Receptor tyrosine kinases

Receptor tyrosine kinases (RTKs) are part of the larger family of protein tyrosine kinases. They are the high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. Approximately 20 different RTK classes have been identified.^[1]

RTK class I Epidermal Growth Factor Receptor family

Lapatinib is a EGFR inhibitor used in breast cancer treatment. EGFRs are overexpressed in many types of human carcinomas including lung, pancreatic, and breast cancer, and are often mutated. This overexpression leads to excessive activation of the anti-apoptotic Ras signaling cascade, resulting in uncontrolled DNA synthesis and cell proliferation. The EGFR tyrosine kinase domain is responsible for activating this Ras signaling cascade. Upon binding ligands like Epidermal Growth Factor, EGFR dimerizes and autophosphorylates several tyrosine residues at its C-terminal domain. Upon phosphorylation, EGFR undergoes a significant conformational shift, revealing an additional binding site capable of binding and activating downstream signaling proteins.

Gefitinib inhibits the EGFR by binding to the ATP-binding site located within the kinase domain. Residues Lys745, Leu788, Ala743, Thr790, Gln791, Met193, Pro794, Gly796, Asp800, Ser719, Glu762, & Met766 tightly bind the inhibitor. Unable to bind ATP, EGFR is incapable of autophosphorylating its C-terminal tyrosines, and the uncontrolled cell-proliferation signal is terminated.

Erlotinib inhibits the EGFR by binding to the ATP-binding site located within the kinase domain. EGFR uses residues Asp831, Lys721, Thr766, Leu820, Gly772, Phe771, Leu694, Pro770, Met769, Leu768, Gln767 & Ala719 to tightly bind the inhibitor. Unable to bind ATP, EGFR is incapable of autophosphorylating its C-terminal tyrosines, and the uncontrolled cell-proliferation signal is terminated.

See also Herceptin - Mechanism of Action

RTK class II Insulin receptor family

Insulin receptor

The insulin receptor (IR) is a dimer of heterodimers made of 2 α-subunits and 2 β-subunits. Within the extracellular ectodomain, there are 4 potential binding sites that can interact with insulin on the extracellular side of the membrane.

The α-subunits make up the extracellular domain of the IR and are the sites of insulin binding. The α-subunit is comprised of 2 Leucine rich domains (L1 & L2), a Cysteine rich domain (CR), and a an α-chain C-terminal helix (α-CT). α-CT has a unique position that allows it to reach across the receptor and interact with the insulin at the binding site on the opposing side of the receptor. The α-subunits are held together by a disulfide bond between cysteine residues on each α-subunit. The disulfide bonds are important to the overall stabilization of the molecule as it binds to insulin. Two types of insulin binding sites are present in the α-subunits, sites 1 and 1' and sites 2 and 2'. The sites are in pairs because of the heterodimeric nature of the receptor. Due to structural differences, as well as greater surface area and accessibility, binding sites 1 and 1' have much higher affinity for insulin binding than sites 2 and 2'. Insulin can also bind at sites 2 and 2', but the location on the back of the β-sheet of the FnIII-1 domain and lack of surface area decreases the likelihood of their binding site becoming occupied as quickly.

The β-subunits spans from the extracellular domain across the TM region and into the intracellular portion of the IR. The β-subunit is composed of part of fibronectin domain III-2 and all of Fibronectin domain III-3. The β-subunit's FnIII-3 domain has links through the TM region into the intracellular part of the membrane. Cryo-EM provided clear representations of the FnIII-2 and FnIII-3 domains, but are missing the TM and intracellular regions. Although the FnIII-3 domain is connected to the TM and intracellular regions, the active T-shape conformation likely extends all the way to the tyrosine kinase domain region (4xlv).

The α and β subunits of the extracellular domains fold over one another and form a "V" shape when the IR is inactivated. Upon activation, the extracellular domain undergoes a conformational change and forms a "T" shape. An additional component to the ectodomain is α-CT. Each of the dimers has an α-CT helix. The α-CT helix is a single α-helix that plays an important role in insulin binding and stabilization of the "T" shape activated conformation. α-CT interacts with a leucine-rich region of the α subunit and a fibronectin type III region of the β subunit to form the insulin binding sites known as site 1 and site 1'.

