Encyclopedia > Orientations of Proteins in Membranes database
 A peripheral protein from the OPM database (P40phox PX domain of of NADPH oxidase). Middle plane of the lipid bilayer - black dots. Boundary of the hydrocarbon core region - blue dots (intracellular side). Layer of lipid phosphates - yellow dots. Orientations of Proteins in Membranes (OPM) database provides spatial positions of protein three-dimensional structures with respect to the lipid bilayer. [1] [2]. The database was used in experimantal and theoretical studies of membrane-associated proteins [3] [4] [5][6] [7] Perhipheral and Integral Membrane Proteins Peripheral membrane proteins are proteins that adhere only loosely to the biological membrane with which they are associated. ...
A diagonal molecular slab from the DPPC lipid bilayer simulation1; color scheme: PO4 - green, N(CH3)3 - violet, water - blue, terminal CH3 - yellow, O - red, glycol C - brown, chain C - grey. ...
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. The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. ...
Implicit solvation (sometimes known as continuum solvation) is a method of representing solvent in molecular dynamics simulations and molecular mechanics (e. ...
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 Structural Classification of Proteins (SCOP) database is a largely manual classification of proteins based on similarities which can be observed in their amino acid sequences and three-dimensional structures. ...
In biochemistry, the membrane topology of an transmembrane protein describes which portions of the amino-acid sequence of the protein lie within the plane of the surrounding lipid bilayer and which portions protrude into the watery environment on either side. ...
It has been suggested that Net flux be merged into this article or section. ...
The site allows visualization of protein structures with membrane boundary planes through Jmol, MDL Chime and WebMol. Jmol is molecule viewer for use in chemistry and biochemistry. ...
MDL Chime is a plugin used by web browsers to display the three dimensional structures of molecules. ...
Advantages This is the only database that includes structures of peripheral membrane proteins. Calculated positions of proteins are compared with relevant experimental data whenever possible. Wikipedia does not yet have an article with this exact name. ...
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. Wikipedia does not yet have an article with this exact name. ...
The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. ...
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
- ^ 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.
See also A transmembrane protein is a protein that spans the entire biological membrane. ...
An Integral Membrane Protein (IMP) is a protein molecule (or assembly of proteins) that is permanently attached to the biological membrane. ...
Peripheral membrane proteins are proteins that adhere only temporarily to the biological membrane with which they are associated. ...
External links
OPM database
Reviews Science is the journal of the American Association for the Advancement of Science (AAAS). ...
Other related resources |
Feeds |
Contact