies to different selections and compose trajectories as needed for analysis. The result is streamlined post-processing, easier segmented analysis by .dcd file, and faster data transfers.

Activation of coagulation factor X (FX) is arguably the most important step in the formation of blood clots. When tissues are damaged by external injury, FX activation is initiated by the formation of a complex between FVIIa and tissue factor, which binds and activates FX after anchoring into negatively charged cellular membranes. This key step involves the formation of a tripartite complex on the membrane, which was earlier modeled by Resource researchers and published in Blood Advances. In collaboration with the Ohi lab and Morrissey lab at the University of Michigan, the previous model is now largely confirmed by the first cryo-EM structure of the complex on the membrane, a study reported as a cover story in Blood.