Cell Signaling 2. The components of signaling pathways

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1 Cell Signaling 2. The components of signaling pathways A simple intracellular signaling pathway The first step of the pathway is the binding of the ligand (first messenger) to the receptor (a G protein-coupled receptor is shown on the slide). The G protein is the transducer (converter), which affects the first (primary) effector (this is the adenylate cyclase in the camp system, the phospholipase C in the phosphoinositol system). The primary effector produces the second messenger molecules, which are usually small chemical compounds. The second messenger is the camp itself in the camp system, and IP 3 and DAG in the phosphoinositol system (these latter two molecules derive from the PIP 2 ). The second messenger activates the secondary effector molecules; these are the protein kinase A in the camp system, protein kinase C and Ca 2+ in the phosphoinositol system. Note that the Ca 2 + is often regarded as a second messenger. The secondary effector molecule activates further effector molecules (the effect may be negative). The most common mechanism for activation is the phosphorylation cascade, in which the different kinase molecules phosphorylate each other in a well-defined sequential order. The protein phosphorylation changes the conformation of the proteins, which usually means switching to an active state. Various phosphorylase enzymes carry out the deactivation by removing the phosphate groups. There are hundreds of different kinase enzyme coding genes in the mammalian genome, which signifies their important role. The signal transduction cascades change the function of the target proteins which may cause change in the function of the cells (cellular response). The target proteins could be enzymes of metabolism (it can change the metabolism), ion channel (it can change the ion milieu), transcription factor (it can change the gene expression), a cytoskeleton protein (change of the shape and / or movement). The conditional use is justified because the cell is a decision machine that can override the effect of a signal (another effect of signals), or neglect the command, because intensity of the signal is too low. The cell responses are usually dependent on signal intensity; in case of stronger signal, the response is greater. The incoming input (neurotransmitters) of the neurons exerts a gradual response in the body of the cell (continuous ion gradient), but the output signal (action potential) is discrete, in particular, is always the same size, and therefore comparable to digital (yes or no basis). The signal intensity of neurons is encoded by the frequency of action potentials (and not the strength of individual action potential). SIGNAL MOLECUES (ligands) responsible for transmission of the information between cells. The signaling molecules are produced by signaling cells, they have to move through the gap between the cells in order to bind to the receptor of the receiving cells and evoke a response in the target cells. The main types of the signaling molecules are as follows: hormones, growth and differentiation factors, chemokines, cytokines, neurotransmitters, nitrogen oxide (NO), etc. Molecules similar to the signal molecules of the organism can be found in nature too, and we can produce them synthetically, too. Caffeine, nicotine and certain drugs are similar to certain naturally occurring ligands and therefore, they can be recognized by the appropriate receptors. Some drugs also bind to our receptors. With these substances, we can control cell communication and bodily functions. Cytokines are small protein or peptide molecules that are secreted by the glial cells and by numerous cells of the immune system, and are a category of signaling molecules used in intercellular communication. As we learn more about them, the distinctions between cytokines and hormones are fading. Cytokines are not limited to their immunomodulatory role; these molecules are also involved in several developmental processes during embryogenesis. The effect of a particular cytokine on a given cell depends on its extracellular abundance, the presence and abundance of their receptors on the cell surface, and downstream signals activated by receptor binding; these last two factors can vary by cell type. Cytokines have been classed as lymphokines, interleukins, and chemokines, based on their presumed function, cell of secretion, or target of action. Cytokines are CELL SIGNALING II. The components of signaling pathways page 1

