The Role of Key Players in Cell Signaling Pathways

Lipid-Modifying Enzymes

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Protein Kinases

Serine/ Threonine kinases

cGMP dependent PK (PKG)

multifunctional calcium/calmodulin-dependent protein kinases (CAMKs)

Protein kinase C (PKC)

5' AMP activated protein kinase (AMPK)

Haem regulated protein kinase (HRI)

cAMP dependent PKA
(Protein Kinase A)

-enzyme attaches a phosphate to a protein


-turn on a protein


-activate signaling molecule


-phosphorylation occur

Protein phosphate

Tyrosine kinase
-"on" or "off" switch

Cytosolic tyrosine kinases

cAMP activates PKA

-enzyme remove a phosphate from a protein


-turn off a protein


-inactive signaling molecule**


-Dephosphorylation occur

Serine/Threonine phosphate

Tyrosine phosphate

Intracellular phosphates

Receptor linked

cAMP is derived from ATP
ATP --> cAMP
by enzyme adenylyl cyclase

exists as a heterotetrameric complex consisting of two catalytic (Cα, Cβ and Cγ,) and two regulatory subunits ( type I (RIα and RIβ) and type II (RIIα and RIIβ).

cGMP activates PKG

cAMP bind to the R subunits causing release of active C subunits, this causing a conformational change in the regulatory subunits

activation of the catalytic subunits, allowing them to phosphorylate specific serine and threonine residues on target proteins within the cell

PKA phosphorylates transcription factors, including CREB and NFκB

Second messenger: cAMP

leading to a variety of cellular responses

Termination of cAMP
cAMP--> AMP
by phosphodiesterases

deactivation of PKA as the regulatory subunits rebind to the catalytic subunits, returning them to an inactive state

contains a catalytic domain and a regulatory domain, and for its activation requires cGMP, which is synthesized by guanylyl cyclases

cGMP binds to PKG causing a conformational change, which removes a pseudosubstrate domain and frees the catalytic site.

GTP--> cGMP
by activated guanylyl cyclase

Second messenger: cGMP

-Membrane-bound guanylyl cyclases: These are activated by natriuretic peptides.


-Soluble guanylyl cyclases: These are activated by nitric oxide (NO).

PKG exists in three isoforms in mammalian cells:
PKGIα and PKGIβ in the cytosol
PKGII in cell membrane at the N-terminus.

The catalytic domain of PKG becomes active and phosphorylates various serine and threonine residues on target proteins.

leading to a variety of cellular responses

Termination of cGMP
cGMP--> GMP
by phosphodiesterases

Deactivation of PKG as the regulatory subunits rebind to catalytic subunits, returning them to an inactive state.

Second messenger: NO gases

Calcium ions, Ca2+ bind to calmodulin, a small, ubiquitous protein that can bind up to 4 Ca²⁺ ions in cytoplasm.

The binding of Ca²⁺ causing a conformational change in calmodulin, enabling it to interact with target proteins

The activated Ca2+-calmodulin binding then will binds to CAMKs and activated the kinase.

This activation of kinase causing a conformational change that exposes the kinase’s active site or releases an inhibitory domain.

Most characterized: calcium/calmodulin-dependent protein kinase II (CAM kinase II)

CAMKs use ATP to phosphorylate serine and threonine residues on target proteins.

leading to a variety of cellular responses

CaMKII is a prominent member of this kinase family and is a multimeric enzyme consisting of multiple subunits (usually 12) that form a holoenzyme complex.


These subunits can be identical or different isoforms, with each subunit having a molecular weight of approximately 50-60 kDa.

CAMKs phosphorylate several transcription factors

In the presence of Ca²⁺-calmodulin binding, CaMKII activation involves autophosphorylation.

Termination of Ca2+ involve dissociation of Ca²⁺-calmodulin from the CAMKs.

Protein phosphatases
-dephosphorylate the target proteins, reversing the effects of CaMK-mediated phosphorylation and deactivated.

