PMC

A space-filling model of a typical phospholipid bilayer.

An example of an α-helical bundle integral membrane protein (halorhodopsin from Halobacterium salinarum).

A plot of the potentials of the bilayer potentials (in units of kcal mol⁻¹) for the charged amino acids.

Validation results for FILM2 potential function applied to decoy sets based on (a) bacteriorhodopsin and (b) rhodopsin.

Dendrogram of the sequences shown in based solely on the pairwise correlation coefficients of the variphobicity scores.

Diagrammatic representation of an integral membrane (transmembrane) protein. The first two helices fully span both leaves of the bilayer, but the third helix (typically an amphipathic helix) is shown not fully penetrating the bilayer.

(a) FILM model for glycophorin A (predicted transmembrane helix from T93 to I118); (b) superposition of FILM model with NMR model (RMSD=3.6 Å); (c) FILM model of subunit C of the F1Fo ATPase (predicted transmembrane helices from E2 to R41 and from L48 to A77); (d) superposition of FILM model with NMR model (RMSD=4.2 Å); (e) FILM model of major fd coat protein (predicted transmembrane helix from W49 to T69 and predicted amphipathic helix from A32 to A41); and (f) superposition of FILM model with NMR model (RMSD=4.8 Å).

An outline of the decoy generation procedure using a polyhedral model of transmembrane helix bundles (). In the first step, different tracings are generated through a hexagonal close packed lattice (packed cylinder model). Tracings that violate obvious structural constraints (e.g. loops too short to make a particular connection) are eliminated. Given a tracing through the lattice, helix axes are generated taking into account the normal packing angles between helices in close packed helix bundles. Finally, using these axes, alpha-carbon coordinates are generated by means of distance geometry and real-space refinement.