Classification
OPM consists of quaternary complexes (biological units) that are classified based on the structure of their main transmembrane or membrane-associated domain. The classification was built using SCOP and TCDB, but it differs from both systems in certain aspects. There are four levels of hierarchy in the classification:
- Type: transmembrane proteins, monotopic/peripheral proteins, or membrane-active peptides.
- Class: all-α, all-β, α+β, α/β, or nonregular proteins.
- Superfamily: evolutionarily related proteins with superimposable 3D structures.
- Family: proteins with detectable sequence homology.
OPM allows sorting of membrane proteins by hydrophobic thicknesses, tilt angles, destination membranes, number of transmembrane helices or subunits, structural family and superfamily, or biological source.
The proposed method can reliably distinguish transmembrane and integral monotopic proteins from peripheral and non-membrane proteins based on their transfer energies and penetration depths into the lipid bilayer.
Figure 3. Hydrophobic thickness or membrane penetration depth vs transfer energy (ΔGtransf) plot for membrane proteins. For hydrophobic non-membrane proteins both calculated values are close to zero.