2 characterized by considerable redundancy (many cytokines share similar functions) and pleiotropism (a single cytokine affects a number of processes). Cytokines may be divided into six groups: interleukins, colonystimulating factors, interferons, tumor necrosis factor, growth factors, and chemokines. The term chemokine refers to a specific class of cytokines that mediates chemo-attraction between cells. A growth factor is a naturally occurring substance capable of stimulating cellular growth, proliferation and cellular differentiation. Usually it is a protein or a steroid hormone. Growth factors are important for regulating a variety of cellular processes. They often promote cell differentiation and maturation, which varies between growth factors. For example, bone morphogenic proteins (BMPs) stimulate bone cell differentiation, while fibroblast growth factors (FGFs) and vascular endothelial growth factors (VEGFs) stimulate blood vessel differentiation (angiogenesis). Growth factor is sometimes used interchangeably among scientists with the term cytokine. While growth factor implies a positive effect on cell division, cytokine is a neutral term with respect to whether a molecule affects proliferation. While some cytokines can be growth factors, such as granulocyte colony-stimulating factor (G-CSF), others have an inhibitory effect on cell growth or proliferation. Some cytokines, such as Fas-ligand, are used as "death" signals; they cause target cells to undergo programmed cell death (apoptosis). Foreign signals Beside endogenous ligands, many signaling pathways can be targeted by natural or synthetic exogenous substances, such as snake venom, drugs, nicotine, kaffein, products of pharmaceutical industries, etc. RECEPTORS are responsible for the perception of signals and converting them into other types of signals, which then are recognized by the signal processing apparatus of the cell eliciting a response. The relationship between receptors and ligands is characterized by the key lock relationship, the steric configuration/shape of the receptor allows only the ligand that fits into this structure to bind (the recognition site). The three-dimensional "complementarity" is not enough, the two molecules should be able to establish chemical bond formation (e.g.: H-bonds, ionic bonds, etc). The receptors can be categorized on the basis of their position in the cell. Thus we talk about cytoplasmic (nuclear) and cell-surface receptors. The steroid hormones are typical ligands of cytoplasmic receptors, are relatively low in molecular weight lipophilic (fat-soluble) molecules can easily penetrate through the cell membrane, bind to the receptor, the receptor-ligand complex becomes active as transcription factor. The receptor-ligand complex crosses the nuclear membrane and binds to the recognition site of its promoter or enhancer DNA sequences, and thereby stimulates the expression of corresponding genes. The cell surface receptors have three main types, which are ionotropic (ion channel-coupled), G-protein-linked, and enzyme-coupled receptors. 1. Signal pathways without receptors Nitric oxide (NO) Nitric oxide (NO) acts by a direct activation on an enzyme. Acetyl-choline released by nerve terminals in the blood vessel wall stimulates endothelial cells lining the blood vessel to make and release NO. No is made from the amino acid arginine by the enzyme NO synthase. The gas has a very short half-life (about 5-10 seconds) because it is quickly converted to nitrates and nitrites by cellular enzymes. The NO diffuses out of the endothelial cells and into adjacent smooth muscle cells, causing the muscle cells to relax, allowing the vessel to dilate, so that blood flows through it more freely. The effects of NO on blood vessels accounts for the action of nitroglycerine (it is converted to NO in the body), which has been used for almost 100 years to treat patients with angina (pain caused by inadequate blood flow to the heart muscle from the coronary blood vessels). Inside many target cells, NO binds to the enzyme guanylate cyclase stimulating the formation of cyclic GMP from the nucleotide GTP. Cyclic GMP itself is a small intracellular signaling molecule that forms the next link in the signaling chain that leads to the cell s ultimate response. The impotence drug Viagra enhances penis erection by blocking the degradation of cyclic GMP, prolonging the NO signal. CELL SIGNALING II. The components of signaling pathways page 2

3 2. Intracellular receptor-mediated signaling pathways Hydrophobic signal molecules such as the steroid hormones including cortisol (glucocorticoid), estradiol and testosterone (sex steroids) and the thyroid hormones such as thyroxin all pass through the plasma membrane of the target cells, where they bind to an intracellular receptor. The intracellular receptor is in fact, an inactive transcription factor, which is activated upon binding to the steroid hormone. Steroid hormone receptors play an essential role in human physiology, as illustrated by the dramatic consequences of a lack of the receptor for testosterone in humans. These individuals are genetically males (they have Y chromosomes) but they develop as females. An example: Glucocorticoid receptors are located in the cytoplasm in an inactive state (hsp90 chaperons inhibit them). Steroid hormone binding dislocates hsp90, and results in the formation of a dimeric (twosubunit) molecule, which in turn, enter to the nucleus, bind to its response DNA