The structure of the extracellular domain is stabilized through multiple disulfide bonds. The α-subunits are linked through 2 disulfide bonds, with the main one being between Cys524 of 2 adjacent α-subunits. Cys683 of both α-subunits are also held together with a disulfide bond. The α-subunit is also attached to the β-subunit by a disulfide bond between the Cys647 of the α-subunits and Cys872 of the β-subunit. The IR unit has 4 separate sites for the insulin binding. There are 2 pairs of 2 identical binding sites referred to as sites 1 and 1' and sites 2 and 2'.

The insulin molecules bind to these sites mostly through hydrophobic interactions, with some of the most crucial residues at sites 1 and 1' being between Cys A7, Cys B7, and His B5 of insulin and Pro495, Phe497, and Arg498 of the IR FnIII-1 domain. Despite some of the residues included being charged, the main interactions are still hydrophobic in this binding site. For example, due to arginine carrying its positive charge at the end of the side chain, the side chain is bent to allow the hydrophobic part of the side chain to interact with the other hydrophobic residues. The α-subunits also have significant disulfide linkages that help maintain a compact binging site. At sites 2 and 2', the major residues contributing to these hydrophobic interactions are the Leu 486, Leu 552, and Pro537 of the IR and Leu A13, Try A14, Leu A16, Leu B6, Ala B14, Leu B17 and Val B18 of the insulin molecule.

Sites 1 and 1' have a higher binding affinity than sites 2 and 2' due to site 1 having a larger surface area (706 Ų) exposed for insulin to bind to compared to site 2 (394 Ų). The binding interactions of the insulin molecules in sites 1 and 1' are facilitated by hydrophobic residues of an α-helix of the IR. The insulin molecules in sites 2 and 2' primarily interact with the residues that comprise some of the β-sheets of the IR.

At binding sites 1 and 1', a tripartite interaction occurs between 3 critical parts of the α subunits of the IR. The entire interface of the tripartite interaction involves many residues that are involved with intra-protomer ionic and hydrogen bonding at the binding site. The α-CT chain and the FnIII-1 domain region come into close proximity during the conformational change of the IR and their interaction involves the following residues: ASP496, ARG498, and ASP499 on the FnIII-1 domain and the LYS703, GLU706, and ASP707 on the α-CT domain. This duo then interacts with the L1 region, specifically ARG14, creating an ideal binding site for the insulin ligand. The FnIII-1 and α-CT are interacting from the 2 different α-subunits, which displays a "cross linking" scenario where the domains of the heterodimer can intertwine with each other. The tripartite interaction between α-CT, the FnIII-1 domain, and the L1 region is important because it allows for a strong interaction between 2 subunits of the IR that maintains and stabilizes the T-shape activation state for the rest of the downstream signaling to occur.

It has been hypothesized that activation of the IR can change based on the concentration of insulin. These structures of the IR have demonstrated that at least 3 insulin molecules have to bind to the IR to induce the active "T" shape conformation, as binding of 2 insulin molecules is insufficient to induce a full conformational change. However, this conclusion has not yet been widely confirmed. In low concentrations of insulin, the IR may not require binding of 3 insulin molecules in order to exhibit activation. Rather, the level of activity will change in accordance to the availability of insulin. When higher concentrations of insulin are present, the conformational difference between the 2-insulin-bound state and the 3-insulin-bound state is drastic as the IR transitions from the inactive "V" shape to the active "T" shape. However, in conditions of low insulin availability, the 2-insulin-bound state may be enough to induce partial activation of the receptor.

The conformational change between the inverted, inactive "V" shape and the active "T" shape of the IR is induced by insulin binding. The T shape conformation is well observed in the α subunit. It is horizontally composed of L1, CR (including the α-CT chain), and L2 domains and vertically composed of the FnIII-1, 2, and 3 domains. The proper conformational change of the ectodomain of the IR is crucial for transmitting the signal into the cell. The movements extracellularly cause the 2 receptor tyrosine kinase domains intracellularly to become close enough to each other to autophosphorylate. This autophosphorylation activates the tyrosine kinase domain, initiating intracellular insulin signaling cascades.

