Transmembrane (cell surface) receptors
Contents
Ion channel-linked (ionotropic) receptorsG protein-linked (metabotropic) receptorsThis is the largest family of receptors and includes the receptors for several hormones and slow transmitters (dopamine, metabotropic glutamate). They are composed of 7 transmembrane α-helices. The loops connecting the α-helices form extracellular and intracellular domains. The binding-site for larger peptide ligands is usually located in the extracellular domain whereas the binding site for smaller non-peptide ligands is often located between the seven α-helices and one extracellular loop. These receptors are coupled to different intracellular effector systems via G proteins You can check out the structure in the window on the right. It shows the mu opioid receptor bound to a peptide ligand and a G protein . The G protein ("G" because it binds to GTP) consists of three parts A , B , and C ). In this crystal structure of the μ opioid receptor it is bound to β-funaltrexamine (β-FNA), a close relative of morphine that is bound in the pocket. The binding of an opioid induces a conformational change in the μ-opioid receptor that activates an inhibitory G-protein (Gαi/o). This results in the dissociation of the G-protein complex. The Gα subunit then inhibits adenylyl cyclase. The Gβγ subunit acts to inhibit Ca2+ channels and activate K+ channels. Activation mechanism. The κ-opioid receptor is a homodimer. The extracellular side is home to the proteins primary active site. These 2 units will span the length for the cell membrane to form the basis of the receptor molecule. The each subunit is attached to the other by the I, II and VIII α-helices, where helices I (in light blue) and helices VIII (in dark blue). This area will make up the basis for the intermembrane surface area. A distinguishing feature that separates the κ-opioid receptor from other receptors, is the large β-hairpin, ECL2, located near the main active site of the protein. It is believed that its function is to cap the active site of the receptor. Although in general, this protein is primarily composed of α-helices, not β-sheets (Compare β-sheet to α-helices). This evidence reinforces the idea that this protein is a transmembrane protein rather than one found inside the cytosol. In general transmembrane protein are composed almost entirely of α-helices (or β-sheet arranged in special fashion called a β-barrel), in order to have maximum stability inside the membrane. Interesting feature of the κ-opioid receptor is the disulfide bond formed by Cys131 and Cys210 which is conserved across all opioid receptors. Active site of κ-opioid receptor. The human κ-opioid receptor ligand binding pocket displays a unique combination of key characteristics both shared with and distinct from those in the chemokine and aminergic receptor families. Opioid receptors typically have 2 big portions: the upper portion, zoomed in here with active site shown in indigo, that is ligand specific and recognizes a particular ligand, and the lower portion which is highly conserved amongst all receptors. When Naltrindole approaches δ-opioid receptor, it is distinguished by the high hydrophobic interaction between the indole group on the ligand and leucine 300 on the receptor. As it glides deeper into the binding site facilitated by the hydrophobic interaction, the hydroxyl group of the tyrosine-like phenol group hydrogen bonds with water molecules which are hydrogen bound to a critical histidine 248. This holds the ligand by having both the phenol group and histidine anchored by a water molecule. The water molecules within the binding pocket flank both the ligand and receptor, serving almost as a scaffolding on which for both components to act. Adjacent to the phenol group, the oxygen of an ether is hydrogen bound to tyrosine 129 of the receptor. On the opposite side of the binding site, Asp128 forms a salt bridge with the charged amino group on the ligand. The rest of the ligand maintains hydrophobic contact with non-polar residues of the binding site. The phenol to water interaction is a conserved interaction between many opioid receptors and their respective ligands as evidenced by many natural antagonists having a tyrosine that interacts with a water molecule in a similar fashion. Like other G protein-coupled receptors, NTSR1 is composed of 3 distinct regions. An extracellular binding site where neurotensin binds and causes a conformational change of the protein. A region containing 7 transmembrane alpha helices (PDB code:4GRV) that transduce the signal from the extracellular side of the cell membrane to the intracellular side. Lastly, an intracellular region that when activated by a conformational change in the protein activates a G-protein associated with this receptor. The hydrophobic binding pocket in NTSR1 is located at the top of the protein (Figure 1). NTSR1 also contains an allosteric sodium binding pocket, which is located directly beneath the ligand binding pocket and the two pockets, which are separated by the residue Trp321. NTSR1 has been mutated to exist in both active and active-like states. Ligand binding cavity with antagonist citrulline (PDB code 3oe0). Ligand binding cavity with antagonist citrulline, receptor is in spacefill representation. Ligand binding cavity with antagonist citrulline, receptor surface is shown. The Suvorexant (Belsomra) binding pocket is open to the extracellular space through a constricted solvent-accessible channel. A complex network of electrostatic interactions includes salt bridges between the protein and the drug, on both sides of the entry channel.