Second messenger: Ca2+

has a regulatory domain that binds to autoinhibitory pseudosubstrate and inhibits its catalytic domain. This binding prevents the kinase from phosphorylating target proteins. (inactive state)

PKC activated by Ca2+, DAG, IP3 and phosphatidylserine

The binding induces a conformational change in PKC, leading to the dissociation of the regulatory domain/pseudosubstrate from the catalytic domain.

This conformational change exposes the catalytic site, allowing PKC to become active and phosphorylate serine and threonine residues on target proteins.

leading to a variety of cellular responses

Activation of some PKC forms can also be through PI-3kinase pathway

Receptor tyrosine kinases (RTKs)

This activation of AMPK occurs through phosphorylation of the Thr-72 residue in the AMPKα subunit by by AMPK kinase(AMPKK)

By phosphorylating targets like acetyl-CoA carboxylase 1 (ACC1) or sterol regulatory element-binding protein 1c (SREBP1c), AMPK effectively inhibit the synthesis of lipids (fatty acids, cholesterol, and triglycerides) while promoting fatty acid uptake and β-oxidation.

In its active form, AMPK phosphorylates various metabolic enzymes, leading to the inhibition of pathways involved in the synthesis of fatty acids and cholesterol.

Function: insulin signaling. Inhibition of AMPK in the presence of glucose can activate insulin secretion.

High level AMP activates AMPK
ATP--> AMP

Promoting catabolic pathways that generate more ATP

Inhibit anabolic pathways that consume ATP

Activated by upstream kinases such as LKB1 and CAMKK2 in response to various physiological stresses2.

acts as sensor for cellular energy status in some cells

Sensitive to changes in intracellular haem levels, thus important for the regulation of hemoglobin synthesis

conditions like iron deficiency or oxidative stress


If haem is absent, regulatory domain of HRI undergoes a conformational change which exposes the catalytic domain and lead to activation of kinase domain.

If haem is present, kinase not active as haem binds to it, protein synthesis occurs

This activation involves autophosphorylation of HRI, which then phosphorylates the eukaryotic initiation factor 2 (eIF-2).

When haem levels are restored, haem binds to HRI again, leading to the re-inhibition of the kinase activity.

all possess an extracellular ligand binding domain, a single transmembrane domain and a cytoplasmic domain which contains the kinase activity

Ligand binds to extracellular binding site of the receptor causing a conformational change which activates the kinase activity on the cytoplasmic side of the receptor.

Turn on :Phophotidylinositol 3-kinase (inositol pathway), GTPase-activating protein (G-Protein signaling) and mitogen activated protein kinase cascades (MAP kinases)

Phosphorylation of this kinase activity then leads to intracellular signaling

Involve in:
-Vascular Endothelial Growth Factor (VEGF)
-Neurotrophins
-Insulin-like Growth Factor-1 (IGF-1)

contain tyrosine phosphorylation capacity which membrane bound, soluble and reside in the cytoplasm of the cell or associated with the membrane proteins

Janus Kinases (JAKs)

-contain tandem, but non-identical, catalytic domains
-involved in interactions with the other proteins they
-lack both SH2 and SH3

The activated JAKs phosphorylate each other and the receptor, creating docking sites for other proteins.

Signal transducers and activators of transcription (STAT) proteins, which have SH2 domains, bind to these phosphorylated sites and are themselves phosphorylated by JAKs.

Phosphorylated STAT proteins dimerize by binding ofphosphotyrosine residues of one STAT with another STAT's SH2 domain.

The STAT dimers move to nucleus to bind to DNA and regulate gene transcription.

In humans there are at least seven different STAT proteins and seven JAK homology domains

Different types of these enzymes :PP1, PP2A, PP2B, PP2C, PP4 and PP5.

