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Signal TransductionSignal Transduction
LECTURE 2
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The meaning of transductionThe meaning of transductionTransduction originates from the archaic English word Traduce
1533 – to lead along; to lead along as a spectacle1678 – to translate, render; to alter, modify1733 – to transmit by generation of 1850 – to transfer from one use to another1947 – the action or process of transducing a signal1975 – Nature 17, 625: The transduction of light energy into neural signals is mediated in all known visual systems by a common typeof visual pigment
First appeared in the title of a paper in 1979Springer et al., Nature, 1979, 280:279‐84.
Widespread use in biologysince the publication of Martin Rodbell 1980
to describe the role of GTP and GTP‐binding proteins in metabolic regulation
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What drove the evolution of signal What drove the evolution of signal transductiontransductionThe membrane of cells (3‐6 nm) are effectively impermeable to ions and polar molecules
K+ ion which achieves diffusional equilibrium in water in 5 ms will require 280 h to equilibrate across a phospholipid bilayerFor a hormone such as adrenaline the rate is too small to measure
Signal transduction is concerned with how external molecules (first messengers (including hormones) hydrophilic molecules) influences what happens inside target cells.Evolution of mechanisms that enabled the specific and precise control of events inside a cell was necessary as the complexity of biological systems increased.
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Which came first Which came first –– hormones or hormones or
receptors?receptors?The first messenger, and the related intracellular (second) messenger, date far back on the biological timescale.
Biomolecules whose structures are closely related to hormones have been discovered in algae, sponges and invertebrates.Catecholamines have been found in protozoa. Ephedrine, c;loselyrelated to catecholamines, has been isolated from the Chinese herb (Ephedra sinica)α‐typemating factors in yeast has a structure similar to gonadotrophin secreted in anterior pituitary gland in mammals.Adrenocorticotrophic hormone and β‐endorphin are present in protozoa and also contain high molecular weight precursors of these peptides similar to invertebrate pro‐opiomelanocortin(POMC). The biosynthetic pathway was established before the evolution of membrane receptors.
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Which came first Which came first ––
hormones or receptors?hormones or receptors?
There is sufficient evidence that many hormone‐like molecules arose long before the receptors that they control. Consider the cross‐species function of the hormone prolactin
Regulator of mammary growth and differentiation in mammalsControlling factor for fat deposition and migratory behavior in birdsRegulator of water balance in newts and salamanders
SerotoninControls mood in humansStimulates spawning in molluscs (and mood??)
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ProtoendocrinologistsProtoendocrinologistsCharles Edouard Brown‐Séquard
Associate of Charles Darwin & Thomas HuxleySelf‐administration of the testicular extracts of dogs and guinea pigsReported in the Lancet (IF2013 = 42)
Edward BerdoeOpposed the practices of Brown‐Séquard
George OliverPhysician from Harrogate, experimented on his family using apparatus of his own devising for measurementsHe injected an extract of the suprarenal gland supplied by a local butcher into his son and observed a contraction of the radial artery
Edward SchäferOliver visited Schäfer’s lab and injected the extract into a dog and they observed an immediate startling increase in the blood pressure of the dogIn 1895 they reported the findings; the active compound was later identified as epinephrine
John Jacob AbelAbel and Crawford in 1897 purified the substance they called epinephrine (Greek)
Jokichi TakamineHad an arrangement with Parke Davis CompanyGained advantage by visiting Abel’s lab in 1899Takamine never published reports until his preparation was protected by patentsHis compound was called adrenalin (Latin)
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NeurotransmittersNeurotransmittersNeurotransmitters induce electrical response – for examples transmission of impulses between nerves, and between nerves and musclesOtto Loewi (1903) induced contractions by electrical stimulation of the vagalnerve in an isolated heart. He then transferred some of the fluid from this heart into another heart undergoing similar stimulation; this slowed down and reduced the contraction. The active substance was identified as acetylcholineHenry H Dale and Otto Loewi received the Nobel prize in 1936 for their discoveries relating to chemical transmission of nerve impulsesThe discovery of adrenergic receptors or adrenoceptors led to the development of drugs for treatment of cardiologic disorders. Sir James Black shared the Nobel prize for Physiology or medicine in 1988 for the development of β‐adrenoceptor blockers used in the treatment of hypertension, angina pectorisand arrhythmiasAdrenoceptors such as β‐adrenoceptor transmit information by signal‐transducing G‐proteins (guanine‐nucleotide regulatory proteins), located near the receptors on the inner portion of the cell membrane. Alfred G. Gilman and Martin Rodbell received the Nobel prize in Medicine in 1994 for discovery the G‐proteins and their significance in cellular activation of adrenalin.W. Sutherland received the Nobel for Physiology or Medicine in 1971 for his discovery of cAMP as the first intracellular messenger “second messenger”Stanley CohenU. S. von Euler
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Receptors and LigandsReceptors and LigandsDefinitionReceptors are proteins imbedded in the plasma membrane of cells
that possess sites accessible to the extracellular milieu. These
bind with specificity, soluble molecules called ligands. The binding of a few ligands brings about a remarkable change within the cell which
attains an “activated”
or “triggered”
state.