element (GRE: glucocorticoid response element) and activate transcription from the linked gene. (1) Steroid hormones, which include the cortisol, the steroid sex hormones and vitamin D, are all made from cholesterol. (a) Cortisol is produced in the cortex of the adrenal gland and influences the metabolism of many cell types. (b) The steroid sex hormones are made in the testis and ovaries, and they are responsible for the primary and secondary sex characteristics that distinguish males from females. (c) Vitamin D is synthesized in the skin in response to sunlight; after it has converted to its active form in the liver or kidneys, it regulated Ca 2+ metabolism. (2) The thyroid hormones, which are made from the amino acid tyrosine, act to increase the metabolic rate in many cell types. (3) Retinoids, such as retinoic acid, are made from vitamin A, and have important role as local mediators in vertebrate development. Nuclear receptors Some of the nuclear receptors, such as those for cortisol, are located primarily in the cytosol and enter the nucleus only after ligand binding; others, such as thyroid and retionid receptors, are bound to the DNA in the absence of ligand. In either case the inactive receptors are usually bound to inhibitory protein complexes. Ligand binding alters the conformation of the receptor protein, causing the inhibitory complex to dissociate, while also causing the receptor bind co-activator proteins that stimulate gene transcription. In other cases, however, ligand binding to a nuclear receptor inhibits transcription: some thyroid hormone receptors, for example, act as transcriptional activators in the absence of their hormones and become transcriptional repressors when hormone binds. The transcriptional response usually takes place in multiple steps. Some of the primary-response proteins turn on secondary-response genes, whereas others turn off the primary-response genes. The intracellular receptors are all structurally related, being part of the very large nuclear receptor superfamily. Many family members are so called orphan receptors, indicating that their ligands are unknown. 3. Cell surface receptor-mediated signaling pathways The vast majority of signal molecules are too large or hydrophilic to cross the plasma membrane of the target cell. This bulky molecules bind to receptor proteins that span the plasma membrane. These receptors detect a signal on the outside and relay the message, in a new form, into the interior of the cell. The cell surface receptors belong to one of the three large families: (1) ion-channel linked receptors; (2) G protein-linked receptors, or (3) enzyme-linked receptors. The number of different types of receptors is greater than the extracellular signal that act on them, because for many extracellular signal molecules there is more than one type of receptor. The neurotransmitter acetylcholine, for example, acts on skeletal muscle cells via an ion-channel-linked receptor, whereas in heart muscle it acts through G-protein linked receptor. These two types of receptors generate different intracellular signals, and thus enable the two types of muscles to react to acetylcholine in different ways, increasing contraction in skeletal muscle and decreasing the frequency of contractions in heart. Many foreign targets can interfere with our physiology. These substances either mimic the natural ligand for a receptor, occupying the normal ligand-binding site, or bind to the receptor at some other site, blocking or over-stimulating the receptor s natural activity. Many drugs and poisons act in this way. CELL SIGNALING II. The components of signaling pathways page 3

4 3a. Ion channel-coupled receptors (in other names: ionotropic receptors, or ligand-gated ion channels, neurotransmitter-gated ion channels). When a neurotransmitter binds, this type of receptor alters its conformation so as to open or close a channel for the flow of specific types of ions - such as Na +, K +, Ca 2+, or Cl - - across the plasma membrane. Driven by electrochemical gradient, the ions rush into or out of the cell, creating a change in the membrane potential within a millisecond, or so. This change in potential may trigger a nerve impulse, or alter the ability of other signals to do so. Whereas ionchannel-linked receptors are specialty of the nervous system and other electrically excitable cells such as muscle, G-protein linked receptors and enzyme-linked receptors are used by practically every cell type of the body. See this topic in more detail in Neural communication lecture. 