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Encyclopedia > Transmembrane protein

A transmembrane protein is a protein that spans the entire biological membrane. Transmembrane proteins 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. A biological membrane or biomembrane is a membrane which acts as a barrier within or around a cell. ... To meet Wikipedias quality standards, this article or section may require cleanup. ...

Contents

Types

There are two basic types of transmembrane proteins:

  1. Alpha-helical. These proteins are present in all types of biological membranes including outer membranes. This is major category of transmembrane proteins.
  2. Beta-barrels. These proteins are found only in outer membranes of Gram-negative bacteria, cell wall of Gram-positive bacteria, and outer membranes of mitochondria and chloroplasts. All beta-barrel transmembrane proteins have simplest up-and-down topology, which may reflect their common evolutionary origin and similar folding mechanism.

Alpha-helical and beta-barrel transmembrane proteins have very different thermodynamic properties and folding mechanisms. A biological membrane or biomembrane is a membrane which acts as a barrier within or around a cell. ... Mitochondria structure : 1) Inner membrane 2) Outer membrane 3) Crista 4) Matrix The outer membrane refers to the outside membranes of Gram-negative bacteria, the chloroplast, or the mitochondria. ... Mitochondria structure : 1) Inner membrane 2) Outer membrane 3) Crista 4) Matrix The outer membrane refers to the outside membranes of Gram-negative bacteria, the chloroplast, or the mitochondria. ... Bacteria that are Gram-negative are not stained dark blue or violet by Gram staining, in contrast to Gram-positive bacteria. ... A cell wall is a more or less solid layer surrounding a cell. ... Gram-positive bacteria are those that are stained dark blue or violet by gram staining, in contrast to Gram-negative bacteria, which are not affected by the stain. ... Mitochondria structure : 1) Inner membrane 2) Outer membrane 3) Crista 4) Matrix The outer membrane refers to the outside membranes of Gram-negative bacteria, the chloroplast, or the mitochondria. ... In cell biology, a mitochondrion is an organelle found in the cells of most eukaryotes. ... Chloroplasts are organelles found in plant cells and eukaryotic algae which conduct photosynthesis. ...


Thermodynamic stability and folding

Transmembrane α-helical, transmembrane β-barrel, and typical water-soluble proteins have different thermodynamic stabilities and folding mechanisms. Unlike water soluble proteins that fold spontaneously in vitro, transmembrane proteins require help from numerous protein chaperones, because they must fold in a significantly more "difficult" and highly heterogeneous environment. In biology, chaperones are proteins whose function is to assist other proteins in achieving proper folding. ...


Stability of α-helical transmembrane proteins

Transmembrane α-helical proteins can be considered extremely stable based on their thermal denaturation studies because they do not unfold completely to the coil in membranes (such transition requires breaking down too many α-helical H-bonds in the nonpolar media). On the other hand, these proteins can very easily misfold due non-native aggregation in membranes, transition to the molten globule-like states, formation of non-native intermolecular disulfide bonds, or unfolding of peripheral regions and nonregular loops that are locally less stable. Denaturation is a structural change in biomolecules such as nucleic acids and proteins, usually caused by heat, acids, bases, detergents, or certain chemicals such as urea. ... In chemistry, a hydrogen bond is a type of attractive intermolecular force that exists between two partial electric charges of opposite polarity. ... A molten globule (MG) is a stable, partially folded protein structure found in mildly denaturing conditions such as low pH (generally pH = 2), mild denaturant, or high temperature. ... A disulfide bond (SS-bond), also called a disulfide bridge, is a strong covalent bond between two sulfhydryl groups. ...


This also depends on definition of the unfolded state. The unfolded state of membrane proteins in detergent micelles is different from that in the thermal denaturation experiments. It represents a combination of folded hydrophobic α-helices and partially unfolded segments covered by the detergent. For example, the unfolded state of bacteriorhodopsin in SDS micelles has only four transmembrane α-helices folded, while the remainder of the polypeptide chain is either coil and fully accessible to water or situated at the micelle-water interface and can adopt different types of non-native amphiphilic structures. The corresponding experimental free energy differences between such detergent-denatured and native states are relatively small and comparable with stabilities of water-soluble proteins. A denatured protein is one which has lost its functional conformation. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... Schematic of a micelle. ... Denaturation is a structural change in biomolecules such as nucleic acids and proteins, usually caused by heat, acids, bases, detergents, or certain chemicals such as urea. ... Bold textLink titleLink title Bacteriorhodopsin is the photosynthetic pigment used by archaea, most notably halobacteria. ... The initialism SDS can abbreviate: Satellite Data System Scientific Data Systems Secondary database server Serb Democratic Party Sodium dodecyl sulfate SDS-PAGE Students for a Democratic Society Slovenian Democratic Party Solstice Disksuite Sozialistischer Deutscher Studentenbund (Socialist German Student Union) A drill bit fixing system - see Chuck (engineering) Subdivision surface System... An amphipathic (a. ...


