Orientations of Proteins in Membranes database
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Orientations of Proteins in Membranes (OPM) database provides spatial positions of protein three-dimensional structures with respect to the lipid bilayer. [1] [1]. [1]. The database was used in experimantal and theoretical studies of membrane-associated proteins [1] [1] [1][1] [1]
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.
Advantages
This is the only database that includes structures of peripheral membrane proteins. Calculated positions of proteins have been compared with relevant experimental data for 24 tranmembrane and 53 peripheral membrane proteins [1] including site-directed spin labeling,[1] chemical labeling, measurement of membrane binding affinities of protein mutants,[1] fluorescence spectroscopy,[1] solution or solid-state NMR spectroscopy,[1] ATR FTIR spectroscopy,[1] and X-ray or neutron diffraction studies [1]
Deficiencies
The set of peripheral membrane proteins in OPM is incomplete. The database probaly 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 [1]
Notes
See also
External links
OPM database
Reviews
- ST NetWatch: Protein Databases review of OPM in Signal Transduction NetWatch list from Science
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
Acknowledgement and Attribution Regarding Sources of Content
Some of the initial content on this page may be incorporated in part from copyleft sources in the public domain including wikis such as Wikipedia and AskDrWiki. Drug information for patients came from the The National Library of Medicine. Infectious disease information may have come from the Centers for Disease Control (CDC). Differential Diagnoses are drawn from clinicians as well as an amalgamation of 3 sources: 1.The Disease Database; 2. Kahan, Scott, Smith, Ellen G. In A Page: Signs and Symptoms. Malden, Massachusetts: Blackwell Publishing, 2004:3; 3. Sailer, Christian, Wasner, Susanne. Differential Diagnosis Pocket. Hermosa Beach, CA: Borm Bruckmeir Publishing LLC, 2002:7 .