Soluble, associated with the cytoplasm

extracellular domain , a transmembrane domain and domain containing phosphatase activity

Example: PTP 1B

Example: CD45

Tyrosine-specific Protein Phosphatases (PTPase):

These enzymes catalyze the removal of a phosphate group from a tyrosine residue using a cysteinyl-phosphate enzyme intermediate

Are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control1.

Important in controlling cell growth, proliferation, differentiation, transformation, and synaptic plasticity.

PP2B
*PP2B(calcineurin) heterodimer (calcium dependent enzyme

PP2C
*Monomeric(Mg2+ dependent enzyme)

PPA2
trimeric protein and have similarities to PP1 Include the control of DNA replication and apoptosis

PP5
*Found in nucleus(RNA and DNA binding)

Cell proliferation,cell death, embryonic development and cell differentiation

PP1
Has broad substrate specificity Catalytic subunits of 37 kDa inhibit activity og PP1
Involved in regulation of glycogen (under control of phosphorylation)metabolism PP1 is under control of cAMP signaling pathway

Second messenger: diacylglycerol (DAG), inositol trisphosphate (IP3)

SECOND MESSENGER

  • Relay signals at receptor on cell surface

Transcription factors

proteins that bind to DNA-regulatory sequences (enhancers and silencers), usually localized in the 5-upstream region of target genes, to modulate the rate of gene transcription. This may result in increased or decreased gene transcription, protein synthesis, and subsequent altered cellular function. Many transcription factors have now been identified and a large proportion of the human genome appears to code for these proteins.

How does it function in cell signalling pathways?

Lipid-modifying enzymes are a diverse group of enzymes that play critical roles in the metabolism of lipids, which include fats, oils, waxes, and certain vitamins, among others. These enzymes are essential for various biological processes, including energy storage, cell membrane structure, signal transduction, and the synthesis of hormones. Here’s an in-depth look at different types of lipid-modifying enzymes, their functions, and their importance:

Lipases

Triacylglycerol Lipase (TG Lipase): This enzyme catalyzes the hydrolysis of triacylglycerol (TAG) into free fatty acids and glycerol, which can be used for energy production. TG lipase is highly active in adipose tissue, where it mobilizes stored fats during fasting or exercise.

Hormone-Sensitive Lipase (HSL): HSL is an enzyme that is activated in response to hormonal signals like adrenaline and glucagon. It breaks down stored triglycerides in adipocytes (fat cells) to release fatty acids for energy production during periods of low carbohydrate availability.

Pancreatic Lipase: This enzyme is critical for the digestion of dietary fats. It breaks down triglycerides in the small intestine into monoglycerides and free fatty acids, which can be absorbed by the intestinal cells.

Phospholipases

Phospholipase A2 (PLA2): PLA2 enzymes hydrolyze the sn-2 acyl bond of phospholipids, releasing arachidonic acid, a precursor for eicosanoids (prostaglandins, thromboxanes, leukotrienes). These signaling molecules are involved in inflammation and other physiological processes.

Phospholipase C (PLC): PLC enzymes cleave the phosphodiester bond of phosphatidylinositol 4,5-bisphosphate (PIP2), generating inositol triphosphate (IP3) and diacylglycerol (DAG). IP3 mediates calcium release from intracellular stores, while DAG activates protein kinase C (PKC), both of which are important for signal transduction.

Phospholipase D (PLD): PLD hydrolyzes phosphatidylcholine (PC) to produce phosphatidic acid (PA) and choline. PA is a lipid second messenger that plays a role in membrane trafficking, cytoskeletal organization, and cell signaling.

Fatty Acid Synthase (FAS)

FAS: Fatty Acid Synthase is a multi-enzyme complex that catalyzes the synthesis of long-chain fatty acids from acetyl-CoA and malonyl-CoA in the cytosol. It is crucial in adipocytes for the storage of energy as fat and in the liver for the synthesis of fatty acids that are incorporated into lipoproteins.

Sphingomyelinases

Acid Sphingomyelinase (ASM): This enzyme hydrolyzes sphingomyelin, a type of sphingolipid found in cell membranes, to produce ceramide. Ceramide is a bioactive lipid that plays a role in apoptosis (programmed cell death), cell growth arrest, and inflammation.