hGPR40 contains 7 transmembrane helices (top view of TM helices). hGPR40 and peptide-binding and opioid GPCRs, they share structural similarities such as a conserved hairpin loop motif on extracellular loop 2 (ECL2). A conserved disulphide bond is formed between TM helix 3 (Cys 79) and the C-terminus of ECL2 (Cys170). A unique feature of hGPR40 is the presence of an additional 13 residues (Pro147-Gly159) on ECL2, which is absent on all the other peptide/opioid receptors. These extra residues form a separate auxiliary loop between the B-sheet-like region and TM4. Together, the auxiliary loop and ECL2 of hGPR40 function as a roof over the canonical binding site covering it from the central extracellular region. The canonical binding pocket for many other GPCRs is solvent exposed and centrally located between the TM helices allowing ligands to directly bind from the extracellular space. However, because ECL2 acts as a roof to this site, it inhibits ligands from entering directly from the extracellular region. Instead, the highly lipophilic nature of hGPRC40’s ligands allow it to enter a noncanonical binding pocket by moving through the lipid bilayer. FFAs bind to hGPR40 by coordinating its free carboxyl group to 3 amino acids Arg183, Tyr2240, and Arg258, which are located close to the extracellular domain of hGPR40. The binding site for the partial agonist TAK-875 has been identified, but other binding sites were hypothesized. hGPR40 has a distinct binding pocket that is established by 8 key residues: Tyr91, Glu172, Arg183, Ser187, Tyr240, Asn241, Asn244, and Arg258 (all individual residues shown in chartreuse). The importance of these residues for agonist binding was determined by alanine site-directed-mutagenesis studies. When the substrat/agonist enters the binding pocket, 4 of the 8 key binding residues interact directly with the carboxylate moiety of the agonist by hydrogen bonding to it. These residues include 2 key arginines in the binding pocket, Arg183 and Arg258, and 2 key tyrosines, Tyr91 and Tyr240. Tyr240 is especially important for binding. hGPR40 contains a highly conserved hairpin extracellular loop (ECL2) is the longest and most divergent of the extracellular loops found in proteins (top view of ECL2). The loop is accompanied by a disulfide bond (Cys79-Cys170) that forms between TM4 and the C-terminus of the ECL2 loop. The only exception to the low flexibility is the tip of the auxiliary loop, which corresponds to residues Asp152-Asn155. This area of greater mobility allows for substrates to enter the binding site. Tak-875 is tested for the treatment of type 2 diabetes. The binding of TAK-875 to hGPR40 occurs by the ligand entering the binding site through the membrane bilayer. This membrane insertion is performed via a method similar to ligand binding to sphingosine 1-phosphate receptor 1, retinal loading of GPCR opsin, and the entry of anandamide in cannabinoid receptors, in which the extracellular loops block the binding from the extracellular matrix. TAK-875 binds to the noncanonical binding site. The carboxylate of TAK-875 is buried within a very hydrophobic region and in a complex complex charge network involving Glu172, Ser187, Asn241, and Asn 244 from hGPR40 forming ionic and polar interactions by coordinating TAK-875 with Arg183, Arg258, Tyr91, and Tyr240. LPA1 lies in the membrane as shown by the fatty acid bound in the crystallization of LPA1. Most polar amino acids (red) reside on the intracellular and extracellular areas of the receptor, while most residues positioned on the trans membrane helices inside the membrane are hydrophobic (blue). The intracellular region of this membrane protein is coupled to a heterotrimeric G protein. Three native disulfide bonds in the extracellular region of this receptor provide fold stability. The 1st disulfide bond constrains the N terminal helix to extracellular loop (ECL) 2. The 2nd disulfide bond shapes ECL2, and the 3rd binds ECL3 to one of the TM α-helices. These disulfide bonds provide intramolecular stabilization along the extracellular region of the LPA1 receptor, where the substrate enters into the binding pocket. The N-terminus is a 6 turn α-helix and functions