Identification of the pore-lining residues of the BM2 ion channel protein of influenza B virus.

The influenza B virus BM2 proton-selective ion channel is essential for virus uncoating, a process that occurs in the acidic environment of the endosome. The BM2 channel causes acidification of the interior of the virus particle, which results in dissociation of the viral membrane protein from the ribonucleo-protein core. The BM2 protein is similar to the A/M2 protein ion channel of influenza A virus (A/M2) in that it contains an HXXXW motif.

Protein-protein docking with multiple residue conformations and residue substitutions.

The protein docking problem has two major aspects: sampling conformations and orientations, and scoring them for fit. To investigate the extent to which the protein docking problem may be attributed to the sampling of ligand side-chain conformations, multiple conformations of multiple residues were calculated for the uncomplexed (unbound) structures of protein ligands. These ligand conformations were docked into both the complexed (bound) and unbound conformations of the cognate receptors, and their energies were evaluated using an atomistic potential function.

Novel pulse-delayed scheme for degenerate optical parametric amplification in chi((3)) waveguides.

We describe a novel pulse-delayed scheme to realize degenerate optical parametric amplification in chi((3)) planar waveguides. The scheme utilizes two identical birefringent plates placed before and after a chi((3)) planar waveguide to implement a single-arm, pulse-multiplexed nonlinear Mach-Zehnder interferometer. Using this scheme, we demonstrate ultrafast degenerate optical parametric amplification in AlGaAs waveguides.