John Newport Langley (J. Physiol
1878)Work based on the mutual antagonism between the poisons atropine and pilocarpine (active at muscarinic cholinergic receptors)
HMRBASE: http://crdd.osdd.net/raghava/hmrbase
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Signal TransductionSignal TransductionThe response of the cell to hydrophilic material in the environment depends on interactions that occur on the extracellular side of the membraneThere are two fundamental ways that a cell can respond to an external extracellular stimulation
Material transport through a proteinaceouschannel in the lipid bilayerSignal transmission by means of a change in a membrane protein that activates its cytosolic domain
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Physical transport of materialPhysical transport of material
Channels – control the passage of ionsK+, Na+ and Ca2+ specially in nerve cells
Transporters – small molecules bind to the transporter on the extracellular side and are released on the cytosolic side.
Glucose‐PTS systemEndocytosis – internalization process that involves the passage of the proteins from one surface to another via coated vesicles
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Organization of the Organization of the PhosphotransferasePhosphotransferase systemssystems
The EI
and HPr
are general proteins for all PTS, whereas there are many specific EII
proteins. The EII
proteins contain three domains A, B and C which may be combined
in a single membrane protein or split into two or more proteins.
For glucose, B and C
are combined together into one membrane‐bound protein IIBC, while A is soluble;
For mannose, A and B are combined together into a soluble IIAB
protein, while C is
membrane‐bound.
A
B
C
C
C
D
B
B
A
AP P
P P
PP
Mannitol
Glucose
Mannose
PEP
Pyr P-EI
EI P-HPr
HPr
Mannitol-1-P
Glucose-1-P
Mannose-6-P
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Transmission of signalTransmission of signalThe transmission of a signal involves the binding of a ligand to a protein that has domains on both sides of the membrane. Binding of the ligand converts the receptor from the inactive to active form. The activation of the receptor on the cytosolic side is called signal transduction. The amplitude of the signal on the cytosolic side is much larger compared to the signal on the extracellular side. The cytosolic modification can either
Increase the quantity of a small molecule (second messenger)Activate a protein whose role is to active other proteins (GTP‐binding protein)
Autophosphorylation: receptor has a protein kinase activity in cytosolic domain. The kinase phosphorylates its own domain.G‐Protein: receptor interacts with trimeric G‐protein in the cytosolic side. This release a monomer unit that can act on other proteins; stimulates the production of second messenger like cAMP
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Reaction Reaction Pathway for Pathway for
AndrostenedioneAndrostenedione SynthesisSynthesis
Androstenedioneis the precursor molecule for many steroids such as testosterone and progesterone which also act as hormones
H RH
OAc
H RH
AcOOH
H RH
AcOO-
OI
H RH
AcOO-
OI
Cl
RH
AcOO-
OI
O
ROO-
OI
H RH
AcOO-
OI
1. β-Sitosterol2. Campesterol3. Cholesterol 4. R=H
5. R=Et6. R=Me
7. R=H8. R=Et9. R=Me
10. R=H11. R=Et12. R=Me
Method 1• Solution prepared in CCl4 • Treatment of CCl4 solution with
sulfuryl chloride in presence of UV/-100C for 150 min
Method 2• Solution prepared in CHCl3• Treatment of CHCl3 solution
with iodobenzene dichloride in presence of 2000C/300W sun lamp for 5 min
13. R=H
H RH
AcOO-
OI
Cl
14. R=Et 15. R=H 16. R=H
17. R=Ac
1,5-diazabicyclo [5.4.0] undecane-5
at 900C
Chlorination
+
+
+ RH
AcOO-
OI16. R=H
O
ROO-
OI18. R=H
H RH
AcOO-
OI15. R=H
Heating in Pyridine solution
O
ROO-
OI18. R=H
Heating in presence of THF and lithium hydroxide for 4 h
Pyridinium chlorochromate, THF and lithium hydroxide (aqueous) at 200C
Treatment with ozone
4-Androsten-3,17-dione
H RH
OAc
H RH
AcOOH
H RH
AcOO-
OI
H RH
AcOO-
OI
Cl
RH
AcOO-
OI
O
ROO-
OI
H RH
AcOO-
OI
1. β-Sitosterol2. Campesterol3. Cholesterol
1. β-Sitosterol2. Campesterol3. Cholesterol 4. R=H
