Chapter 14

Principles of Cell SignalingBy

Melanie H. Cobb & Elliott M. Ross

14.2 Cellular signaling is primarily chemical

• Cells can detect both chemical and physical signals.

• Physical signals are generally converted to chemical signals at the level of the receptor.

14.3 Receptors sense diverse stimuli but initiate a limited repertoire of

cellular signals• Receptors contain:

– a ligand-binding domain– an effector domain

• Receptor modularity allows a wide variety of signals to use a limited number of regulatory mechanisms.

• Cells may express different receptors for the same ligand.

• The same ligand may have different effects on the cell depending on the effector domain of its receptor.

14.3 Receptors sense diverse stimuli but initiate a limited repertoire of cellular signals

14.4 Receptors are catalysts and amplifiers

• Receptors act by increasing the rates of key regulatory reactions.

• Receptors act as molecular amplifiers.

14.5 Ligand binding changes receptor conformation

• Receptors can exist in active or inactive conformations.

• Ligand binding drives the receptor toward the active conformation.

14.6 Signals are sorted and integrated in signaling pathways

and networks• Signaling pathways usually have

multiple steps and can diverge and/or converge.

• Divergence allows multiple responses to a single signal.

• Convergence allows signal integration and coordination.

14.7 Cellular signaling pathways can be thought of as biochemical logic

circuits• Signaling networks are composed of

groups of biochemical reactions.– The reactions function as mathematical

logic functions to integrate information.

• Combinations of such logic functions combine as signaling networks to process information at more complex levels.

14.8 Scaffolds increase signaling efficiency and enhance spatial

organization of signaling• Scaffolds:

– organize groups of signaling proteins – may create pathway specificity by

sequestering components that have multiple partners

• Scaffolds increase the local concentration of signaling proteins.

• Scaffolds localize signaling pathways to sites of action.

14.8 Scaffolds increase signaling efficiency and enhance spatial organization of signaling

14.9 Independent, modular domains specify protein-protein interactions

• Protein interactions may be mediated by small, conserved domains.

• Modular interaction domains are essential for signal transmission.

• Adaptors consist exclusively of binding domains or motifs.

14.10 Cellular signaling is remarkably adaptive

• Sensitivity of signaling pathways is regulated to allow responses to change over a wide range of signal strengths.

• Feedback mechanisms execute this function in all signaling pathways.

• Most pathways contain multiple adaptive feedback loops to cope with signals of various strengths and durations.

14.10 Cellular signaling is remarkably adaptive

14.11 Signaling proteins are frequently expressed as multiple

species• Distinct species (isoforms) of

similar signaling proteins expand the regulatory mechanisms possible in signaling pathways.

• Isoforms may differ in:– function– susceptibility to regulation – expression

• Cells may express one or several isoforms to fulfill their signaling needs.

14.11 Signaling proteins are frequently expressed as multiple species

14.12 Activating and deactivating reactions are separate and independently controlled

• Activating and deactivating reactions are usually executed by different regulatory proteins.

• Separating activation and inactivation allows for fine-tuned regulation of amplitude and timing.

14.13 Cellular signaling uses both allostery and covalent modification

• Allostery refers to the ability of a molecule to alter the conformation of a target protein when it binds noncovalently to that protein.

• Modification of a protein’s chemical structure is also frequently used to regulate its activity.

14.14 Second messengers provide readily diffusible pathways for

information transfer• Second messengers can propagate

signals between proteins that are at a distance.

• cAMP and Ca2+ are widely used second messengers.

14.15 Ca2+ signaling serves diverse purposes in all eukaryotic cells

• Ca2+ serves as a second messenger and regulatory molecule in essentially all cells.

• Ca2+ acts directly on many target proteins.– It also regulates the activity of a

regulatory protein calmodulin.

• The cytosolic concentration of Ca2+ is controlled by organellar sequestration and release.

14.15 Ca2+ signaling serves diverse purposes in all eukaryotic cells

14.16 Lipids and lipid-derived compounds are signaling molecules

• Multiple lipid-derived second messengers are produced in membranes.

• Phospholipase Cs release soluble and lipid second messengers in response to diverse inputs.

• Channels and transporters are modulated by different lipids in addition to inputs from other sources.

• PI 3-kinase synthesizes PIP3 to modulate cell shape and motility.

• PLD and PLA2 create other lipid second messengers.

14.16 Lipids and lipid-derived compounds are signaling molecules

14.17 PI 3-kinase regulates both cell shape and the activation of essential

growth and metabolic functions

• Phosphorylation of some lipid second messengers changes their activity.

• PIP3 is recognized by proteins with a pleckstrin homology domain.

14.18 Signaling through ion channel receptors is very fast

• Ion channels allow the passage of ions through a pore.– This results in rapid (microsecond)

changes in membrane potential.

• Channels are selective for particular ions or for cations or anions.

• Channels regulate intracellular concentrations of regulatory ions, such as Ca2+.

14.18 Signaling through ion channel receptors is very fast

14.19 Nuclear receptors regulate transcription

• Nuclear receptors modulate transcription by binding to distinct short sequences in chromosomal DNA known as response elements.

• Receptor binding to other receptors, inhibitors, or coactivators leads to complex transcriptional control circuits.

• Signaling through nuclear receptors is relatively slow, consistent with their roles in adaptive responses.

14.19 Nuclear receptors regulate transcription

14.20 G protein signaling modules are widely used and highly

adaptable• The basic module is:

– a receptor– a G protein – an effector protein

• Cells express several varieties of each class of proteins.