like a cap on the extracellular side of the protein, packing tightly against ECL1 and ECL2. The N-terminus helix also provides polar amino acids that interact with the ligand when bound. The biological ligand of the LPA1 receptor is lysophosphatidic acid (LPA), a phospholipid that contains a long, nonpolar tail, a phosphate head, a chiral hydroxyl group, and an ester group. This receptor provides specificity for its ligand by the amphipathic binding pocket; the positive region on the left hand side of the pocket stabilizes the LPA's phosphate group, the nonpolar region at the bottom of the binding pocket stabilizes the hydrophobic tail of LPA, and the polar region at the top of the pocket stabilize binding of the ester and hydroxyl group. The binding pocket for LPA consists of both polar and nonpolar residues. Polar residues are located on the N terminus and within the binding pocket. A hydrophobic pocket also interacts with the long acyl chain of LPA. The shape and polarity of the binding pocket makes it specific for molecules with a polar head and long hydrophobic tail shaped like LPA. ONO-9780307 (ON7) is an antagonist for LPA due to its large nonpolar region, chiral hydroxyl group, ester, and carboxylic acid which all resemble portions of the LPA molecule. 4 separate interactions with this antagonist of LPA1 help demonstrate the key interactions that stabilize the binding of the LPA to this receptor. In the nonpolar region of the binding pocket, 3 nonpolar residues of LPA1 stabilize the nonpolar group of ON7. At the polar region, the ligand binding is stabilized by Arg124 and Glu125 forming ionic and polar interactions with the carboxylic acid and the hydroxyl group of ON7. Interplay between Glu293 and Lys39 causes another stabilizing component with the ON7 antagonist. Glu293 forms polar interactions with Lys39, positioning it in close proximity to to the carboxylic acid of ON7, which then interactions with Lys39 via ionic bonding. While Lys39 is highly conserved among all 6 LPA receptors, a neighboring His residue is specific to the LPA1 receptor. His40 forms both ionic and polar interactions with the carboxylic acid of ON7. Sphingosine-1-phosphate receptor (S1P1) has altered ligand binding pathway (compared to LPA) includes global changes in the positioning of the extracellular loops and transmembrane helices. Specifically, a slight divergence of TMI, which is positioned 3 Å closer to TMVII compared to S1P1, and a repositioning of ECL3, resulting in a divergence of 8 Å from S1P1 result in ligand access via the extracellular space. This narrowing of the gap between TMI and TMVII blocks membrane ligand access in LPA1, while the greater distance between ECL3 and the other extracellular loops promotes extracellular access for LPA1. Additionally, ECL0 is helical in S1P1, but lacks secondary structure in LPA1. This increased flexibility that results from ECL0 lack of secondary structure in LPA1 further promotes favorable LPA access to the binding pocket from the extracellular space. Rhodopsin consists of seven mostly α-helical transmembrane domains (H1-H7) linked sequentially by extracellular and cytoplasmic loops (E1-E3 and C1-C3 respectively), with the extracellular amino-terminal tail and the cytoplasmic carboxyl-terminal tail. Four of the helices are tilted and three of the helices are approximately perpendicular to the membrane plane. There is notable interaction between the four extracellular domains, but only a few associations are observed with the cytoplasmic domains. Helix 7 is close to being elongated around the Lysine 296 retinal attachment site, and also contains the residues Proline 291 and Proline 303, with Proline 303 being part of a conserved motif. Near the retinal region, there is a β4 strand (Serine 186-Cysteine 187-Glycine 188-Isoleucine 189) within the Extracellular Helix 2 that runs almost parallel to the chromophore held in place and is stabilized by the essential conserved disulfide bond between Cysteine 110 and Cysteine 187. This loop also potentially contacts the chromophore through Glutamine 181 and Tyrosine 191. Water molecules are observed to be located in the extracellular domains of