Folding of α-helical transmembrane proteins

Refolding of α-helical transmembrane proteins in vitro is technically difficult. There are relatively few examples of the successful refolding experiments, as for bacteriorhodopsin. In vivo all such proteins are normally folded co-translationally within the large transmembrane translocon. The translocon channel provides a highly heterogeneous envoronment for the nascent transmembane α-helices. A relatively polar amphiphilic α-helix can adopt a transmembrane orientation in the translocon (although it would be at the membrane surface or unfolded in vitro), because its polar residues can face the central water-filled channel of the translocon. Such mechanism is necessary for incorporation of highly polar α-helices into structures of transmembrane proteins. The amphiphilic helices remain attached to the translocon until the protein is completely synthesized and folded. If the proteins remains unfolded on the translocon for too long, they are recognized, modified, and degraded by specific "quality control" cellular systems. Bold textLink titleLink title Bacteriorhodopsin is the photosynthetic pigment used by archaea, most notably halobacteria. ... The translocon is the complex of proteins associated with the translocation of nascent polypeptides into the cisternal space of the endoplasmic reticulum from the cytosol. ...


Stability and folding of β-barrel transmembrane proteins

Stability of β-barrel transmembrane proteins is relatively low based on chemical denaturation studies, similar to water-soluble proteins. Their folding in vivo is facilitated by water-soluble (unlike the transmembrane translocon) chaperones, such as protein Skp [1]. The translocon is the complex of proteins associated with the translocation of nascent polypeptides into the cisternal space of the endoplasmic reticulum from the cytosol. ... In biology, chaperones are proteins whose function is to assist other proteins in achieving proper folding. ...


Classification of 3D structures

Light absorption-driven transporters

Bacteriorhodopsin-like proteins including rhodopsin [2] Bold textLink titleLink title Bacteriorhodopsin is the photosynthetic pigment used by archaea, most notably halobacteria. ... A rhodopsin molecule (yellow) with bound retinal (orange), embedded in a cell membrane (lipids shown as green, head groups as red/blue). ...


Bacterial photosynthetic reaction centres and photosystems I and II [3] An electron micrograph of a series of reaction centres and light harvesting complexes from the surface of the thylakoid membrane inside a chloroplast. ... REDIRECT [[In the process of photosynthesis, light is absorbed by a photosystem (ancient Greek: phos = light and systema = assembly) to begin an energy-producing reaction. ...


Light harvesting complexes from bacteria and chloroplasts [4] A light-harvesting complex is one or more polypeptide chains containing photosynthetic pigments, which surrounds a photosynthetic reaction centre and focuses light inward toward its core. ... Subgroups Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Bacteria (singular: bacterium) are microscopic, unicellular organisms. ... Chloroplasts are organelles found in plant cells and eukaryotic algae which conduct photosynthesis. ...


Oxidoreduction-driven transporters

Transmembrane cytochrome b-like proteins [5]: coenzyme Q - cytochrome c reductase (cytochrome bc1 ); cytochrome b6f complex; formate dehydrogenase, respiratory nitrate reductase; succinate - coenzyme Q reductase (fumarate reductase); and succinate dehydrogenase. See electron transport chain. CoQ Cytochrome c reductase The Coenzyme Q - cytochrome c reductase complex, sometimes called the cytochrome bc1 complex, and at other times Complex III, is the third complex in the electron transfer chain (PDB 1KYO, EC 1. ... CoQ Cytochrome c reductase The Coenzyme Q - cytochrome c reductase complex, sometimes called the cytochrome bc1 complex, and at other times Complex III, is the third complex in the electron transfer chain (PDB 1KYO, EC 1. ... The cytochrome b6f complex (plastoquinol—plastocyanin reductase; EC 1. ... Nitrate reducatse are group of enzymes which reduce nitrate to nitrite This article belongs in one or more categories. ... Succinate—coenzyme Q reductase (EC 1. ... Succinate - coenzyme Q reductase also called succinate dehydrogenase is an enzyme complex found in the matrix part of the inner mitochondrial membrane. ... The Electron Transport Chain. ...


