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
Organisms All
Contact
Research center University of Michigan College of Pharmacy
Primary citation PMID   16397007
Release date2005
Access
Data format modified PDB format
Website http://opm.phar.umich.edu
Download URL OPM files
Tools
Web Server for calculating positions of proteins in membranes
Miscellaneous
License CC-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]

Related Research Articles

A transmembrane domain (TMD) is a membrane-spanning protein domain. TMDs may consist of one or several alpha-helices or a transmembrane beta barrel. Because the interior of the lipid bilayer is hydrophobic, the amino acid residues in TMDs are often hydrophobic, although proteins such as membrane pumps and ion channels can contain polar residues. TMDs vary greatly in size and hydrophobicity; they may adopt organelle-specific properties.

<span class="mw-page-title-main">Integral membrane protein</span> Type of membrane protein that is permanently attached to the biological membrane

An integral, or intrinsic, membrane protein (IMP) is a type of membrane protein that is permanently attached to the biological membrane. All transmembrane proteins can be classified as IMPs, but not all IMPs are transmembrane proteins. IMPs comprise a significant fraction of the proteins encoded in an organism's genome. Proteins that cross the membrane are surrounded by annular lipids, which are defined as lipids that are in direct contact with a membrane protein. Such proteins can only be separated from the membranes by using detergents, nonpolar solvents, or sometimes denaturing agents.

<span class="mw-page-title-main">Lipid bilayer</span> Membrane of two layers of lipid molecules

The lipid bilayer is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many viruses are made of a lipid bilayer, as are the nuclear membrane surrounding the cell nucleus, and membranes of the membrane-bound organelles in the cell. The lipid bilayer is the barrier that keeps ions, proteins and other molecules where they are needed and prevents them from diffusing into areas where they should not be. Lipid bilayers are ideally suited to this role, even though they are only a few nanometers in width, because they are impermeable to most water-soluble (hydrophilic) molecules. Bilayers are particularly impermeable to ions, which allows cells to regulate salt concentrations and pH by transporting ions across their membranes using proteins called ion pumps.

<span class="mw-page-title-main">Membrane protein</span> Proteins that are part of, or interact with, biological membranes

Membrane proteins are common proteins that are part of, or interact with, biological membranes. Membrane proteins fall into several broad categories depending on their location. Integral membrane proteins are a permanent part of a cell membrane and can either penetrate the membrane (transmembrane) or associate with one or the other side of a membrane. Peripheral membrane proteins are transiently associated with the cell membrane.

<span class="mw-page-title-main">Transmembrane protein</span> Protein spanning across a biological membrane

A transmembrane protein is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently undergo significant conformational changes to move a substance through the membrane. They are usually highly hydrophobic and aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of them (beta-barrels) can be also extracted using denaturing agents.

<span class="mw-page-title-main">Peripheral membrane protein</span> Membrane proteins that adhere temporarily to membranes with which they are associated

Peripheral membrane proteins, or extrinsic membrane proteins, are membrane proteins that adhere only temporarily to the biological membrane with which they are associated. These proteins attach to integral membrane proteins, or penetrate the peripheral regions of the lipid bilayer. The regulatory protein subunits of many ion channels and transmembrane receptors, for example, may be defined as peripheral membrane proteins. In contrast to integral membrane proteins, peripheral membrane proteins tend to collect in the water-soluble component, or fraction, of all the proteins extracted during a protein purification procedure. Proteins with GPI anchors are an exception to this rule and can have purification properties similar to those of integral membrane proteins.

<span class="mw-page-title-main">Membrane topology</span>

Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to the inner or outer sides of the biological membrane occupied by the protein.

<span class="mw-page-title-main">Antimicrobial peptides</span> Class of peptides that have antimicrobial activity

Antimicrobial peptides (AMPs), also called host defence peptides (HDPs) are part of the innate immune response found among all classes of life. Fundamental differences exist between prokaryotic and eukaryotic cells that may represent targets for antimicrobial peptides. These peptides are potent, broad spectrum antimicrobials which demonstrate potential as novel therapeutic agents. Antimicrobial peptides have been demonstrated to kill Gram negative and Gram positive bacteria, enveloped viruses, fungi and even transformed or cancerous cells. Unlike the majority of conventional antibiotics it appears that antimicrobial peptides frequently destabilize biological membranes, can form transmembrane channels, and may also have the ability to enhance immunity by functioning as immunomodulators.

<span class="mw-page-title-main">Inner mitochondrial membrane</span>

The inner mitochondrial membrane (IMM) is the mitochondrial membrane which separates the mitochondrial matrix from the intermembrane space.