3b. G protein-coupled receptors (GPCRs) G-protein-linked receptors form the largest family of receptors, with hundreds of members already identified in mammalian cells. They mediate most responses to signals from the external world, as well as signals from other cells, including hormones, neurotransmitters, and local mediators. There are more than 800 GPCRs in humans, and in mice there are about 1000 concerned with the sense alone (in mice receptor genes were generated by gene duplications followed by functional divergence, while these genes were lost and mutated in the human genome). The signal molecules that act on GPCRs include proteins and small polypeptides, as well as derivatives of amino acids and fatty acids, not to mention photons of light and all the molecules that we can smell or taste. The same signal molecule can activate many different GPCR family members; for example, adrenaline activates at least 9 distinct GPCRs, acetyl choline another 5, and serotonin at least 14. The different receptors for the same signal are usually expressed in different cell types and elicit different responses. GPCR kinases (GRK; G protein-coupled receptor kinase) A GRK phosphorylates only activated receptors. The binding of an arrestin to the phosphorylated receptor prevents the receptor from binding to its G protein. GRK-mediated inactivation of GPCRs is a mechanism act to desensitization of the receptor in case of prolonged exposition to a high concentration of ligand molecules. G proteins (trimeric G proteins) When an extracellular signal molecule binds to a GPCR, the receptor undergoes a conformational change that enables it to activate a G protein. In some cases, the G protein is physically associated with the receptor before the receptor is activated, whereas in others it binds only after receptor activation. There are various types of G proteins, each specific for a particular set of GPCRs and for a particular set of target proteins in the plasma membranes. G proteins are composed of three subunits, and. In the unstimulated state, the subunit has GDP bound and the G protein is inactive. When a GPCR is activated, it acts like a guanine nucleotide exchange factor (GEF) and induces the subunit to release its bound GDP, allowing GTP to bind in its place. When a ligand binds to its receptor, the altered receptor activates the G protein by causing the subunit to lose its affinity to GDP, which it exchanges for a molecule of GTP. The activated GTP-bound subunit then dissociate from the complex (thereby activating them). The two activated parts of a G protein - the subunit and complex - then interact with their targets to elicit intracellular response. The amount of time that the two parts of G protein remain dissociated, and - hence available to relay signals is limited by the intrinsic GTPase activity of the subunit. The reassociation generally occurs within seconds after the G protein has been activated. The cholera toxin enters the cells that lines the intestine and modifies the subunit in such a way that it can no longer hydrolyze its bound GTP, thereby the subunit remains in the active state indefinitely. This results in excessive outflow of water into the gut, and thus dehydration. 3c. Enzyme-linked receptors are the receptors for many growth factors, cytokines and hormones. The cytoplasmic domain of enzyme linked receptors act as enzymes or form complexes with other proteins act as enzymes. These receptors came to light through their role in responses to extracellular signal proteins that regulate growth, proliferation, differentiation, and survival of cells. Most of these proteins act as local mediators and act at very low concentrations. Mutations in receptor tyrosine CELL SIGNALING II. The components of signaling pathways page 4

5 kinases are responsible for a wide array of diseases, including cancers, neurodegeneration, achondroplasia and atherosclerosis. There are five main types of enzyme-linked receptors: 1. Receptor tyrosine kinase (RTK): Contains intrinsic tyrosine kinase activity (EGFR, VEGFR) 2. Receptor serine/threonine Kinase: Contains intrinsic serine/threonine kinase activity (TGF-βR) 3. Receptor guanylate cyclase: Contain intrinsic cyclase activity (ANP) 4. Tyrosine-kinase associated receptors: Receptors that associate with proteins that have tyrosine kinase activity (cytokine receptors) 5. Receptor tyrosine phosphatases The largest class of enzyme-linked receptors made up of those with a cytoplasmic domain that functions as a tyrosine protein kinase, phosphorylating tyrosine side chains on selected intracellular proteins. Such receptors are called receptor tyrosine kinases. The binding of a signal molecule to the extracellular domain of a receptor tyrosine kinase causes two receptor molecules to associate into a dimer. The signal molecule (as shown in our example) is itself a dimer and thus can physically cross-link the two receptors. In other cases, binding the signal molecule changes the conformation of the receptor molecules in such a way that they dimerize. Dimer formation brings the kinase domains of each intracellular receptor tail into contact with the other; this activates the kinases and enables them to phosphorylate each other at several tyrosine side chains. Each phosphorylated tyrosine serves as a specific site for different (as many as 10 or 20) intracellular signaling proteins, which in turn, transmit their signals along several routes simultaneously to many destinations inside the cell, thus activating