Cytochrome c oxidases [6] from bacteria and mitochondria Cytochrome c oxidase The enzyme cytochrome c oxidase (PDB 2OCC, EC 1. ... Subgroups Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Bacteria (singular: bacterium) are microscopic, unicellular organisms. ... In cell biology, a mitochondrion is an organelle found in the cells of most eukaryotes. ...


Electrochemical potential-driven transporters

Proton or sodium translocating F-type and V-type ATPases [7] ATPases are a class of enzymes that catalyze the decomposition of adenosine triphosphate (ATP) into adenosine diphosphate (ADP) and a free phosphate ion. ...


P-P-bond hydrolysis-driven transporters

P-type calcium ATPase (five different conformations) [8] Calcium ATPase is a form of ATPase which transfers calcium after a muscle has contracted. ...


Calcium ATPase regulators phospholamban and sarcolipin[9] Phospholamban is a 52 amino acid integral membrane protein that regulates the Ca2+ pump in cardiac muscle cells. ...


Vitamine B12 transporter-like (ABC transporter BtuCD) [10] The ATP-binding cassette (ABC) transporter superfamily of membrane proteins function in the transport of a wide variety of substrates across extra- and intracellular membranes, including metabolic products, lipids and sterols, and drugs. ...


Lipid flippase-like ABC transporters (three different structures of closely homologous proteins) [11] Flippases (rarely, flipases) are membrane proteins responsible for aiding the movement of phospholipid molecules between the two leaflets that compose a cells membrane. ... The lipid flippase Msba, and example of an ABC-transporter ATP-binding cassette transporter genes (ABC-transporter genes) are a superfamily of genes which encode the ABC-transporter proteins. ...


General secretory pathway (Sec) translocon (preprotein translocase SecY) [12] A secretory pathway is a term used to describe different methods that cells use to transport material to the outside, usually from the endoplasmic reticulum via the Golgi apparatus. ... The translocon is the complex of proteins associated with the translocation of nascent polypeptides into the cisternal space of the endoplasmic reticulum from the cytosol. ...


Porters (uniporters, symporters, antiporters)

Mitochondrial carrier proteins [13] A symporter, also known as a cotransporter, is an integral membrane protein that is involved in secondary active transport. ... Antiporter illustration An antiporter is an integral membrane protein that is involved in secondary active transport. ... ... Carrier proteins are proteins that transport a particular substance in the blood or across the cell membrane. ...


Major Facilitator Superfamily (Glycerol-3-hosphate transporter, Lactose permease, and Multidrug transporter EmrD) [14] The permeases are a class of cell membrane proteins that facilitate the transport of a specific molecule in or out of the cell. ...


Resistance-nodulation-cell division (multidrug efflux transporter AcrB, see multidrug resistance)[15] Active efflux is a mechanism responsible for extrusion of toxic substances and antibiotics outside the cell. ... Multidrug resistance is the ability of pathologic cells to withstand chemicals that are designed to aid in the eradication of such cells. ...


Dicarboxylate/amino acid:cation symporter (proton glutamate symporter) [16]


Monovalent cation/proton antiporter (Sodium/proton antiporter 1 NhaA) [17]


Neurotransmitter sodium symporter [18] Chemical structure of D-Aspartic Acid, a common Amino Acid neurotransmitter. ...


Ammonia transporters [19]


Drug/Metabolite Transporter (small multidrug resistance transporter EmrE) [20]


Alpha-helical channels including ion channels

Voltage-gated ion channel like, including potassium channels KcsA and KvAP, and inward-rectifier potassium ion channel Kirbac [21] Ion channels are present in the membranes that surround all biological cells. ... Voltage-gated ion channel is a ion channel that is specifically activated, or gated, by the surrounding potential difference near the channel (or near the cell, neuron or synapse). ... In cell biology, potassium channels are the most common type of ion channel. ... Inwardly rectifing potassium channels (Kir or IRK) are potassium selective ion channels. ...


Large conductance mechanosensitive ion channel (MscL) [22]


Small conductance mechanosensitive ion channel (MscS) [23]


CorA metal ion transporters [24]


Ligand-gated ion channel of neurotransmitter receptors (acetylcholine receptor) [25] Chemical structure of D-Aspartic Acid, a common Amino Acid neurotransmitter. ... An acetylcholine receptor (abbreviated AChR) is an integral membrane protein that responds to the binding of the neurotransmitter acetylcholine. ...


Major intrinsic protein family (aquaporins) [26] Sideview of Aquaporin 1 (AQP1) Channel Aquaporins are a class of integral membrane proteins that form pores in the membrane of biological cells and selectively conduct water molecules in and out, while preventing the passage of ions and other solutes. ...