• Effectors are heterogeneous and initiate diverse cellular functions.

14.20 G protein signaling modules are widely used and highly adaptable

14.21 Heterotrimeric G proteins regulate a wide variety of effectors

• G proteins convey signals by regulating the activities of multiple intracellular signaling proteins known as effectors.

• Effectors are structurally and functionally diverse.

• A common G-protein binding domain has not been identified among effector proteins.

• Effector proteins integrate signals from multiple G protein pathways.

14.21 Heterotrimeric G proteins regulate a wide variety of effectors

14.22 Heterotrimeric G proteins are controlled by a regulatory GTPase

cycle• Heterotrimeric G proteins are

activated when the Gαsubunit binds GTP.

• GTP hydrolysis to GDP inactivates the G protein.

• GTP hydrolysis is slow, but is accelerated by proteins called GAPs.

• Receptors promote activation by allowing GDP dissociation and GTP association. – Spontaneous exchange is very slow.

• RGS proteins and phospholipase C-βs are GAPs for G proteins.

14.22 Heterotrimeric G proteins are controlled by a regulatory GTPase cycle

14.23 Small, monomeric GTPbinding proteins are multiuse switches

• Small GTP-binding proteins are:– active when bound to GTP – inactive when bound to GDP

• GDP/GTP exchange catalysts known as GEFs (guanine nucleotide exchange factors) promote activation.

• GAPs accelerate hydrolysis and deactivation.

• GDP dissociation inhibitors (GDIs) slow spontaneous nucleotide exchange.

14.23 Small, monomeric GTPbinding proteins are multiuse switches

14.24 Protein phosphorylation/ dephosphorylation is a major

regulatory mechanism in the cell

• Protein kinases are a large protein family.

• Protein kinases phosphorylate:– Ser and Thr– or Tyr– or all three

• Protein kinases may recognize the primary sequence surrounding the phosphorylation site.

• Protein kinases may preferentially recognize phosphorylation sites within folded domains.

14.24 Protein phosphorylation/ dephosphorylation is a major regulatory mechanism in the cell

14.25 Two-component protein phosphorylation systems are

signaling relays• Two-component signaling systems

are composed of sensor and response regulator components.

• Upon receiving a stimulus, sensor components undergo autophosphorylation on a histidine (His) residue.

• Transfer of the phosphate to an aspartyl residue on the response regulator serves to activate the regulator.

14.25 Two-component protein phosphorylation systems are signaling relays

14.26 Pharmacological inhibitors of protein kinases may be used to understand and treat disease

• Protein kinase inhibitors are useful both:– for signaling research – as drugs

• Protein kinase inhibitors usually bind in the ATP binding site.

14.27 Phosphoprotein phosphatases reverse the actions of kinases and

are independently regulated

• Phosphoprotein phosphatases reverse the actions of protein kinases.

• Phosphoprotein phosphatases may dephosphorylate:– phosphoserine/threonine– phosphotyrosine– or all three

• Phosphoprotein phosphatase specificity is often achieved through the formation of specific protein complexes.

14.27 Phosphoprotein phosphatases reverse the actions of kinases and are independently regulated

14.18 Covalent modification by ubiquitin and ubiquitinlike proteins is another way of regulating protein

function• Ubiquitin and related small

proteins may be covalently attached to other proteins as a targeting signal.

• Ubiquitin is recognized by diverse ubiquitin binding proteins.

• Ubiquitination can cooperate with other covalent modifications.

• Ubiquitination regulates signaling in addition to its role in protein degradation.

14.18 Covalent modification by ubiquitin and ubiquitinlike proteins is another way of regulating protein function

14.29 The Wnt pathway regulates cell fate during development and

other processes in the adult

• Seven transmembrane-spanning receptors may control complex differentiation programs.

• Wnts are lipid-modified ligands.

• Wnts signal through multiple distinct receptors.

• Wnts suppress degradation of β-catenin, a multifunctional transcription factor.

14.29 The Wnt pathway regulates cell fate during development and other processes in the adult

14.30 Diverse signaling mechanisms are regulated by protein tyrosine

kinases• Many receptor protein tyrosine

kinases are activated by growth factors.

• Mutations in receptor tyrosine kinases can be oncogenic.

• Ligand binding promotes:– receptor oligomerization– autophosphorylation

• Signaling proteins bind to the phosphotyrosine residues of the activated receptor.

14.30 Diverse signaling mechanisms are regulated by protein tyrosine kinases

14.31 Src family protein kinases cooperate with receptor protein

tyrosine kinases• Src is activated by release of intrasteric

inhibition.

• Activation of Src involves liberation of modular binding domains for activation-dependent interactions.

• Src often associates with receptors, including receptor tyrosine kinases.

14.32 MAPKs are central to many signaling pathways

• MAPKs are activated by Tyr and Thr phosphorylation.

• The requirement for two phosphorylations creates a signaling threshold.

• The ERK1/2 MAPK pathway is usually regulated through Ras.

14.33 Cyclin-dependent protein kinases control the cell cycle

• The cell cycle is regulated by cyclin-dependent protein kinases (CDKs).

• Activation of CDKs involves:– protein binding– dephosphorylation– phosphorylation

14.34 Diverse receptors recruit protein tyrosine kinases to the

plasma membrane• Receptors that bind protein

tyrosine kinases use combinations of effectors similar to those used by receptor tyrosine kinases.

• These receptors often bind directly to transcription factors.