Signal networks and pathways

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Signal networks and pathways

• Chitta Baral
• Arizona State University

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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

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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

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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.

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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).

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G protein activation/inactivation cycle
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cAMP
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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.

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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.

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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.)

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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/BIOL2060_W2
  003/CellBiol10/CB10.html
• Look for signal transduction, pathways, signal
  pathways, G protein, biochemical networks etc.

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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

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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.

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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 Load causes loaded.
• S2 Shoot causes alive if loaded.
• S3 Intially alive.
• S4 Initially loaded.
• Planning D alive after X. XLoadShoot.
• Explanation S1, S2, S3, alive after shoot
  Initially loaded
• Prediction
• D alive after Load? D loaded after Load?

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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.

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Glossary

• Activation
• A process of (i) initiating a chemical or
  biochemical reaction (ii) converting an inactive
  component to a functionally active form.
• Adenylate Cylase
• The enzyme that catalyzes the synthesis of
  cyclic AMP (cAMP) from ATP,
• ATP lt--gt 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.

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Glossary (cont)

• Channel Protein
• Proteins that form water-filled pores or
  channels across the membrane and are responsible
  for transporting solutes across the membrane.
• conformational change
• change in the form differing in secondary or
  tertiary structure.
• cyclic AMP (cAMP)
• 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
• 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
• Bioactive protein that catalyzes the biochemical
  reactions in the living cell.
• GAPs (growth-associate proteins)
• 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.)

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Glossary (cont.)

• G-Protein
• A GTP binding membrane protein that is capable of
  hydrolyzing GTP, activating membrane bound CAMP,
  and mediating a variety of signal transducing
  systems.
• GRK G-Protein receptor kinase
• GTP Guanosine 5'-Triphosphate
• GTPase (Guanosine triphosphatase)
• Enzyme that catalyzes the reaction GTP H20
  lt---gt 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
• An increase in the rate of enzyme synthesis due
  to the presence of substrate or inducer.
• Inhibition
• (i) reduction or prevention in the rate of
  enzymatic activity (ii) repression of physical or
  chemical activity.
• Kinase
• 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)

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Glossary (cont.)

• Nucleotide The basic building blocks of nucleic
  acids it consists of a nucleoside and a
  phosphate.
• phosphatase (two kinds acidic and alkaline)
• acidic phosphatase is an enzyme that catalyzes
  the hydrolysis of a number of phosphomonoesters
  at acid pH but not phosphodiesters.
• Phosphoric monoester H2O lt--gt Alcohol
  Phosphoric acid.
• alkaline phosphatase is an enzyme that catalyzes
  the hydrolysis of phosphomonoester at alkaline
  pH.
• phosphodiesterase
• The enzyme that catlyzes the hydrolysis of
  phosphodiester bond in the polynucleotides or
  cyclic nucleotides.
• PKA Protein kinase A
• Protein
• 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.
• Regulatory enzyme
• The enzyme that possesses a regulatory site for
  binding effector molecules in addition to the
  catalytic binding site.
• RGS (Regulators of G-Protein signalling)
• 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.