Orientations of Proteins in Membranes database

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

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]

  1. ^ ST NetWatch: Protein Databases Archived 2013-06-02 at the Wayback Machine review of OPM in Signal Transduction NetWatch list from Science
  2. ^ Cite error: The named reference OPM-cite was invoked but never defined (see the help page).
  3. ^ Cite error: The named reference OPM1 was invoked but never defined (see the help page).
  4. ^ a b c Cite error: The named reference peripheral was invoked but never defined (see the help page).
  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. ^ Cite error: The named reference Malmberg was invoked but never defined (see the help page).
  8. ^ Cite error: The named reference Spencer was invoked but never defined (see the help page).
  9. ^ Cite error: The named reference Lathrop was invoked but never defined (see the help page).
  10. ^ Cite error: The named reference Kuta was invoked but never defined (see the help page).
  11. ^ Cite error: The named reference Tatulian was invoked but never defined (see the help page).
  12. ^ Cite error: The named reference Hristova was invoked but never defined (see the help page).
  13. ^ Cite error: The named reference park-helms was invoked but never defined (see the help page).
  14. ^ Cite error: The named reference marsh-jost-peggion was invoked but never defined (see the help page).
  15. ^ Cite error: The named reference pfb-2007 was invoked but never defined (see the help page).
  16. ^ Cite error: The named reference cyl-2006 was invoked but never defined (see the help page).
  17. ^ Cite error: The named reference pbm-2006 was invoked but never defined (see the help page).
  18. ^ "PDBTM: Protein Data Bank of Transmembrane Proteins". Archived from the original on 2013-12-25. Retrieved 2007-06-20.