Computational protocol: Direct visualization of the small hydrophobic protein of human respiratory syncytial virus reveals the structural basis for membrane permeability

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Protocol publication

[…] Purified SH-FLAG fusion protein was applied to copper grids in PBS/1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), or in liposomes. Samples were blotted, negatively stained using 3% ammonium molybdate, and examined using a Tecnai F20 at a magnification of 62 000. Images were aligned and classified to generate groups of equivalently orientated projections. Separate class-averages were generated using SPIDER and IMAGIC programs . [...] SH protein secondary structure was predicted using MEMSAT3 and PSIPRED and monomer models built using Maestro (Schrodinger). Models were energy minimized with residues 15-38 defined as the trans-membrane domain. Multiple monomers were aligned, with clusters of polar trans-membrane residues facing the pore lumen, and rearranged to regain symmetry and energy minimized as before. […]

Pipeline specifications

Software tools MEMSAT, PSIPRED
Application Protein sequence analysis
Organisms Human orthopneumovirus, Hydrangea ringspot virus, Homo sapiens
Diseases Respiratory Tract Diseases