Cell Communication and Signaling

Cell Communication

• Cells must perceive and respond to their microenvironment for development, tissue repair, immunity, and homeostasis.
• Faulty cellular information processing leads to diseases such as cancer and autoimmunity.

Drug Targets

• Cell signaling components are the major drug targets.
• 33% of small-molecule drugs target GPCRs (7TM1).
• 18% of small-molecule drugs target ion channels.
• 16% of small-molecule drugs target kinases.
• 3% of small-molecule drugs target nuclear receptors.
• Remaining 30% is comprised of small-molecule drugs labelled as other.

Receptors

• Information in the form of signal molecules is perceived by cell-surface or intracellular receptors.
• Receptors bind signal molecules to initiate a response in the target cell.

Signaling Molecules

• Signaling molecules include amino acids, peptides, proteins, nucleotides, steroids, fatty acids, and gases.

Endocrine Signaling

• Hormones are secreted by specialized cells, often in glands.
• Hormones travel by simple diffusion or via the bloodstream.
• Examples of hormones include insulin (secreted by the pancreas), vasopressin (secreted by the hypothalamus), and adrenaline (secreted by the adrenal gland).

Paracrine Signaling

• It signals across short distances.
• Short range due to rapid degradation or hindrance by the extracellular matrix.
• Autocrine signaling is a special form of short-distance signaling, where auto equals self.
• EGF (epidermal growth factor) and IL-2 (interleukin 2) are examples of paracrine signaling molecules.

Contact-Dependent Signaling

• It uses precision, it is important for integrating multiple signals or decisive signals like cell death induction.
• A variant of contact-dependent signaling is gap junction dependent.
• Examples include Notch signaling and TNF signaling.

Synaptic/Neuronal Signaling

• Synaptic/neuronal signaling resembles paracrine signaling but features a synapse between sending and receiving cells.
• Signaling molecules are called neurotransmitters.
• It is a process that is fast and precise.

Cell Signaling Complexity

• Cells are typically exposed to hundreds of different signals like soluble, surface-bound, mechanical, activating, or inhibitory signals.
• Signal concentration, or morphogen gradient, affects cellular response.
• The cellular response to a signal is determined by the repertoire of receptors and intracellular signaling molecules expressed in a given cell type, resulting in a cell-type-specific response.

Pleiotropy

• A single signaling molecule can exert different functions in different target cells.
• The outcome depends on how the target cell receives/interprets the signal via receptors and signal transduction.

Signal Transduction Process

• It converts extracellular signals into intracellular signals that alter the behavior of target cells.
• Cell-surface receptors bind membrane-impermeable ligands, converting them into specific cellular responses.
• 10-15% of eukaryotic proteins participate in signal transduction as signaling proteins, receptors, or intracellular effectors.

Stages in a Signaling Cascade

• Reception: detecting the signal
• Transduction: relaying the signal
• Silencing / desensitization: inhibiting the signal
• Response: reacting to the signal

Glucose Homeostasis

• Regulated by two hormones.
• Insulin stimulates glucose uptake from the blood when blood sugar is high and is released by the pancreas.
• Glucagon stimulates glycogen breakdown to raise blood sugar, it is produced by the pancreas.

Glycogen

• It is a large, branched polysaccharide for energy storage.
• Glycogen consists of glucose units linked primarily by α(1→4) glycosidic bonds, with α(1→6) glycosidic bonds creating branches approximately every 8 to 10 glucose units.

Second Messenger Concept

• Second messengers are part of signal transduction.
• Earl Wilbur Sutherland Jr. won the Nobel Prize in 1971 for work on second messengers.

Second Messenger Molecules

• Low molecular weight intracellular signaling molecules mediate cell signaling.
• Transient concentration changes occur after ligands ("first messenger") bind to receptors.
• These rapid changes trigger alterations in conformation or enzymatic activity of target proteins.
• They can be water-soluble, like cAMP, or lipid-soluble, examples include DAG.
• Examples: cAMP, cGMP, 1,2-Diacylglycerol (DAG), Inositol 1,4,5-triphosphate (IP3), Ca2+, and NO

Signal Transduction via Post-Translational Modifications

• Edwin G. Krebs and Edmond H. Fischer won the Nobel Prize in 1992 for discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism.

Protein Kinases

• Protein kinases: Protein kinases modify other proteins by chemically adding phosphate groups.
• Phosphorylation often results in a functional change in the target protein, affecting enzyme activity, cellular localization, or binding to other proteins.
• The human system has approximately 500 protein kinases and 150 protein phosphatases.
• In eukaryotes, most phosphorylated amino acid residues are serine (Ser) and threonine (Thr). Only 1% are tyrosine (Tyr).
• Frequently organized into phosphorylation cascades, such as MAPK pathways.
• Catalytic domain ≈250 amino acids, consisting of an N and C-terminal lobe that form an active-site cleft.
• Catalytic domain consists of an N- and C-terminal lobe, forming an active-site cleft.
• The cleft binds and anchors substrates, and is responsible for catalysis
• ATP is buried in pocket, the γ phosphate moiety “sticks out”.
• The phosphorylatable amino acid residue is positioned adjacent to the γ phosphate moiety.
• Protein kinases often function in phosphorylation cascades.
• Phosphorylation of the "lip" of a MAPK results in activation.
• Seven superfamilies of protein kinases exist, including tyrosine kinase, tyrosine kinase-like, STE (homologs of yeast Sterile kinases), casein kinase 1 (CK1), AGC (containing PKA, PKG, PKC families), CAMK (calcium/calmodulin-dependent protein kinase), and CMGC (containing CDK, MAPK, GSK3, CLK families).