Chloride channels [27] Ion channels are present in the membranes that surround all biological cells. ...


Enzymes

Methane monooxygenase [28] Methane monooxygenase, or MMO, is an enzyme capable of oxidizing the C-H bond in methane. ...


Rhomboid protease [29]


Proteins with alpha-helical transmembrane anchors

Steryl-sulfate sulfohydrolase [30]


Stannin [31]


Glycophorin A dimer [32] A Glycophorin is a sialoglycoprotein of the membrane of a red blood cell. ...


Inovirus (filamentous phage) major coat protein [33] There are very few or no other articles that link to this one. ...


Pilin subunits [34] Pilin protein from Neisseria gonorrhoeae, a parasitic bacterium that requires functional pili for pathogenesis. ...


Pulmonary surfactant-associated protein [35] Diagram of the alveoli with both cross-section and external view Pulmonary surfactant is a surface-active lipoprotein formed by type II alveolar cells. ...


Monoamine oxidases A and B [36], Monoamine oxidase Monoamine oxidases (singular abbreviation MAO) (EC 1. ...


Cytochrome P450 oxidases [37], Cytochrome P450 Oxidase (CYP2E1) Cytochrome P450 oxidase (commonly abbreviated CYP) is a generic term for a large number of related, but distinct, oxidative enzymes (EC 1. ...


Corticosteroid 11β-dehydrogenases [38].


Signal Peptide Peptidase [39] Please wikify (format) this article or section as suggested in the Guide to layout and the Manual of Style. ...


Membrane protease specific for a stomatin homolog [40]


β-Barrels from outer membranes of Gram-negative bacteria

(n and S are number of beta-strands and "share number" [41] of beta-barrel) A beta barrel is a protein fold containing a series of beta sheets, typically arranged in an antiparallel fashion. ...


Outer membrane protein A like (n=8,S=10) [42]


Outer membrane protein T like (n=10,S=12) [43]


Autotransporter (n=12,S=14) [44]


Trimeric autotransporter (n=12,S=12) [45]


Outer membrane phospholipase (n=12,S=16) [46]


Nucleoside-specific channel-forming membrane porin (n=12,S=16) [47]


FadL outer membrane protein (n=14,S=14) [48]


Outer membrane protein G porin (n=14,S=16) [49]


Trimeric porins (n=16,S=20) (see porin (protein)[50] The introduction to this article provides insufficient context for those unfamiliar with the subject matter. ...


Sugar porins (n=18,S=22) [51]


Ligand-gated channels (n=22,S=24) [52]


Trimeric outer membrane factors (n=12,S=18) (TolC-like)[53]


Oligomeric β-barrels of Gram-positive bacteria

Leukocidin-like proteins (n=S) [54]. These proteins are secreted.


See also Gramicidin A [55], a peptide that forms a dimeric transmembrane β-helix. It is also secreted by Gram-positive bacteria. The discontinuous diamer is seen showing the antiparallel hydrogen bonding between the amid hydrogens and carbonyl oxygens. ... Gram-positive bacteria are those that are stained dark blue or violet by gram staining, in contrast to gram-negative bacteria, which are not affected by the stain. ...


Examples

Schematic of cell adhesion The study of cell adhesion is part of cell biology. ... Transmembrane receptors are integral membrane proteins, which reside and operate typically within a cells plasma membrane, but also in the membranes of some subcellular compartments and organelles. ... A Glycophorin is a sialoglycoprotein of the membrane of a red blood cell. ... In molecular biology, the insulin receptor is a transmembrane receptor that is activated by insulin. ... An integrin, or integrin receptor, is an integral membrane protein in the plasma membrane of cells. ... Cadherins are a class of proteins which are expressed on the surface of cells. ... A rhodopsin molecule in the cell membrane. ...

External links

TCDB Transporter classification database from Milton H. Saier, Jr. laboratory


TransportDB Genomics-oriented database of transporters from TIGR


Membrane PDB Database of 3D structures of integral membrane proteins and hydrophobic peptides with an emphasis on crystallization conditions


Membrane proteins of known 3D structure from Stephen White laboratory


PDBTM All 3D models of transmembrane peptides and proteins currently in the PDB including theoretical models. Approximate positions of membrane boundary planes were calculated for each PDB entry.


Orientations of proteins in membranes database Calculated spatial positions of transmembrane, integral monotopic, and peripheral proteins in membranes


See also


 
 

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