When an insulin molecule binds to site 1 of the α-subunit, the respective protomer is recruited and a slight inward movement of the Fibronectin type III domains of the β-subunit is initiated. This is accomplished by the formation of several salt bridges, specifically between Arg498 and Asp499 of the FnIII-1 and Lys703, Glu706, and Asp707 of the α-CT. Binding of insulin to both protomers establishes a full activation of the IR. This activation is demonstrated through the inward movement of both protomers. This motion has been referred to as a "hinge" motion as both protomers "swing" in towards one another. The conformational change and "hinge motion" between the inactive and active forms of an IR protomer. Upon insulin binding, the β subunits of the inactive form, shown in blue, are "swung" inward to the active form, shown in orange. When the receptor is in an inverted V shape, the FnIII-3 domains are separated by about 120Å. This distance prevents the initiation of autophosphorylation and downstream signaling by the tyrosine kinase domains on the intracellular side of the receptor. Upon the binding of insulin to multiple binding sites, this conformation change brings the FnIII-3 domains within 40Å of each other to induce the T shape conformation. As the fibronectin type III domains of the β subunit swing inward, the α subunits also undergo a conformational change upon insulin binding. As insulin binds to site 1, the leucine-rich region of one protomer interacts with α-CT and the FNIII-1 domains of the other protomer to form the tripartite interface binding site. For the tripartite interface to form, the α subunits of each protomer must undergo a "folding" motion.

Human IR tyrosine kinase catalytic domain complex with IR substrate 2 peptide, Mg+2 ion and ATP (3bu5).

TK domain of IR contains an activation loop and a catalytic loop and 3 phosphorylated tyrosine residues. The bound IR substrate 2 peptide tyrosine is the phosphorylated residue^[2].

In type 2 diabetes, the TK domain is thought to be down-regulated through phosphorylation of threonine 1160 by protein kinase C^[3].

ATP/Mg binding site. Water molecules shown as red spheres.

Student Projects for UMass Chemistry 423 Spring 2012-1

RTK class III Platelet-derived growth factor receptor family

RTK class IV Vascular Endothelial Growth Factor Receptor family

Vascular Endothelial Growth Factor Receptors (VEGFRs) are tyrosine kinase receptors responsible for binding with VEGF to initiate signal cascades that stimulate angiogenesis among other effects. The tyrosine kinase domain of VEGFR-2 is separated into 2 segments with a 70 amino acid long kinase insert region. Upon binding VEGFA and subsequent dimerization, VEGFR-2 is autophosphoryalted at the carboxy terminal tail and kinase insert region, 6 tyrosine residues of VEGFR2 are autophosphorylated. Auto-phosphorylation of residues 1054 and 1059 within the activation loop of VEGFR2 leads to increased kinase activity. Anti-tumor inhibitor binding site (3c7q).

See also Bevacizumab.

RTK class V Fibroblast growth factor receptor family

FGFR consist of an extracellular ligand-binding domain (LBD), transmembrane helix domain and cytoplasmic tyrosine kinase activity domain (TKD) with phosphorylated tyrosine designated PTR. FGFR LBD contains 3 immunoglobulin-like domains D1, D2 and D3.

Human fibroblast growth factor receptor 1 ligand-binding domain modules D2 and D3 with 2 molecules of fibroblast growth factor 1 (PDB code 1evt).