Neutral Sphingomyelinase (NSM): NSM also hydrolyzes sphingomyelin to generate ceramide but operates optimally at a neutral pH. It is involved in signal transduction pathways that regulate cell stress responses.

Lipoprotein Lipase (LPL)

LPL: Lipoprotein lipase is an enzyme located on the endothelial surface of capillaries in adipose tissue, muscle, and the heart. It hydrolyzes triglycerides in circulating chylomicrons and very low-density lipoproteins (VLDL) into free fatty acids, which are then taken up by cells for energy or storage.

Cholesterol Esterases

Cholesteryl Ester Hydrolase (CEH): CEH enzymes catalyze the hydrolysis of cholesteryl esters to free cholesterol and fatty acids. This reaction is essential in the mobilization of cholesterol from intracellular stores, particularly in steroidogenic tissues where cholesterol is a precursor for steroid hormones.

Hormone-Sensitive Cholesteryl Esterase: Similar to hormone-sensitive lipase, this enzyme is activated by hormonal signals and plays a crucial role in the regulation of cholesterol homeostasis, particularly during stress or fasting.

Desaturases

Stearoyl-CoA Desaturase (SCD): SCD introduces a double bond into saturated fatty acyl-CoAs, producing monounsaturated fatty acids (MUFAs) like oleic acid. These MUFAs are key components of membrane phospholipids, triglycerides, and cholesterol esters.

Delta-5 and Delta-6 Desaturases: These enzymes are involved in the biosynthesis of polyunsaturated fatty acids (PUFAs) from essential fatty acids like linoleic acid and alpha-linolenic acid. PUFAs are important for the fluidity of cell membranes and serve as precursors for eicosanoids, which have various signaling roles in inflammation and immunity.

Lipid Kinases

Phosphatidylinositol-4-Phosphate 5-Kinase (PIP5K): This enzyme phosphorylates phosphatidylinositol 4-phosphate (PI4P) to produce phosphatidylinositol 4,5-bisphosphate (PIP2), a crucial lipid that serves as a substrate for PLC and regulates various cellular processes, including cytoskeletal organization and membrane trafficking.

Diacylglycerol Kinase (DGK): DGK phosphorylates diacylglycerol (DAG) to produce phosphatidic acid (PA). This reaction is critical in terminating DAG-mediated signaling and in generating PA, which has signaling functions in its own right.

Lysosomal Lipid-Modifying Enzymes

Acid Lipase: Found in lysosomes, this enzyme is responsible for breaking down cholesteryl esters and triglycerides within lysosomes, releasing free cholesterol and fatty acids that can be used by the cell. Mutations in this enzyme can lead to lysosomal storage diseases like Wolman disease and cholesteryl ester storage disease.

Ceramide Synthases (CerS)

Ceramide Synthases: These enzymes catalyze the formation of ceramide from sphinganine (a long-chain base) and fatty acyl-CoA. Ceramide is a central molecule in sphingolipid metabolism and plays important roles in regulating cell growth, differentiation, and apoptosis.

Acetyl-CoA Carboxylase (ACC)

ACC1 and ACC2: ACC is a key enzyme in the biosynthesis of fatty acids. It catalyzes the carboxylation of acetyl-CoA to form malonyl-CoA, the first committed step in fatty acid synthesis. ACC1 is primarily involved in lipogenesis (fatty acid synthesis), while ACC2 regulates fatty acid oxidation by controlling the levels of malonyl-CoA, which inhibits carnitine palmitoyltransferase 1 (CPT1), the enzyme responsible for transporting fatty acids into mitochondria for oxidation.

Acyl-CoA Synthetases

Acyl-CoA Synthetase (ACS): This family of enzymes activates fatty acids by attaching them to Coenzyme A (CoA), forming acyl-CoA. This activation is necessary for the fatty acids to participate in various metabolic pathways, including β-oxidation, where they are broken down to generate ATP.