GTP-Binding Proteins

• GTP-binding proteins switch between an active (GTP-bound) and inactive (GDP-bound) state.
• Once activated by GTP, they can hydrolyze GTP, and regulate with the help of GEFs and GAPs
• GTP:GDP ratio is 10:1.
• GTP binding proteins are regulated by GEFs (guanine nucleotide exchange factors) and GAPs (GTPase activating proteins).
• There are two major forms: monomeric GTPases (small GTPases) and heterotrimeric G proteins (α,β,γ subunits).
• Five superfamilies exist: Ras, RAB, ARF, Ga, and RHO.
• Alfred G. Gilman and Martin Rodbell won the Nobel Prize in 1994 for their discovery of G-proteins.

Mobilization of Glucose

• Glucagon and adrenaline can activate the GPCR.
• Which then activates Gs.
• This then converts ATP to cAMP.
• Which activates PKA.
• Which activates PPK using ATP.
• Finally it phosphorylates glycogen to UDP-Glc.

Specificity in Signaling

• High affinity and specificity exists between interacting partners. Also there are docking sites that promote specific and high affinity interactions.
• Protein kinases contain an active interaction site with a specific amino acid sequence around the phosphorylation site in the target protein
• Thresholding provides a way to avoid any unwanted background signalling. This is done by activating a protein and messenger using higher than 'normal' amounts of protein or signal.
• Robustness: Signaling cascades downstream from a receptor often have more than one way of performing the same function meaning signalling is redundant among different mechanisms.

Domain Building Blocks

• Signaling cascades use domain building blocks such as modified peptides, peptides, Domains, and phospholipids

Intracellular Signaling Complexes

• Intracellular Signaling Complexes form at Activated Receptors by: Preformed Signaling Complex on a Scaffold Protein or Assembly of Signaling Complex on an Activated Receptor or Assembly of Signaling Complex on Phosphoinositide Docking Sites

Signaling Cascade Function

• Signaling cascades often function in double negative steps

Response Timing

• Response timing varies dramatically between different signaling systems and takes significantly less or more time depending on the function.
• The speed of a response depends on the turnover of signaling molecules.
• Signal processing can produce smoothly graded or switch-like responses.
• Switch-like responses are generated by positive feedback loops.
• Switch-like responses are due to allosteric regulatory mechanisms.
• Signaling must be effectively turned off.

Turning Off Signals

• Signaling is turned off via receptor sequestration, receptor down-regulation, receptor inactivation, inactivation of signaling protein, or production of inhibitory protein.

Intracellular Receptors

• Important signal molecules that signal via intracellular receptors:
• NO (= nitric oxide; gas)
• Ligands of nuclear receptors (steroid hormones, thyroxine)
• Nitric oxide is a gaseous signaling mediator that passes between cells and increases cGMP levels through binding and activation of guanylyl cyclase leading to the relaxation of smooth muscle cells
• Nitroglycerine is a therapeutic drug which uses NO to reduce blood pressure
• Nuclear receptors sense small lipophilic substances such as steroid or thyroid hormones and act directly on gene expression and To solubilise them in the bloodstream they are bound to specific carrier proteins.
• There are 48 nuclear receptors in the human body.

Summary of Lecture

• Four forms of intercellular signaling exist, differing in speed and selectivity.
• Signal transduction converts extracellular signals into intracellular signals that alter the behavior of target cells.
• Second messengers, molecular switches, and scaffolding proteins are key components of signal transduction cascades.
• Key 2nd messenger systems: cAMP, DAG, and Ca2+.
• The lecture also covered G-proteins: monomeric, trimeric, GEFs, gaps, protein kinases, common interaction motifs, scaffolding systems, signalosomes.
• Enzyme cascades enable signal amplification and fine tuning.
• A cell's response to a signal can be fast or slow, depending on whether it involves changes in gene expression/protein synthesis or only alters protein function.
• Switchlike responses are caused by positive feedback loops or allosteric regulation.
• Turning off signaling pathways is as important as activating them.
• Small hydrophobic extracellular signals such as steroid hormones and nitric oxide diffuse directly across the plasma membrane to activate intracellular receptors.
• Signal molecules that cannot cross the membrane bind to cell-surface receptors, converting (transducing) the extracellular signal into an intracellular signal.
• Core Classes of cell-surface receptors: (1) Ion-channel-coupled receptors, (2) G-protein-coupled receptors, and (3) Enzyme-coupled receptors.