5. R=Et6. R=Me
7. R=H8. R=Et9. R=Me
10. R=H11. R=Et12. R=Me
Method 1• Solution prepared in CCl4 • Treatment of CCl4 solution with
sulfuryl chloride in presence of UV/-100C for 150 min
Method 2• Solution prepared in CHCl3• Treatment of CHCl3 solution
with iodobenzene dichloride in presence of 2000C/300W sun lamp for 5 min
Method 1• Solution prepared in CCl4 • Treatment of CCl4 solution with
sulfuryl chloride in presence of UV/-100C for 150 min
Method 2• Solution prepared in CHCl3• Treatment of CHCl3 solution
with iodobenzene dichloride in presence of 2000C/300W sun lamp for 5 min
13. R=H
H RH
AcOO-
OI
Cl
14. R=Et 15. R=H 16. R=H
17. R=Ac
1,5-diazabicyclo [5.4.0] undecane-5
at 900C
Chlorination
+
+
+ RH
AcOO-
OI16. R=H
O
ROO-
OI18. R=H
O
ROO-
OI18. R=H
H RH
AcOO-
OI15. R=H
Heating in Pyridine solution
O
ROO-
OI18. R=H
O
ROO-
OI18. R=H
Heating in presence of THF and lithium hydroxide for 4 h
Pyridinium chlorochromate, THF and lithium hydroxide (aqueous) at 200C
Treatment with ozoneTreatment with ozone
4-Androsten-3,17-dione4-Androsten-3,17-dione
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Receptor Tyrosine Receptor Tyrosine KinaseKinase RTKRTKLigand‐induced RTK activation
induces receptor dimerization, leading to activation of
catalytic domainsReceptor autotransphosphorylation: Further stimulates kinaseactivity
Leads to phosphorylation of additional proteins involved in receptor signalling pathwayProvides “docking sites” for downstream signalling proteins (PI3‐kinase, phospholipase Cg, etc.)
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GTP binding proteinsGTP binding proteins
GTP Binding proteinsG‐Proteins –reserved for a class of GTP‐binding proteins that interact with 7TM receptorsG‐Proteins and GTPases–all are capable of hydrolyzing GTP ( technically, all are GTPases)
All are composed of three subunits ‐α, β and γ referred to as the class of heterotrimericG‐proteins
GPCR=G protein coupled receptor
GPCR mechanism
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GG‐‐Protein StructureProtein Structure
These G proteins bind to the inner surface of the cell membrane, holding them close to their receptors. The G protein system plays a central role in many signalingtasks, making it a sensitive target for drugs and toxins.
heroin, cocaine and marijuana, act at G‐protein‐coupled receptors in these signalingchainsCholera toxin attacks G‐proteins directly. An heterotrimeric G protein. GDP is in
purple. Alpha chain in orange. Beta chain in blue. Gamma chain in green.
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GTPaseGTPase cyclecycle
Association with activated receptor is transientG‐protein remains associated with the activated receptor through its α‐or βγ‐subunitsThe selectivity and activity is determined by the 10‐fold excess of GTP over GDP in cellsAct as “molecular switches”
Active/inactive = on/off= Gα‐GTP/ Gα‐GDP= kdiss
/kcat
= dissociation rate of GDP/ hydrolysis rate of GTP
Adrenaline binds its receptor, that associates with a heterotrimeric G protein. The G protein associates with adenylate cyclase, which converts ATP to cAMP, spreading the signal
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Yeast signal transduction: examplesYeast signal transduction: examplesBudding yeast cells
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Nature, August (2001)
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Function of signaling pathwaysFunction of signaling pathways
Signal transduction pathways describe how signals received by receptors at the cell membrane are processed inside the cell via biochemical reactions. Signal is transferred into the nucleus, where it causes a change in the currently active genetic program of the cell. Understanding this flow of information inside a cell is fundamental for an in‐depth understanding of the functioning of a cell as a whole. Modeling and simulating this information flow is beneficial, because it helps to understand the flow of signals in a complex network, to test hypotheses in‐silico before validating them with experiments and to validate the data collected about a certain pathway.
