Signal networks and pathways
Chitta Baral
Arizona State University
Goal: Decoding the cell and …
• Ultimate goal
– Decoding the cell (understand what is happening
inside the cell)
– Control cell behavior
• It involves
– Accurate description of cellular biochemistry that
allows
• Explanation of particular cell behaviors and phenotypes
(such as proliferation, cell migration, cell death, etc.)
• Prediction of future behavior
• Planning interactions with the cell to control the cell behavior
Biochemistry, network of
interactions
• Relation between various molecules is often expressed
using network of interactions (called Biochemical
networks)
• Three kinds of biochemical networks
– Metabolic networks
• Represent the chemical transformation between metabolites
• Example: Glycolysis (breakdown of glucose)
– Signal networks (also called protein networks)
• Representing protein-protein interactions
– Gene networks
• Representing relationship between genes that encode the impact of
the expression level of one gene on another
• Pathways: Specific series of interaction in a network
G proteins
• 1994 Nobel prize. Discovery of G-protein coupled
receptors and their role in signal transduction. Gilman,
Alfred G. and Rodbell, Martin.
http://www.nobel.se/medicine/laureates/1994/index.html
• 43,409 articles in Medline that mention G proteins.
• 1. Basic facts about G proteins
– Each G-protein consists of 3 sub-units: Ga, Gb, and Gg.
– These sub-units can be together or separated.
– Each G-protein has a binding site that can be occupied by either
GDP or GTP.
– A G-protein is said to be inactive when it is bound to GDP.
– A G-protein is said to be active when it is bound to GTP.
cyclicAMP (cAMP) pathway
• 2. Up regulation: When a ligand binds to a
receptor in a cell membrane the effect is that
– A. the receptor becomes activated
– B. the nucleotide binding site on the G-protein is
altered,
– C. GTP replaces GDP,
– D. GDP is released,
– E. and Ga-GTP gets disassociated from GbGg.
– F. Ga being active triggers the binding of Ga-GTP to a
membrane bound adenylate cyclase molecule,
• activating it for production of cyclicAMP (cAMP).
G protein activation/inactivation
cycle
cAMP
cyclicAMP (cAMP) pathway
• 3. Down regulation – when the ligand
dissociates from the receptor the effects are
– A. GTP is hydrolyzed by a GTPase activity on Ga
– B. Ga-GTP becomes Ga-GDP,
– C. and disassociates from adenylate cyclase
molecule, making the later inactive.
– D. Ga then reassociates with GbGg
– E. CyclicAMP (in the cytoplasm) is then inactivated
by the enzyme phosphodiesterase, which hydrolyzes
it to AMP.
Interference with cAMP
• A. Cholera toxin inhibits the GTPase activity of
the G-proteins of Gs subfamily, thus impacting
3A.
• B. The ras gene produces a G-protein that lacks
GTPase activity, thus impacting 3A.
• C. Pertussis toxin inactivates the process that
downregulates adenylate cyclase activity with
respect to G-proteins of the Gi subfamily, with a
few exceptions such as Gz, thus impacting 3C.
• D. G-proteins of the Gq subfamily are not
modifiable by pertussis toxin or cholera toxin,
thus nullifying A and C above.
A specific example of CAMP
mediated regulation – Glycogen
degradation
• In liver or muscle cells in presence of the ligand
epinephrine hormone (also called adernalin) increase in
the cAMP concentration (in the cytoplasm)
– activates protein kinase,
– active protein kinases then converts inactive phosphorylase
kinase to active form by ATP dependent phosphorylation,
– active phosphorylase kinase then phosphorylates (i.e., converts)
less active phosphorylase-b to more active phosphorylase-a,
and
– phosphorylase-a then catalyzes the phosphorolytic cleavage of
glycogen into molecules of glucose-1-phosphate. (i.e., glycogen
breakdown happens.)
References (for stuff so far)
• The world of cell 2nd ed. Becker, Deamer.
Chapter 21. (Latest one is 5th ed, by Becker,
Kleinsmith and Hardin; has a nice Cd-Rom with
the book and explains signal transduction very
well)
• Biochemistry of signal transduction and
regulation. G. Krauss. Sec 5.5.1
• http://www.mun.ca/biology/desmid/brian/BIOL20
60_W2003/CellBiol10/CB10.html
• Look for signal transduction, pathways, signal
pathways, G protein, biochemical networks etc.
Reasoning about cAMP and
Glycogen degradation
• Observation: cAMP concentration way above
normal
– Possible explanation: presence of Cholera toxin or
Pertussis toxin
– Planning: How to overcome it using drugs.
• Predicting the impact of not having enough
adernalin.
• Observation: Lack of glycogen breakdown.
– Explained by low cAMP concentration
• Explained by G proteins not getting activated in adequate
concentration
Computer Science (AI) challenges
• Represent signal networks
– Such that we can reason with it
– We can elaborate on it (add more details)
without making wholesale changes
• Reason with them
– Explain observations.
– Predict effect of particular actions.
– Plan to make the cell behave a particular way.
Analogy with current AI research
• Goal: To represent effect of actions on the world,
executability condition of actions, relation between
objects in the world, etc.
