A peripheral protein from the OPM database (P40phox PX domain of NADPH oxidase). Middle plane of the lipid bilayer - black dots. Boundary of the hydrocarbon core region - blue dots (intracellular side). Layer of lipid phosphates - yellow dots.

Orientations of Proteins in Membranes (OPM) database provides spatial positions of protein three-dimensional structures with respect to the lipid bilayer.^[1][2][3] The database was used in experimental and theoretical studies of membrane-associated proteins^{[4][5][6][7][8]}

[edit] Description

Proteins structures are taken from the Protein Data Bank. Positions of the proteins in a hydrophobic slab are calculated using the implicit solvation model.

OPM provides structural classification of membrane-associated proteins into families and superfamilies (based on SCOP classification), membrane topology, and the type of a destination membrane for each protein. All protein coordinate files with calculated membrane boundaries are freely downloadable.

The site allows visualization of protein structures with membrane boundary planes through Jmol, MDL Chime and WebMol.

[edit] Advantages

This database provides spatial positions of transmembreane and peripheral membrane proteins in the lipid bilayer, along with PDBTM database that includes only transmembrane proteins. Calculated positions of proteins have been compared with relevant experimental data for 24 tranmembrane and 53 peripheral membrane proteins^[3] including site-directed spin labeling,^[9] chemical labeling, measurement of membrane binding affinities of protein mutants,^[10] fluorescence spectroscopy,^[11] solution or solid-state NMR spectroscopy,^[12] ATR FTIR spectroscopy,^[13] and X-ray or neutron diffraction studies of proteins in lipid bilayers^[14]

[edit] Deficiencies

The set of peripheral membrane proteins in OPM is incomplete. The database probably includes less than 50% of peripheral proteins from the Protein Data Bank, because membrane-anchoring elements of peripheral proteins (amphiphilic alpha helices, exposed nonpolar residues, or lipid anchors) are missing or disordered in the experimental protein structures, and therefore the mode of protein-membrane association can not be computationally predicted^[3].

Another feature is the use of only one "representative" PDB entry for every protein complex, unlike PDBTM that includes all crystal structures of the same protein in the PDB. The "representative" structure of each protein was selected as one with the "most complete coverage" (smallest total length of disordered segments in the crystal structure, or a quarternaly complex with the larger number of subunits), rather than a structure determined with the highest resolution.

[edit] Notes

[edit] See also

• Transmembrane protein
• Integral membrane protein
• Peripheral membrane protein

[edit] External links

[edit] OPM database

• Official site

[edit] Reviews

• ST NetWatch: Protein Databases review of OPM in Signal Transduction NetWatch list from Science

[edit] Other related resources

• TCDB Transporter classification database from Milton H. Saier, Jr. laboratory
• TransportDB Genomics-oriented database of transporters from TIGR
• Membrane PDB Database of 3D structures of integral membrane proteins and hydrophobic peptides with an emphasis on crystallization conditions
• Integral membrane proteins of known 3D structure from Stephen White laboratory
• PDBTM All 3D models of transmembrane proteins currently in the PDB including theoretical models. Approximate positions of membrane boundary planes were calculated for each PDB entry.
• Membrane targeting domains (MeTaDoR)
• Antimicrobial Peptide Database