RTK class VIII Hepatocyte growth factor receptor family

The A loop of the wt receptor contains 2 tyrosines at position 1234 and 1235. When these 2 residues become phosphorylated, the kinase can become active. A unique part of the c-met structure is the pair of tyrosine residues (1349 and 1356). These tyrosines are necessary for normal c-met signaling. When these 2 tyrosines were substituted with with phenylalanine in mice, the mice had an embryonically lethal phenotype and defects were found in placenta, liver, muscles and nerves. In a wt c-met, these sites will become phosphorylated and act as docking sites for many different transducers and adapters. Upon phosphorylation, these tyrosines can bind with Src homology 2 (SH2) domains and phophotyrosine-binding (PTB), and therefore bind many effectors that will cause downstream effects such as cell proliferation, scattering and inhibition of apoptosis. This receptor follows the typical structure of a protein kinase, with a bilobal structure. The N-terminal contains β-sheets and is linked through a hinge to the C lobe, which is full of α helices. This particular kinase domain is very similar to the domains of the insulin receptor kinase and fibroblast growth factor receptor kinase.^[4] This structure is made up of many α-helices that move in the transformation from inactive to active kinase. Some of these helices are conserved in many different tyrosine kinases. C-met does show a divergence from other tyrosine kinases (such as IRK and FGFRK) in the helix formed at the N-terminus, before the core kinase domain, in residues 1060-1069. The αA is in contact with αC and so causes αC to be in a slightly different orientation than in FGFRK and IRK. Residues Leu-1062, Val-1066, and Val-1069 of αA intercalate with with residues Leu-1125 and Ile-1129 of αC. There is another interaction between the residues Ile-1053, Leu-1055 and Leu-1058 of αA and Ile-1118 and Val-1121 of αC. Because of the movement of αC during activation of the kinase, it is an assumption that αA is also part of the kinase activation upon ligand binding.

The particular structure of the hepatocyte growth factor tyrosine kinase domain is one harboring a human cancer mutation. The 2

tyr1234 and tyr1235 are replaced by a phenylalanine and aspartate, respectively. This mutation normally causes the receptor to be constitutively active, and is found in HNSC (Head, Neck squamous cell) carcinoma. Although there is no longer phosphorylation at these sites, it is believed that the negative charge of the aspartate resembles the negative phosphate that would normally cause activation, and therefore keeps the protein in its active form. ^[5] There is a 3rd mutation at Tyr-1194 which is substituted for a phenylalanine. This is shown to point into the pocket formed by Lys-1198 and Leu-1195 from αE. ^[6] This structure is conserved in the wild type protein, suggesting that the mutation at residue 1149 is not changing the structure at this position.

K-252a is a staurosporine analog. Staurosporine is an inhibitor of many Ser/Thr Kinases, and has been shown to also inhibit c-Met activation by inhibiting its autophosphorylation. The structures of K-252a and staurosporine are very similar, with the main difference being that K-252a has a furanose instead of a pyranose structure. The binding of K-252a causes the c-Met to adopt an inhibitory conformation of the A-loop, specifically with residues 1231-1244. This segment blocks the place where the substrate tyrosine side chain would bind, if the protein were in an active conformation. Residues

1223-1230 also enhance this inhibitory conformation, as they constrain αC into a conformation that does not allow the catalytic placement of Glu-1127 keeping αC in an inactive conformation. In an active kinase, Glu-1127 would form a salt bridge with Lys-1110. Residues 1229-1230 pass through the triphosphate subsite of bound ATP blocking ATP binding. The K-252a itself binds in the adenosine pocket, therefore also inhibiting the binding of ATP. The binding of K-252a is very favorable. This is probably due to polar interactions as well as a change in conformation upon binding. There is a concerted conformational change in the complex upon K-252a binding. One of these changes involves the A-loop, specifically residues 1228-1230. In the Apo-Met structure, the side chain of Met-1229 would pass through the ring of the inhibitor, and so, in order to make room for K-252a, the segment must move, with residues 1229 and 1230 moving by 3-4 Å. In order to make room for the side chain of Tyr-1230, Arg-1208 moves by 8 Å toward Asp-1204. Arg-1208, which in the uninhibited complex would stack with tyr-1230, now stacks with Phe-1234. K-252a binds in the adenosine pocket. It has 4 hydrogen bonds to the enzyme, with two of these mimicking hydrogen bonds of an adenine base. There is a hydrogen bond between the K-252a nitrogen and the carbonyl oxygen of Pro-1158, and another between the K252-a carbonyl oxygen and the hydrogen of the amide of Met-1160. There are 2 more hydrogen bonds between the 3' hydroxyl and carbonyl oxygen and the tyr-1230 of the A loop. There are also many hydrophobic interactions between the interface of the enzyme and K-252a. The residues involved in this are Ile-1084, Gly-1085, Phe-1089, Val-1092, Ala-1108, Lys-1110, and Leu-1140 (N lobe); Leu-1157, Pro-1158, Tyr-1159, and Met-1160 (hinge region); and Met-1211, Ala-1226, Asp-1228, Met-1229, and Tyr-1230 (C lobe). Met-1229, Met-1211 and Met-1160 all make up the platform for the indolocarbazole plane as they are all within van der Waals distance of it.