• An example:
– Description D.
•
•
•
•
S1
S2
S3
S4
Load causes loaded.
Shoot causes ~ alive if loaded.
Intially alive.
Initially ~loaded.
– Planning: D |= ~alive after X.
X=Load;Shoot.
– Explanation: {S1, S2, S3, ~alive after shoot} |= Initially loaded
– Prediction:
• D |= ~alive after Load? D |= loaded after Load?
Home work 3 (Due Feb 17th) – 100
pts
• Describe a particular signal pathway.
– Draw the figure.
– Write in English similar to the slides
– Write in English-like syntax. (such as in the
previous slide and make up specific terms like
`causes’ that you may need.)
– Source (journal: Cellular signaling; signal
transduction chapter in books on cell biology;
www.afcs.org. etc.) 50% bonus if you use a
journal instead of a book.
Glossary
•
Activation
–
•
Adenylate Cylase
–
–
•
A process of (i) initiating a chemical or biochemical reaction (ii) converting an
inactive component to a functionally active form.
The enzyme that catalyzes the synthesis of cyclic AMP (cAMP) from ATP,
ATP <--> cAMP + PP
Allosteric
– Pertaining to the topologically distinct sites on a protein or an enzyme molecule.
•
AMP
– An Adenosine 3'-monophosphate or Adenosine 5'-monophosphate nucleotide
with the
phosphate group linked to the carbon 3 (or 5 resp.) of the
ribose.
•
Arrestin
– Family of inhibitory proteins that bind to tyrosine-phosphorylated receptors,
thereby blocking their interaction with G-proteins and effectively
terminating the signaling.
Glossary (cont)
•
Channel Protein
–
•
conformational change
–
•
Bioactive protein that catalyzes the biochemical reactions in the living cell.
GAPs (growth-associate proteins)
–
•
•
Small, biologically active molecule that acts as a regulator to control the activity of a protein
or an enzyme by binding to a specific region on the protein or enzyme.
Enzyme
–
•
An abbreviation for adenosine 3',5'-monophosphate or adenosine 2',3' -monophosphate.
An important intracellular regulator or second messenger for a number of cellular processes
in animals, bacteria, fungi and plants.
Effector molecule
–
•
change in the form differing in secondary or tertiary structure.
cyclic AMP (cAMP)
–
–
•
Proteins that form water-filled pores or channels across the membrane and are responsible
for transporting solutes across the membrane.
Promote the hydrolysis of bound GTP, thereby switching the G-protein to the inactive form.
GDP (Guanosine 5'-Diphosphate)
GEFs (guanine nucleotide exchange factors)
–
Family of proteins that facilitate the exchange of bound GDP or GTP on small G-proteins
such as ras and rho and thus activate them. (act in the opposite way to GAPs.)
Glossary (cont.)
•
G-Protein
–
•
•
•
GRK: G-Protein receptor kinase
GTP: Guanosine 5'-Triphosphate
GTPase (Guanosine triphosphatase)
–
•
•
•
•
(i) reduction or prevention in the rate of enzymatic activity (ii) repression of physical or
chemical activity.
Kinase
–
•
An increase in the rate of enzyme synthesis due to the presence of substrate or inducer.
Inhibition
–
•
Enzyme that catalyzes the reaction GTP +H20 <---> Guanosine + Triphosphate
Guanine: A constituent base in nucleic acids.
Guanosine: A nucleoside and constitutent of nucleotides
Hydrolysis: Splitting of 1 molecule to 2 by incorporation of 1 water molecule.
Induction
–
•
A GTP binding membrane protein that is capable of hydrolyzing GTP, activating membrane
bound CAMP, and mediating a variety of signal transducing systems.
The enzyme that catlyzes the transfer of a phosphate group from one compound to another.
Nucleoside
–
A component of a nucleotide that consists of a nitrogenous base (purine or pyrimidine) linked
to a pentose sugar (ribose or deoxyribose)
Glossary (cont.)
•
•
Nucleotide: The basic building blocks of nucleic acids it consists of a nucleoside and a
phosphate.
phosphatase (two kinds: acidic and alkaline)
–
–
–
•
phosphodiesterase
–
•
•
A polymer of L-amino acids that folds into a conformation specified by the linear sequence of amino acids
nd functions as an enzyme, a hormone, an antibody or a structural component of the cell.
The enzyme that possesses a regulatory site for binding effector molecules in addition to the catalytic
binding site.
RGS (Regulators of G-Protein signalling)
–
•
Protein kinase A
Regulatory enzyme
–
•
The enzyme that catlyzes the hydrolysis of phosphodiester bond in the polynucleotides or cyclic
nucleotides.
PKA:
Protein
–
•
acidic phosphatase is an enzyme that catalyzes the hydrolysis of a number of phosphomonoesters at acid
pH but not phosphodiesters.
Phosphoric monoester +H2O <--> Alcohol + Phosphoric acid.
alkaline phosphatase is an enzyme that catalyzes the hydrolysis of phosphomonoester at alkaline pH.
RGS is a protein that can increase the GTPase activity by more than one order of magnitude.
Transport protein: A protein that mediates the entry of specific substances into a cell.