Electronic Notes in Theoretical Computer Science 194 (2008) 149–164
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Transmission of Information in Transmission of Information in Biological NetworksBiological Networks
There are multiple levels of interactionAt each level, nearly all processes are nonlinearKinetic parameters are extremely difficult find because the questions being asked are very differentModels are computationally intensive. However, there is a need for theoretical analysis because it will not be feasible to carry out all the experiments required to solve a problem
Signal molecules
Gene
RNA
Proteins
substrates products
11
111 XK
Xvvm
m
+=
22
222 XK
Xvvm
m
+=
X1 X2 X3
11
111 XK
Xvvm
m
+=
22
222 XK
Xvvm
m
+=
X1 X2 X3++
X11
X1222
222 XK
Xvvm
m
+=
α
1−α
A
B
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Block RepresentationBlock Representation
⊗
Signaling molecule binds
to receptor
Evolutionary Constraint
ChangeSecondary Messengers
Gene activation(Protein Synthesis)
Response
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Ideas from Linear Control TheoryIdeas from Linear Control Theory
Feed back control systemsP, PI & PID Controllers
⊗1+s
KP
P
τ)(sy)(su
1+sK
m
m
τ
)(sym
)(sysp ε ⎟⎠
⎞⎜⎝
⎛+
sK
Ic τ
11
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Response AnalysisResponse Analysis
Frequency response analysis, Bode diagrams and stability
Substitute s =
jw; then AR
= |G(jw)| and Phase angle
= ∠
G(jw)
Plot LogAR
versus Logwand Phase angle versus LogwCheck the Bode Stability Criterion at the cross over frequency
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Time domain equationsTime domain equations
Predominantly concerned with time invariant control systems
Unique equilibrium point if A is nonsingularEquilibrium point is stable regardless of initial conditions
In the presence of an external input u(t)
Satisfies principle of superpositionAsymptotic stability implies bounded‐input bounded‐output stability
Axx =&
BuAxx +=&
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Behavior of Nonlinear SystemsBehavior of Nonlinear Systems
Equilibrium need not be unique – multiple equilibrium points commonPrinciple of superposition does not holdLimit cycles – can display oscillations of fixed amplitude and fixed period without external excitationBifurcation – parameter changes can change the number of equilibrium pointsChaos – sensitive to changes in initial conditions often displaying large unpredictable changes input when there are small changes in initial conditions
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State Space RepresentationState Space Representation
The state of a dynamical system are the physical quantities, which when specified completely defines the evolution of the system (
provided external
excitation is absent ).In particular, a set of differential equations using these state variables that describes the dynamical behavior of the system, constitutes the modelThe number of state variables that defines the system is called the order of the systemThe number of constants that need to be determined (or identified) are called the parameters of the system
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Example 1 Example 1 –– Linear Second Order Linear Second Order
SystemSystem
The states of the system are x1
and x2
; the parameters are
ζ and
τ. The order of the system is 2. The system is linear
u
uxx
xx
uxxx
xxyx y x
uydtdy
dtyd
bAxx +=
⎥⎦
⎤⎢⎣
⎡+⎥
⎦
⎤⎢⎣
⎡⎥⎦
⎤⎢⎣
⎡−−
=⎥⎦
⎤⎢⎣
⎡
+−−=
===
=++
&
&
&
&
&
&
or, 1
02110
121
and Let
2
22
12
2
1
22122
21
21
2
22
ττςτ
ττς
τ
ςττ
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State Space Representation of a cells State Space Representation of a cells growing in a reactorgrowing in a reactor
The states of the system are cell mass concentration x
and the substrate concentration s
; the parameters are
μm
, Km
, Yx/s
and sF
; The order of the system is n
=2.
The system is nonlinear
)(1/
Fm
m
sx
m
m
ssDsK
sxY
sdtds
DxsK
sxxdtdx
−−+
−==
−+
==
μ
μ
&
&
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General State Space RepresentationsGeneral State Space Representations
1.
Nonlinear Systems
2.
Control Linear (or Affine) Systems),,,(
),,,(
),,,(
21,21
21,2122
21,2111
pnnn
pn
pn
uuuxxxfx
uuuxxxfx
uuuxxxfx
LL&
M
LL&
LL&
=
=
=
⎥⎥⎥⎥
⎦
⎤
⎢⎢⎢⎢
⎣
⎡
⎥⎥⎥⎥
⎦
⎤
⎢⎢⎢⎢
⎣
⎡
+
⎥⎥⎥⎥
⎦
⎤
⎢⎢⎢⎢
⎣
⎡
=
⎥⎥⎥⎥
⎦
⎤
⎢⎢⎢⎢
⎣
⎡
pnpnn
p
p
nn u
uu
ggg
gggggg
f
ff
x
xx
M
L
MOMM
L
L
M
&
M
&
&
2
1
21
22221
11211
2
1
2
1
),( uxfx =&
g(x)uxfx += )(&
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3.