and coordinating the numerous biochemical changes, that are required to trigger a complex response, such as cell proliferation. To terminate the activation of the receptor, the cell contains protein tyrosine phosphatase enzymes, which remove the phosphates from the receptor (see below for other strategies of receptor inactivation). Different receptor tyrosine kinases recruit different collections of intracellular signaling proteins, producing different effects; but certain components are used quite widely. The main signaling pathway from receptor tyrosine kinases to the nucleus is the MAP-kinase pathway. Monomeric G proteins (monomeric GTPases) The most representative members of monomeric G proteins are the Ras proteins. There are three major, closely related Ras proteins in humans (H-, K-, and N-Ras). Ras contains one or more covalently attached lipid groups that help anchor the protein to the cytoplasmic face of the membrane. Ras functions as a molecular switch, cycling between two distinct conformational states active when GTP is bound and inactive when GDP is bound. Intracellular signaling molecules (I) The small intracellular mediators, or second messengers, are generated in large numbers in response to receptor activation and often diffuse away from their source, spreading the signal to other parts of the cell. In addition to their job as relay molecules, second messengers serve to greatly amplify the strength of the signal. Binding of a ligand to a single receptor at the cell surface may end up causing massive changes in the biochemical activities within the cell. Some, such as cyclic AMP and Ca 2+, are water soluble and diffuse in the cytosol, while others, such as diacylglycerol (DAG), are lipidsoluble and diffuse in the plane of the plasma membrane. In either case, they pass the signal on by binding to and altering the conformation and behavior of selected signaling proteins or effector proteins. There are 4 major classes of second messengers: 1. cyclic nucleotides (e.g., camp and cgmp) 2. inositol triphosphate (IP 3 )and diacylglycerol (DAG) 3. calcium ions (Ca 2+ ) 4. gases (NO, CO) (II) Intracellular signaling proteins help relay the signal into the cell by either generating second messenger molecules or activating the next signaling or effector protein in the pathway. These CELL SIGNALING II. The components of signaling pathways page 5

6 proteins form a functional network, in which each protein helps to process the signal in one or more of the following ways as it spreads the signal s influence through the cell. (1) The protein may simply relay the signal to the next signaling component in the chain. (2) It may act as a scaffold to bring two or more signaling proteins together so that they can interact more quickly and efficiently. (3) It may transform (or transduce) the signal into different form, which is suitable for either passing the signal, or along or stimulating a cell response. (4) It may amplify the signal it receives, either by producing a large amount of small second messenger molecules, or by activating many copies of a down-stream signaling molecule. When there are multiple amplification steps in a relay chain, the chain is often referred to as a signaling cascade. (5) It may receive signals from two or more signaling pathways and integrate them before relaying a signal onward. A protein that that requires input from two or more signaling pathways to become activated, is often referred to as a coincidence detector. 6) It may spread the signal from one signaling pathway to another, creating branches in the signaling stream, thereby increasing the complexity of the response. (7) It may anchor one or more signaling proteins in a pathway to a particular structure in the cell where the signaling proteins are needed. (8) It may modulate the activity of other signaling proteins and thereby regulating the strength of signaling along a pathway. Activation and inhibition of the components of signaling pathways Many intracellular signaling proteins behave like molecular switches. When they receive a signal, they switch from an inactive to an active conformation, until another process switches them off. Two important classes of molecular switches that operate in intracellular signaling pathways depend on the gain or loss of phosphate groups for their activation or inactivation, although the way in which the phosphate is gained and lost is very different in the two classes. One of these processes is the phosphorylation (or dephosphorylation), and the other one is the exchange of GDP to GTP, or vice versa. The modification of the activity of signal proteins can occur in other ways too (see below). 