rhodopsin; specifically, the water molecules around the second extracellular loop between Helix 4 and 5 solvate the loop when the loop interacts with the retinal chromophore and possibly contribute to its flexibility should rearrangement occur. There is the presence of a cationic amphipathic Helix 8, known as the fourth cytoplasmic loop, that spans from Asparagine 310 to Cysteine 323 and is formed from the C-terminal tail anchoring to the membrane by Cysteine 322 and Cysteine 323, which are palmitoylated. This helix runs approximately parallel to the cytoplasmic surface and is involved in Gtγ binding, as well as the modulation of rhodopsin-transducin interactions and rhodopsin-phospholipid interactions. A metal zinc ion bridge chelated by histidine side-chains and connected to the cytoplasmic ends of Helix 3 and 6 is observed to prevent receptor activation. This perhaps indicates that separation of these cytoplasmic ends would contribute to rhodopsin activation. The structure of rhodopsin may provide stability to the important Schiff base linkage with the retinal by affecting its hydrolysis, limiting its interactions with solvent, and inhibiting its release when hydrolyzed, thus encouraging rebinding of the Schiff base linkage. Rhodopsin protein. Fully functional rhodopsin has the typical GPCR structure of a 7 transmembrane helical bundle with the N-terminus on the interior of the rods and the C-terminus in the cytoplasm. The N-terminus is located near the extracellular loops and ends of the transmembrane protein. There are hydrogen bonding between the transmembrane sections and the extracellular loops that are involved in the activation of rhodopsin when a photon is received. The N-terminus is thought to play a role in orientation of the extracellular loops. TM1 and TM2 play a role in stabilizing the protein and giving the protein functionality. Rhodopsin has 2 components: opsin (a membrane-bound polypeptide) and 11-cis-retinal (a chromophore that is bound to opsin via a protonated Schiff-base). 11-cis retinal is derived from vitamin A, is necessary for rhodopsin function. The ligand performs an inverse agonist suppressing activity on the photon receptor and is associated with the protein via protonated Schiff-bases linked to a lysine reside on the TM7. A negative agonist means the ligand, when present in the binding pocket of the protein, inhibits the receptor activity. The isomerization of cis to trans causes the protein complex to relax which allows for binding of transducin and the signal cascade to progress. Rhodopsin and Ligand. This is rhodopsin with 11-cis retinal bound. After 11-cis retinal becomes activated and becomes all-trans, rhodopsin undergoes the conformational change to become metarhodopsin I and then metarhodopsin II which is the fully active form of rhodopsin. Metarhodopsin II then associates with the G protein transducin and the signal cascade can continue. 5-HT1B receptor The 5-HT1B receptor couples to G-protein α subunits Gi and Go. In the CNS, this receptor is an inhibitory presynaptic receptor that can alter the release of serotonin, as well as other neurotransmitters, from the presynaptic neuron. The structure of this receptor includes 7 transmembrane α-helices. The N-terminal tail of 5-HT1B is close to the ligand binding pocket suggesting some interaction with its ligand. The ligand binding pocket, also called the orthosteric binding pocket, is characterized as a cavity formed from residues of the 3rd, 5th, 6th, and 7th α-helices and the ECL2. 5-HT2B receptor The 5-HT2B receptor is important in utilizing serotonin signals to encourage proper development and continuing function of the cardiovascular system. Overexpression of 5-HT2B has been linked to congestive heart failure. 