Orientations of Proteins in Membranes database
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 experimantal and theoretical studies of membrane-associated proteins [4] [5] [6][7] [8]
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 [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 [14]
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 [3]
Notes
- ↑ Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: Orientations of Proteins in Membranes database. Bioinformatics 22, 623-625. Full text
- ↑ Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI (2006) Positioning of proteins in membranes: A computational approach. Protein Science 15, 1318-1333. Full text
- ↑ 3.0 3.1 3.2 Lomize AL, Pogozheva ID, Lomize MA and Mosberg HI. The role of hydrophobic interactions in positioning of peripheral proteins in membranes BioMed Central Structural Biology 2007, 7:44 Full text online
- ↑ Park Y, Helms V. On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins. Bioinformatics 23: 701-708. 2007
- ↑ Marsh D, Jost M, Peggion C, et al. TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes. Biophys. J. 92 (2): 473-481. 2007
- ↑ Punta M, Forrest LR, Bigelow H, et al. Membrane protein prediction methods. Methods 41 (4): 460-474. 2007
- ↑ Cherezov V, Yamashita E, Liu W, et al. In meso structure of the cobalamin transporter, BtuB, at 1.95 angstrom resolution. J. Mol. Biol. 364 (4): 716-734. 2006
- ↑ Pali T, Bashtovyy D, Marsh D. Stoichiometry of lipid interactions with transmembrane proteins - Deduced from the 3D structures. Protein. Sci. 15 (5): 1153-1161. 2006.
- ↑ Malmberg N, Falke J (2005). "Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains". Annu Rev Biophys Biomol Struct. 34: 71–90. PMID 15869384.
- ↑ Spencer A, Thuresson E, Otto J, Song I, Smith T, DeWitt D, Garavito R, Smith W (1999). "The membrane binding domains of prostaglandin endoperoxide H synthases 1 and 2. Peptide mapping and mutational analysis". J Biol Chem. 274 (46): 32936–42. PMID 10551860.
- ↑ Lathrop B, Gadd M, Biltonen R, Rule G (2001). "Changes in Ca2+ affinity upon activation of Agkistrodon piscivorus piscivorus phospholipase A2". Biochemistry. 40 (11): 3264–72. PMID 11258945.
- ↑ Kutateladze T, Overduin M (2001). "Structural mechanism of endosome docking by the FYVE domain". Science. 291 (5509): 1793–6. PMID 11230696.
- ↑ Tatulian S, Qin S, Pande A, He X (2005). "Positioning membrane proteins by novel protein engineering and biophysical approaches". J Mol Biol. 351 (5): 939–47. PMID 16055150.
- ↑ Hristova K, Wimley WC, Mishra VK, Anantharamiah GM, Segrest JP, White SH. (1999). "An amphipathic alpha-helix at a membrane interface: a structural study using a novel X-ray diffraction method". J Mol Biol. 290 (1): 99–117. PMID 10388560. Unknown parameter
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See also
External links
OPM database
Reviews
- ST NetWatch: Protein Databases review of OPM in Signal Transduction NetWatch list from Science
- 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