1. Phosphorylation 2. GTP-binding 3. Binding to a second messenger 4. Proteolytic cleavage 5. Dissociation of an inhibitory protein (chaperon) 6. Ubiquitination Protein kinases: protein phosphorylation The largest class of signaling proteins are activated or inactivated by phosphorylation. The activity of any protein regulated by phosphorylation depends on the balance between the activities of the kinases that phosphorylate it and phosphatases that dephosphorylate it. About 30% of human proteins contain covalently attached phosphate, and the human genome encodes about 520 protein kinases and about 150 protein phosphatases. Many signaling proteins controlled by phosphorylation are themselves protein kinases, and these are often organized into phosphorylation cascades. In such a cascade, one protein kinase, activated by phosphorylation, phosphorylates the next protein kinase in the sequence, and so on, relaying the signal onward. The great majority of these enzymes are (1) serine/threonin kinases, which phosphorylate proteins on serines and less often on threonines. (2) Others are tyrosine kinases, which phosphorylate proteins on tyrosines. GTP binding proteins: The other important class of molecular switches that function by gaining and losing phosphate groups consists of GTP-binding proteins. These proteins switch between an ON state when GTP is bound and an OFF state when GDP is bound. In the ON state they have intrinsic GTPase activity and shut themselves off by hydrolyzing their GTP to GDP. There are two major types of GTP-binding proteins. (1) Large trimeric GTP-binding proteins (also called G proteins) help relay signal from G-protein-coupled receptors that activate them. (2) Small monomeric GTP-binding proteins (also called monomeric GTPases) help relay signals from many classes of cell-surface receptors. GTPase activator proteins (GAPs) drive the proteins into an OFF state by hydrolyzing the bound GTP to GDP. CELL SIGNALING II. The components of signaling pathways page 6

7 Conversely, G-protein-coupled receptors activate trimeric G proteins, and guanine nucleotide exchange factors (GEFs) activate monomeric GTPases, by promoting the release of bound GDP in exchange for binding of GTP (no phosphorylation of GDP to GTP in a bound state!). Not all signaling proteins act as switches when they are phosphorylated or otherwise modified, covalently added groups can simply mark the protein so that it can interact with other signaling proteins that recognize the modification. Other switches Not all molecular switches in signaling pathways depend on phosphorylation or GTP binding, however. Some signaling proteins are switched on or off by binding of another signaling proteins (e.g. inhibitors, such as chaperons), or a small intracellular mediator (second messenger) such as camp or Ca 2+, or by covalent modifications other than phosphorylation, such as ubiquitylation. Proteolytic cleavage (such as in caspases) is another form of activation. Inhibitors In many signal pathways, beside the lack of incoming signal, the inactivity of a component is further ensured by binding an inhibitory protein. Proteolysis chain reaction In the process of apoptosis the proteases called caspases activate each other by cleaving a short peptide from the pro-caspase molecules. The so generated active caspase does the same with another procaspase molecule, and so on (caspase cascade). The role of calcium in the cell Calcium ions are one of the most widespread second messengers used in signal transduction. They make their entrance into the cytoplasm either from outside the cell through the cell membrane via calcium channels, or from the internal calcium storages such as endoplasmic reticulum or mitochondria. The level of intracellular calcium is regulated by transport proteins. The sodium-calcium exchanger uses energy from the electrochemical gradient of Na + pumps out Ca 2+ from the cell in exchange for the entry of Na +. Additionally, Ca 2+ pumps obtain energy to remove calcium from the cell by the hydrolysis of ATP. In neurons, voltage dependent calciumselective ion channels are important for synaptic transmission through triggering the release of neurotransmitters through the fusion of neurotransmitter vesicles with the plasma membrane of axon terminal of post-synaptic (sending) neuron. CAM-kinase-II An increase of the level of free Ca 2+ in the cytosol is triggered by many different signals. Ca 2+ exerts its effect by binding to and influencing the activity of Ca 2+ binding proteins. The most widespread and common of these is the calmodulin, which is present in the cytosol of all eukaryotic cells. When calmodulin binds to Ca 2+, the protein undergoes conformational change that enables it to wrap around a wide range of target proteins, altering their activities. One particularly important class of targets for calmodulin is the Ca 2+ /calmodulin-dependent kinases (CaM-kinases). When these kinases are activated by binding to calmodulin complexed with Ca 2+, they influence other processes in the cell by the phosphorylation of selected proteins. Chapter 15 Cell signaling and communication in the textbook LIFE is only a facultative material, but it helps understanding the topic, therefore, it is highly recommended to read. CELL SIGNALING II. The components of signaling pathways page 7

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