In c-Met, there are 2 tyrosines located in the C-terminal tail sequence, which, upon phosphorylation, act as the docking sites for many signal transducers. These tyrosines correspond to residues 1349 and 1356. Both of these sites interact with SH2, MBD and PTD domains of signal transducers. The residues 1349-1352 form an extended conformation, which is seen in other phosphopeptides that bind to SH2 domains. Residues

1353-1356 form a type I β turn, which is similar to sequences that bind to Shc-PTB domians. Whether binding to SH2 domains or PTB domains, upon binding, these motifs would move to avoid clashes with the C lobe. The 3rd binding motif is found in residues 1356-1359, which form a type II β turn, and is similar to pohsphopeptides that bind Grb2. When comparing the unphosphorylated conformation of the motif to one that is phosphorylated, and bound to the Grb2 complex, there is a peptide flip between the bind of Val-1357 and Asn-1358. This suggests that when Grb2 docks onto c-Met, there is a change in orientation of this motif. These 3 binding motifs of the mutated structure are very similar to binding motifs that would be recognized by their binding partners, implying that the C-terminal supersite of this structure is very similar to that of an active c-met.

RTK class IX Ephrin receptor family

• Ephrin A3 receptor with peptide substrate, nucleotide derivative and Mg+2 ion. Water molecules are shown as red spheres.
• Nucleotide derivative and Mg+2 ion binding site.
• Peptide substrate binding site (3fxx).

Ephrin Type-A Receptor The extracellular part of Eph receptors includes the N-terminal ephrin (Ligand)-binding domain (LBD), a cysteine-rich domain (CRD), and 2 fibronectin Type-III Repeats (FN3). EphA binds ephrins with its LBD. Most ephrins have a similar rigid structure which includes four loops, AB, CD, FG, & GH. The LBD of EphA4 is said to be a “structural chameleon” able bind both A and B class ephrins. This explains why Ephrin Type-A receptors exhibit cross-class reactivity. The overall structure of the EphA4 LBD includes four important loops, the BC, DE, GH, & JK loops. EphA4 binds the GH loop of the ephrin ligand within a deep pocket created by the EphA4 DE and JK loops. It is these loops, DE and JK, which undergo the greatest conformational shifts when binding either EphrinA2 or EphrinB2. When binding EphrinA2, EphA4-Arg 162 forms a hydrogen bond with EphrinA2-Leu 138, while EphA4-Met 164 and EphA4-Leu 166 participate in hydrophobic interactions with EphrinA2-Leu 138 and EphrinA2-PHe 136. Although EphA4 binds EphrinB2 in the same binding pocket, the local interactions are significantly different. Most notably, the α-helix present in the EphA4-EphrinA2 JK loop is disrupted in the EphA4-EphrinB2 structure. This is due to the steric clash that would occur between EphrinB2-Trp 122 and EphA4 Met 164. Instead, EphA4-Arg 162 and EphrinB2-Trp 122 form hydrophobic stacking interactions among other interactions which stabilize the receptor-ligand complex. A morph of the movements EphA4 undergoes to bind EphrinA2 and EphrinB2 can be seen here.