Long-Chain Acyl-CoA Synthetase (ACSL): ACSL enzymes specifically activate long-chain fatty acids. These activated fatty acids can then be used for the synthesis of complex lipids like triglycerides or for energy production through β-oxidation.

cAMP

  • from ATP by adenylyl cyclase

PKA
( inactive )

2 cAMP binds to regulatory subunit

Thus, dissociate catalytic subunit
( gets phosphorylated )

PKA activate CREB

cGMP

  • from GTP by guanylyl cyclase

Act as second messenger for

  • Atrial natriuretic peptide ( ANP )
  • Nitric oxide ( NO )
  • Response of rods of the retina to light ( vision )

IP3 & DAG

Effects of cGMP mediated through PKG

Dependent protein kinase phosphorylates the
target protein in the cell

cGMP converted back to GTP by
phosphodiesterase enzyme

Extracellular ligand binds to GPCR

GPCR activated

Leads to the activation of
phospholipase C

PIP2

IP3

DAG

enters cytosol
wall

binds to IP3/Ca2+ channel
attached to ER

Opens the channel and
release Ca2+

remain associated with
plasma membrane

recruit PKC

Activation of PKC needs
calcium ions

Available by the action of IP3

Calcium

Ca2+ binds to calmodulin

Calmodulin activate calcium - calmodulin
dependant protein kinase

Calmodulin mediate the
biological effect of Ca2+

Eicosanoid

  • phospholipid bilayer

phospholipase A2 catalise the
release of arachidonic acid

Lipoxygrnase
( LOX )

Cyclooxygenase
( COX )

Cytochrome 450
( cyt P450 )

NO

stimulate nerve to release Ach

Ach binds to receptor
on endothelial cell

activate NO synthase

diffuse across membrane

NO binds to guanylyl cyclase

signal dilation of blood vessels

GROUP 7
-CHAN JIA YI


-NURUL SYAZLIN HAZZAH BINTI ISHAK


-ALEEYA NATASYA


-SHAFIQAH


-BASHIR AL HARITH BIN OMAR

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• Sry-Related HMG-Box (SOX)

• Forkhead Box (FOX)

• Signal Transducer and Activator of Transcription (STAT)

• TATA-Binding Protein (TBP) and TFIID Complex

• Nuclear Receptor

• Helix-Turn-Helix (HTH)

• Zinc Finger

• Basic Helix-Loop-Helix (bHLH)

There are 8 types of transcription factors families:

Signal Reception: Cell signaling pathways often begin with the reception of an external signal, such as a hormone or growth factor, by a cell surface receptor.

Activation of Transcription Factors: As the signal transduction pathway progresses, it frequently leads to the activation or inhibition of transcription factors. This activation can occur through various mechanisms, including phosphorylation (addition of phosphate groups), binding of signaling molecules, or changes in cellular localization.

Signal Transduction: The binding of the signal to its receptor triggers a cascade of intracellular events. This can involve various proteins, second messengers, and other molecules that relay and amplify the signal.

Gene Regulation: Once activated, transcription factors move into the nucleus (if they are not already there) and bind to specific DNA sequences in the promoter or enhancer regions of target genes. This binding can either promote or inhibit the transcription of these genes into mRNA.

Cellular Response: The changes in gene expression lead to alterations in cellular behavior. For example, genes involved in cell growth, differentiation, or apoptosis (programmed cell death) may be turned on or off in response to the signaling pathway.


Feedback and Regulation: Transcription factors can also play roles in feedback loops, where they regulate the expression of other components in the signaling pathway to ensure the proper level of response and prevent overreaction.

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Other covalent modifications
Protein cleavage
-not reversable
Adenylation
-controls nitrogen metabolism
Fatty acid/isoprene addition
-membrane targeting
Reactive oxygen or nitrogen species(ROS,RNS)
-effect protein function