Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane protein structures with respect to the lipid bilayer.[1][2][3][4] Positions of the proteins are calculated using an implicit solvation model of the lipid bilayer.[5][6] The results of calculations were verified against experimental studies of spatial arrangement of transmembrane and peripheral proteins in membranes.[4][7][8][9][10][11][12]
| Content | |
|---|---|
| Description | The database provides spatial arrangement of proteins in the lipid bilayer |
| Data types captured | Protein structures from the PDB |
| Organisms | All |
| Contact | |
| Research center | University of Michigan College of Pharmacy |
| Primary citation | PMID 16397007 |
| Release date | 2005 |
| Access | |
| Data format | modified PDB format |
| Website | http://opm.phar.umich.edu |
| Download URL | OPM files |
| Tools | |
| Web | Server for calculating positions of proteins in membranes |
| Miscellaneous | |
| License | CC-BY 3.0 |
| Version | 2.0 |
| Curation policy | Curated |
Proteins structures are taken from the Protein Data Bank. OPM also provides structural classification of membrane-associated proteins into families and superfamilies, membrane topology, quaternary structure of proteins in membrane-bound state, and the type of a destination membrane for each protein. The coordinate files with calculated membrane boundaries are downloadable. The site allows visualization of protein structures with membrane boundary planes through Jmol.
The database was widely used in experimental and theoretical studies of membrane-associated proteins.[13][14][15][16][17] However, structures of many membrane-associated proteins are not included in the database if their spatial arrangement in membrane can not be computationally predicted from the three-dimensional structure. This is the case when all membrane-anchoring parts of the proteins (amphiphilic alpha helices, exposed nonpolar residues, or lipidated amino acid residues) are missing in the experimental structures.[4] The database also does not include lower resolution structures with only main chain atoms provided by the Protein Data Bank. The calculated spatial arrangements of the lower resolution protein structures in the lipid bilayer can be found in other resources, such as PDBTM.[18]
References
edit- ^ ST NetWatch: Protein Databases Archived 2013-06-02 at the Wayback Machine review of OPM in Signal Transduction NetWatch list from Science
- ^ Lomize, Mikhail A.; Lomize, Andrei L; Pogozheva, Irina D.; Mosberg, Henry I. (2006). "OPM: Orientations of Proteins in Membranes database" (PDF). Bioinformatics. 22 (5): 623–625. doi:10.1093/bioinformatics/btk023. PMID 16397007.
- ^ Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2006). "Positioning of proteins in membranes: A computational approach" (PDF). Protein Science. 15 (6): 1318–1333. doi:10.1110/ps.062126106. PMC 2242528. PMID 16731967.
- ^ a b c Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2007). "The role of hydrophobic interactions in positioning of peripheral proteins in membranes" (PDF). BMC Structural Biology. 7 (44): 44. doi:10.1186/1472-6807-7-44. PMC 1934363. PMID 17603894.
- ^ Lomize, AL; Pogozheva, ID; Mosberg, HI (2011). "Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects". Journal of Chemical Information and Modeling. 51 (4): 918–929. doi:10.1021/ci2000192. PMC 3089899. PMID 21438609.
- ^ Lomize, AL; Pogozheva, ID; Mosberg, HI (2011). "Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes". Journal of Chemical Information and Modeling. 51 (4): 930–946. doi:10.1021/ci200020k. PMC 3091260. PMID 21438606.
- ^ Malmberg, Nathan J.; Falke, Joseph 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. doi:10.1146/annurev.biophys.34.040204.144534. PMC 3637887. PMID 15869384.
- ^ Spencer, Andrew G.; Thuresson, Elizabeth; Otto, James C.; Song, Inseok; Smith, Tim; DeWitt, David L.; Garavito, R. Michael; Smith, William L. (1999). "The membrane binding domains of prostaglandin endoperoxide H synthases 1 and 2. Peptide mapping and mutational analysis". J Biol Chem. 274 (46): 32936–32942. doi:10.1074/jbc.274.46.32936. PMID 10551860.
- ^ Lathrop, Brian; Gadd, Martha; Biltonen, Rodney L.; Rule, Gordon S. (2001). "Changes in Ca2+ affinity upon activation of Agkistrodon piscivorus piscivorus phospholipase A2". Biochemistry. 40 (11): 3264–3272. doi:10.1021/bi001901n. PMID 11258945.
- ^ Kutateladze, Tatiana; Overduin, Michael (2001). "Structural Mechanism of Endosome Docking by the FYVE Domain". Science. 291 (5509): 1793–1796. Bibcode:2001Sci...291.1793K. doi:10.1126/science.291.5509.1793. PMID 11230696.
- ^ Tatulian, Suren A.; Qin, Shan; Pande, Abhay H.; He, Xiaomei (2005). "Positioning membrane proteins by novel protein engineering and biophysical approaches". J Mol Biol. 351 (5): 939–947. doi:10.1016/j.jmb.2005.06.080. PMID 16055150.
- ^ Hristova, Kalina; Wimley, William C.; Mishra, Vinod K.; Anantharamiah, G.M.; Segrest, Jere P.; White, Stephen H. (2 July 1999). "An amphipathic α-helix at a membrane interface: a structural study using a novel X-ray diffraction method". J Mol Biol. 290 (1): 99–117. doi:10.1006/jmbi.1999.2840. PMID 10388560. S2CID 5704597.
- ^ Park, Yungki; Helms, Volkhard (2007). "On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins". Bioinformatics. 23 (6): 701–708. doi:10.1093/bioinformatics/btl653. PMID 17237049.
- ^ Marsh, Derek; Jost, Micha; Peggion, Cristina; Toniolo, Claudio (2007). "TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes". Biophys. J. 92 (2): 473–481. Bibcode:2007BpJ....92..473M. doi:10.1529/biophysj.106.092775. PMC 1751395. PMID 17056731.
- ^ Punta, Marco; Forrest, Lucy R.; Bigelow, Henry; Kernytsky, Andrew; Liu, Jinfeng; Rost, Burkhard (2007). "Membrane protein prediction methods". Methods. 41 (4): 460–474. doi:10.1016/j.ymeth.2006.07.026. PMC 1934899. PMID 17367718.
- ^ Cherezov, V; Yamashita, E; Liu, W; Zhalnina, M; Cramer, WA; Caffrey, M (8 December 2006). "In Meso Structure of the Cobalamin Transporter, BtuB, at 1.95 Ångstrom Resolution". J. Mol. Biol. 364 (4): 716–734. doi:10.1016/j.jmb.2006.09.022. PMC 1808586. PMID 17028020.
- ^ Páli, Tibor; Bashtovyy, Denys; Marsh, Derek (2006). "Stoichiometry of lipid interactions with transmembrane proteins - Deduced from the 3D structures". Protein Sci. 15 (5): 1153–1161. doi:10.1110/ps.052021406. PMC 2242517. PMID 16641489.
- ^ "PDBTM: Protein Data Bank of Transmembrane Proteins". Archived from the original on 2013-12-25. Retrieved 2007-06-20.