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Orientations of Proteins in Membranes database

February 27, 2023

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]

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 centerUniversity of Michigan College of Pharmacy
Primary citationPMID 16397007
Release date2005
Access
Data formatmodified PDB format
Websitehttp://opm.phar.umich.edu
Download URLOPM files
Tools
WebServer for calculating positions of proteins in membranes
Miscellaneous
LicenseCC-BY 3.0
Version2.0
Curation policyCurated

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 2013-06-02 at the Wayback Machine 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" (PDF). Bioinformatics. 22 (5): 623–625. doi:10.1093/bioinformatics/btk023. PMID 16397007.
  3. ^ 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.
  4. ^ 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.
  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. PMC 3089899. 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. PMC 3091260. 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. PMC 3637887. 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. Bibcode:2001Sci...291.1793K. doi:10.1126/science.291.5509.1793. PMID 11230696.
  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.
  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. S2CID 5704597.
  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. Bibcode:2007BpJ....92..473M. doi:10.1529/biophysj.106.092775. PMC 1751395. PMID 17056731.
  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. PMC 1934899. 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. PMC 1808586. 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. PMC 2242517. PMID 16641489.
  18. ^ . Archived from the original on 2013-12-25. Retrieved 2007-06-20.

February 27, 2023
orientations, proteins, membranes, database, orientations, proteins, membranes, database, provides, spatial, positions, membrane, protein, structures, with, respect, lipid, bilayer, positions, proteins, calculated, using, implicit, solvation, model, lipid, bil. 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 Orientations of Proteins in MembranesContentDescriptionThe database provides spatial arrangement of proteins in the lipid bilayerData typescapturedProtein structures from the PDBOrganismsAllContactResearch centerUniversity of Michigan College of PharmacyPrimary citationPMID 16397007Release date2005AccessData formatmodified PDB formatWebsitehttp opm phar umich eduDownload URLOPM filesToolsWebServer for calculating positions of proteins in membranesMiscellaneousLicenseCC BY 3 0Version2 0Curation policyCuratedProteins 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 a 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 Angstrom Resolution J Mol Biol 364 4 716 734 doi 10 1016 j jmb 2006 09 022 PMC 1808586 PMID 17028020 Pali 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 Retrieved from https en wikipedia org w index php title Orientations of Proteins in Membranes database amp oldid 1070327517, wikipedia, wiki, book, books, library,

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