Orientations of Proteins in Membranes database
Encyclopedia
Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane protein
structures
with respect to the lipid bilayer
. Positions of the proteins are calculated using an implicit solvation model
of the lipid bilayer. The results of calculations were verified against experimental studies of spatial arrangement of transmembrane
and peripheral
proteins in membranes.
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
, MDL Chime
and WebMol.
The database was widely used in experimental and theoretical studies of membrane-associated proteins. However, structures of many membrane-associated proteins are not included in the database if they can not be computationally predicted. 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.
Membrane protein
A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. More than half of all proteins interact with membranes.-Function:...
structures
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
with respect to the lipid bilayer
Lipid bilayer
The lipid bilayer is a thin membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around cells. The cell membrane of almost all living organisms and many viruses are made of a lipid bilayer, as are the membranes surrounding the cell nucleus...
. Positions of the proteins are calculated using an implicit solvation model
Implicit solvation
Implicit solvation is a method of representing solvent as a continuous medium instead of individual “explicit” solvent molecules most often used in molecular dynamics simulations and in other applications of molecular mechanics...
of the lipid bilayer. The results of calculations were verified against experimental studies of spatial arrangement of transmembrane
Transmembrane protein
A transmembrane protein is a protein that goes from one side of a membrane through to the other side of the membrane. Many TPs function as gateways or "loading docks" to deny or permit the transport of specific substances across the biological membrane, to get into the cell, or out of the cell as...
and peripheral
Peripheral membrane protein
Peripheral membrane proteins are proteins that adhere only temporarily to the biological membrane with which they are associated. These molecules attach to integral membrane proteins, or penetrate the peripheral regions of the lipid bilayer. The regulatory protein subunits of many ion channels and...
proteins in membranes.
Proteins structures are taken from the Protein Data Bank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
. OPM also provides structural classification of membrane-associated proteins into families and superfamilies, membrane topology
Membrane topology
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...
, quaternary structure
Quaternary structure
In biochemistry, quaternary structure is the arrangement of multiple folded protein or coiling protein molecules in a multi-subunit complex.-Description and examples:...
of proteins in membrane-bound state, and the type of a destination membrane
Biological membrane
A biological membrane or biomembrane is an enclosing or separatingmembrane that acts as a selective barrier, within or around a cell. It consists of a lipid bilayer with embedded proteins that may constitute close to 50% of membrane content...
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
Jmol
Jmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...
, MDL Chime
MDL Chime
MDL Chime is a free plugin used by web browsers to display the three dimensional structures of molecules. It is part of the ISIS product line acquired by Symyx Technologies from scientific publisher Elsevier in October 2007. It is based on the RasMol code.Chime is used by a wide range of...
and WebMol.
The database was widely used in experimental and theoretical studies of membrane-associated proteins. However, structures of many membrane-associated proteins are not included in the database if they can not be computationally predicted. This is the case when all membrane-anchoring parts of the proteins (amphiphilic alpha helices, exposed nonpolar residues, or lipidated amino acid residues
Lipid anchored protein
In lipid-anchored proteins, a covalently attached fatty acid such as palmitate or myristate serves to anchor them to either face of the cell membrane. Examples include G proteins and certain kinases. It is believed that the fatty acid chain inserts and assumes a place in the bilayer structure of...
) are missing in the experimental structures.