Eph-Ephrin complexes form two unique heterotetrameric assemblies consisting of distinct EphA2-EphA2 interfaces. The 1st tetrameric form is generated by Eph-Eph interactions only within the LBD. The 2nd tetrameric form involves complex interactions in the LBD and in the region near the CRD.^[7] These two heterotetramers generate a continuous Eph-ephrin assembly when combined (Alternative Coloring). The proximity of kinase domains in an eph-ephrin tetramer, favors transphosphorylation of tyrosines in the cytoplasmic domains. Phosphorylation promotes kinase activity by orienting the activation segment of the kinase domain in a way that favors subsrate binding and subsequent signaling.

RTK class XIII Epithelial discoidin domain-containing receptor (DDR receptor) family

DDR1 contains a discoidin domain. This domain is about 150 amino acid long and is found in many blood coagulation factors. The structure of the complex between DDR1 and imatinib shows hydrogen bonds interactions between the anti-cancer drug and the kinase domain including bonds with the kinase allosteric site Asp-Phe-Gly (DFG motif)^[8]. Water molecules are shown as red spheres.

Neurotrophin receptor

• High affinity nerve growth factor receptor

TrkA. Trk stands for Topomyosin-Related Kinase. TrkA ligand - nerve growth factor activates the receptor by stabilizing homodimer formation which initiates transautophosphorylation. Structure of Nerve Growth Factor Complexed with the Extracellular Domain of TrkA. An Arg residue, conserved in all neutrophins, forms the most important binding determinant between TrkA and its ligand - nerve growth factor - which forms the active homodimer of the receptor. All interactions between TrkA chain A and NGF.

• Tyrosine kinase receptor TrkA

TRK-A contains an extracellular ligand binding domain (LBD), a transmembrane helix and an intracellular region which contains the kinase domain. The kinase domain (4yne) contains the tripeptide DFG which flips out in TRK-A inactivated form. Inhibitor binding site (4yne). The structure of the complex of TRK-A with the phenylpyrrolidine derivative shows the inhibitor forming hydrogen bonds to Met620 and Lys572 residues and π-π interactions of it with Phe617 and Phe 698.

The complex between TRK-A and the nerve growth factor (2ifg) is a 2:2 dimer. The C-terminal immunoglobulin-like domain interacts with the NGF. The extracellular domain of TRK-A contains 3 Leu-rich regions flanked by Cys-rich regions (in yellow), 2 immunoglobulin-like domains and the nerve growth factor (NGF) binding domain.

• Neurotrophin & its receptor

The complex between NT3 and p75 neurotrophin receptor (p75NTR) shows a homodimer of NT3 with two symmetrically arranged p75NTR molecules. There are 3 sites of interactions between NT3 and p75NTR - site 1, site 2 and site 3.

Site 1.

Site 2.

Site 3.

• TrkB tyrosine kinase receptor

Structure of the TrkB-d5:NT-4/5 Complex, comprising one homodimer of NT-4/5 bound to two monomers of TrkB-d5. TrkB and neutrotrophin-4/5 interact via a specificity interaction site and via a conserved interaction site

Insulin-like growth factor receptor

Memory-Enhancement by Traditional Chinese Medicine? ^[9]

IGF receptor (IGF-IR, in darkmagenta) activation is critical for IGF-I to elicit desirable cognitive functions. Molecular dynamics simulation revealed that the Traditional Chinese medicine (TCM) ligands were secured at the opening of the IGF-IR binding site for the duration of the MD. 3-(2-carboxyphenyl)-4(3H)-quinazolinone was stabilized by Asp1056, (+)-N-methyllaurotetanine was stabilized by Leu975 and Asp1056, and (+)-1(R)-Coclaurine was stabilized by Leu975 and Gly1055 (key residues are colored in yellow).

Enzyme-linked receptor

• TGF-beta receptor
• Activin receptor
• Crystal structure of the extracellular domain of the receptor-like kinase TMK3 from Arabidopsis thaliana
• Bone Morphogenetic Protein 7 and receptor
• Toll-like Receptors

See also:

• Receptor
• Transmembrane (cell surface) receptors