<span class="mw-page-title-main">Phospholipid scramblase</span> Protein

Scramblase is a protein responsible for the translocation of phospholipids between the two monolayers of a lipid bilayer of a cell membrane. In humans, phospholipid scramblases (PLSCRs) constitute a family of five homologous proteins that are named as hPLSCR1–hPLSCR5. Scramblases are members of the general family of transmembrane lipid transporters known as flippases. Scramblases are distinct from flippases and floppases. Scramblases, flippases, and floppases are three different types of enzymatic groups of phospholipid transportation enzymes. The inner-leaflet, facing the inside of the cell, contains negatively charged amino-phospholipids and phosphatidylethanolamine. The outer-leaflet, facing the outside environment, contains phosphatidylcholine and sphingomyelin. Scramblase is an enzyme, present in the cell membrane, that can transport (scramble) the negatively charged phospholipids from the inner-leaflet to the outer-leaflet, and vice versa.

<span class="mw-page-title-main">Voltage-dependent anion channel</span> Class of porin ion channels in the outer mitochondrial membrane

Voltage-dependent anion channels, or mitochondrial porins, are a class of porin ion channel located on the outer mitochondrial membrane. There is debate as to whether or not this channel is expressed in the cell surface membrane.

<span class="mw-page-title-main">GLTP</span> Protein-coding gene in humans

Glycolipid transfer protein is a protein that in humans is encoded by the GLTP gene.

Protein–lipid interaction is the influence of membrane proteins on the lipid physical state or vice versa.

Hydrophobic mismatch is the difference between the thicknesses of hydrophobic regions of a transmembrane protein and of the biological membrane it spans. In order to avoid unfavorable exposure of hydrophobic surfaces to water, the hydrophobic regions of transmembrane proteins are expected to have approximately the same thickness as the hydrophobic region of the surrounding lipid bilayer. Nevertheless, the same membrane protein can be encountered in bilayers of different thickness. In eukaryotic cells, the plasma membrane is thicker than the membranes of the endoplasmic reticulum. Yet all proteins that are abundant in the plasma membrane are initially integrated into the endoplasmic reticulum upon synthesis on ribosomes. Transmembrane peptides or proteins and surrounding lipids can adapt to the hydrophobic mismatch by different means.

Mechanosensitive channels (MSCs), mechanosensitive ion channels or stretch-gated ion channels are membrane proteins capable of responding to mechanical stress over a wide dynamic range of external mechanical stimuli. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya. They are the sensors for a number of systems including the senses of touch, hearing and balance, as well as participating in cardiovascular regulation and osmotic homeostasis (e.g. thirst). The channels vary in selectivity for the permeating ions from nonselective between anions and cations in bacteria, to cation selective allowing passage Ca2+, K+ and Na+ in eukaryotes, and highly selective K+ channels in bacteria and eukaryotes.

<span class="mw-page-title-main">WALP peptide</span> Class of peptides used for studying lipid membranes

WALP peptides are a class of synthesized, membrane-spanning α-helices composed of tryptophan (W), alanine (A), and leucine (L) amino acids. They are designed to study properties of proteins in lipid membranes such as orientation, extent of insertion, and hydrophobic mismatch.

OMPdb is a dedicated database that contains beta barrel (β-barrel) outer membrane proteins from Gram-negative bacteria. Such proteins are responsible for a broad range of important functions, like passive nutrient uptake, active transport of large molecules, protein secretion, as well as adhesion to host cells, through which bacteria expose their virulence activity.

Stephen H. White is an American Biophysicist, academic, and author. He is a Professor Emeritus of Physiology and Biophysics at the University of California, Irvine.

Membranome database provides structural and functional information about more than 6000 single-pass (bitopic) transmembrane proteins from Homo sapiens, Arabidopsis thaliana, Dictyostelium discoideum, Saccharomyces cerevisiae, Escherichia coli and Methanocaldococcus jannaschii. Bitopic membrane proteins consist of a single transmembrane alpha-helix connecting water-soluble domains of the protein situated at the opposite sides of a biological membrane. These proteins are frequently involved in the signal transduction and communication between cells in multicellular organisms.

<span class="mw-page-title-main">Single-pass membrane protein</span> Transmembrane protein

A single-pass membrane protein also known as single-spanning protein or bitopic protein is a transmembrane protein that spans the lipid bilayer only once. These proteins may constitute up to 50% of all transmembrane proteins, depending on the organism, and contribute significantly to the network of interactions between different proteins in cells, including interactions via transmembrane alpha helices. They usually include one or several water-soluble domains situated at the different sides of biological membranes, for example in single-pass transmembrane receptors. Some of them are small and serve as regulatory or structure-stabilizing subunits in large multi-protein transmembrane complexes, such as photosystems or the respiratory chain. A 2013 estimate identified about 1300 single-pass membrane proteins in the human genome.

References

  1. ↑ ST NetWatch: Protein Databases Archived 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. 1 2 3 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. ↑ "PDBTM: Protein Data Bank of Transmembrane Proteins". Archived from the original on 2013-12-25. Retrieved 2007-06-20.
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