Biology:Orientations of Proteins in Membranes database

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Orientations of Proteins in Membranes
Content
DescriptionThe database provides spatial arrangement of proteins in the lipid bilayer
Data types
captured		Protein structures from the PDB
OrganismsAll
Contact
Research centreUniversity of Michigan College of Pharmacy
Primary citationPMID 16397007
Release date2005
Access
Data formatmodified PDB format
Websitehttp://opm.phar.umich.edu
Download URLOPM files
Tools
Web applicationServer for calculating positions of proteins in membranes
Miscellaneous
Software licenseCC-BY 3.0
Version2.0
Curation policyCurated

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]

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

  1. ↑ ST NetWatch: Protein Databases review of OPM in Signal Transduction NetWatch list from Science
  2. ↑ Lomize, Mikhail A.; Lomize, Andrei L; Pogozheva, Irina D.; Mosberg, Henry I. (2006). "OPM: Orientations of Proteins in Membranes database". Bioinformatics 22 (5): 623–625. doi:10.1093/bioinformatics/btk023. PMID 16397007. http://opm.phar.umich.edu/OPM.pdf. 
  3. ↑ Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2006). "Positioning of proteins in membranes: A computational approach". Protein Science 15 (6): 1318–1333. doi:10.1110/ps.062126106. PMID 16731967. PMC 2242528. http://opm.phar.umich.edu/PPM.pdf. 
  4. ↑ 4.0 4.1 4.2 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". BMC Structural Biology 7 (44): 44. doi:10.1186/1472-6807-7-44. PMID 17603894. PMC 1934363. http://opm.phar.umich.edu/PSALM.pdf. 
  5. ↑ 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. PMID 21438609. 
  6. ↑ 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. PMID 21438606. 
  7. ↑ 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. PMID 15869384. 
  8. ↑ 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. 
  9. ↑ 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. 
  10. ↑ Kutateladze, Tatiana; Overduin, Michael (2001). "Structural Mechanism of Endosome Docking by the FYVE Domain". Science 291 (5509): 1793–1796. doi:10.1126/science.291.5509.1793. PMID 11230696. Bibcode: 2001Sci...291.1793K. 
  11. ↑ 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. https://zenodo.org/record/894918. 
  12. ↑ 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. 
  13. ↑ 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. 
  14. ↑ 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. doi:10.1529/biophysj.106.092775. PMID 17056731. Bibcode: 2007BpJ....92..473M. 
  15. ↑ 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. PMID 17367718. 
  16. ↑ 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. PMID 17028020. 
  17. ↑ 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. PMID 16641489. 
  18. ↑ "PDBTM: Protein Data Bank of Transmembrane Proteins". http://pdbtm.enzim.hu/. 



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