5-HT2B utilizes the α Gq protein pathway which triggers intracellular cGMP production through activation of nictric-oxidase synthase (NOS). This receptor is also known for being the target of the drug LSD, which is similar in structure to serotonin. The structure of this receptor is much like that of 5-HT1B, however significant differences are seen in their binding pockets. The pocket of 5-HT1B is much broader than that of 5-HT2B, due to a 3 Å shift of the top of helix V. Perhaps this difference highlights a variation in serotonin affinity between the 2 families. The similar characteristics of the 5-HT1B and 5-HT2B receptor families consist of 7 α-helices and the N-terminus sticking out into extracellular space. Lysergic Acid Diethylamide (LSD) is a highly potent hallucinogen and is derived from ergotamine, an ergopeptine whose structural skeleton is contained in a diverse range of alkaloids. LSD acts as a non-selective 5-HT receptor agonist, meaning it can bind with equal affinity to 2 or more sub-types of receptors. LSD actively binds in the orthosteric binding pocket to both the 5-HT1B and 5HT-2B receptors, suggesting a similar chemical structure and function between the 2 receptor families. The docking is stabilized by all the same residues involved in normal binding in the orthosteric pocket. Hydrogen bonding between the amino group of the 5-membered ring of LSD and the T140 residue of the 5-HT2B receptor, as well as hydrogen bonding between D135 and the other ergoline amino group stabilize the LSD in a similar fashion that 5-HT would bind to the receptor. Serotonin 5-HT2C receptors are targets for treatment of depressive and anxious states. 5-HT2C receptors may be involved in the effects of corticosterone-induced hyperphagia. β-1 Adrenergic receptor is homodimer. Just as is true of most GPCRs, the dimers are each made up of 7 α-helices with different ligands, all of which must span the membrane; the α-helices are connected by external and internal loops and are connected in an anti-parallel form. For these α-helices to be stable, their middle must be made up of mostly hydrophobic amino acids while their ends are hydrophilic. In this scene, hydrophobic amino acids are colored grey, while polar amino acids are purple. Though some polar amino acids exist on the middle of the helices, they are also mostly on the interior of the helix. This keeps them from being exposed to the lipid membrane and destabilizing the protein. The hydrogen bonds (in white) are all between the amino acids in the α-helices and not from interactions with the ligand. The ligand to the protein must also have these similar qualities, or else it would not be able exist within the membrane. As seen in this scene, the ligand consists of hydrocarbon chains and rings in the center with nitrogen (blue) and oxygen (red) atoms only existing on the ends. This gives the ligands a very similar structure to the membrane, with a hydrophobic center and polar ends. Most of the ligands exist between the 2 dimers, allowing them to participate in binding along with the protein.
Kinase-linked, enzyme-linked and related receptorsReceptor tyrosine kinasesEnzyme-linked receptorImmune receptorsLeukocyte immunoglobulin-like receptorCytokine receptorsTNF receptor superfamilyColony-stimulating factor receptorType I cytokine receptorsType II cytokine receptorsInterferon receptors
Interleukin receptorsInterleukin-20 receptor: Chemokine receptors, two of which acting as binding proteins for HIV (CXCR4 and CCR5). They are G protein-coupled receptorsT-cell receptorTGF-beta receptorLDL receptorLDLR complex with proprotein convertase subtilisin/kexin 9-CoA reductase and Ca+2 ions. Ligand-binding domain (LBD) and epidermal growth factor precursor homology domain (EGFP) of LDLR. LDLR consists of a ligand-binding domain (LBD residues 1-292), epidermal growth factor precursor homology domain (EGFP residues 293-699), oligosaccharide-rich domain (residues 700-758), membrane-spanning domain (residues 759-781) and cytoplasmic domain (residues 782-832). LDLR LBD contains 7 ca. 40 amino acid long repeats (LB1 residues 20-67; LB2 residues 55-104; LB3 residues 105-143; LB4 residues 144-196; LB5 residues 196-232; LB6 residues 234-272) containing 6 cysteine residues, making a calcium binding octahedral structure. LDLR EGFP contains 2 EGF repeats followed by 6 YWTD repeats and another EGF repeat. LDLR LBD residues 133-273 are named C-type lectin-like domain. Transferrin receptorHuman transferrin receptor ectodomain dimer complex with transferrin N-lobe and C-lobe (1suv). See also Receptor
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