Linear Systems
⎥⎥⎥⎥
⎦
⎤
⎢⎢⎢⎢
⎣
⎡
⎥⎥⎥⎥
⎦
⎤
⎢⎢⎢⎢
⎣
⎡
+
⎥⎥⎥⎥
⎦
⎤
⎢⎢⎢⎢
⎣
⎡
=
⎥⎥⎥⎥
⎦
⎤
⎢⎢⎢⎢
⎣
⎡
pnpnn
p
p
nnnn
n
n
n u
uu
bbb
bbbbbb
aaa
aaaaaa
x
xx
M
L
MOMM
L
L
L
MOMM
L
L
&
M
&
&
2
1
21
22221
11211
21
22221
11211
2
1
BuAxx +=&
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Exercise Problem Exercise Problem –– 1 1
Find the trajectory of the system
That passes through the point (1,0)21
2
21
25 xxdt
dx
xdtdx
−−=
=
SolutionEquation of isoclines :
Slope at initial point :
hence the trajectory starts vertically downwards at (1,0)
25 hence, 25 12
2
21
+−
==−−
αα xx
xxx
5,0 21 −==dt
dxdtdx
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Construction of Phase PortraitConstruction of Phase Portrait
α
= ∞
α
= 10
α
= 3
α
= 1α
= 0
α
= -1α
= -2α
= -
4
α
= -
12
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The The trptrp Operon of E. Operon of E. colicoli. .
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The Mechanism of Attenuation The Mechanism of Attenuation –– 11
If the environment of the bacteria contains the amino acid, its biosynthesis is superfluous
For example, if histidine or tryptophan is present in the environment, it biosynthesis by the bacteria is superfluousIf tryptophan is added into a culture of growing cells, it stops producing the enzymes in the pathway leading to its synthesisAttenuation – operon is not regulated by the end product
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The Mechanism of Attenuation The Mechanism of Attenuation ––
22
The relative positions of mRNA and how they bindRegions 1 and 2 are complementaryRegion 2 is complementary to 3 and region 3 is complementary to region 4
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The Mechanism of Attenuation The Mechanism of Attenuation ––
33The position of the ribosome plays an important role
It determines if the 1‐2 and 3‐4 segments form hairpins orThe 2‐3 segments forms a hairpin
RNA polymerase binds to leader sequence ~60 basesAttenuator (~140 bases) is passed before polymerase reaches structural geneThe leader sequence contains 2 successive tryptophan codons; so, in the presence of excess tryptophan t‐RNA, the ribosome reaches the stop codon and forces the attenuator into a hairpin loop
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CaCa2+2+ as a secondary messengeras a secondary messenger
Discovery of Ca2+ signalingRinger and Fielder, 1883Kamada and Kinoshita, 1943Heilbrunn and Wiercinski, 1947
Calcium and evolutionDifferences between prokaryotic and Eukaryotic cellsIntracellular calcium stores
Thiovulum
a sulphur‐oxidising
bacterium, possesses endoplasmic
membrane structures
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Free, bound and trapped CaFree, bound and trapped Ca2+2+Cytosol Ca2+ is maintained low
Active transport by Ca2+ ATPasesHigh affinity Ca2+ binding proteinsNa+ ‐ Ca2+ plasma membrane exchangers
Bound Ca2+ in extracellular milleuProtein specificity for Ca2+ over Mg2+
Many are able to bind to Ca2+ in the oresence of a huge excess of Mg2+
Low‐affinity Ca2+ binding protein short termHormonal mechanisms long term
Ca2+ Mg2+
Plasma, extracellular fluid 1‐2 mmol/l pCa ~ 3 1 mmol/l Intracellular cytosolic (resting cells) 50‐100 nmol/l pCa ~ 7 0.5‐1 mmol/l Intracellular luminal (ER) 30‐300 μmol/l pCa ~ 4‐5
Approximate levels of free Ca2+ and Mg2+
Excess circulating Ca2+ (hypercalcaemia) reduces neuromuscular transmission, causes myocardial dysfunction and lethargy
Hypocalcaemia affects excitability of membranes and if untreated, lead to tetany, seizures and death
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Distinguishing Between MgDistinguishing Between Mg& Ca& CaMetal‐ligand coordination complexes
Size of Ca2+ is larger than Mg2+Ca2+ has less difficulty in accommodating ligand atoms and has the ability to form irregular structuresCa2+ has coordination number between 6 and 12Mg2+ has a fixed coordination number of 6
Chelating agents and selectivityAll ions in aqueous solution are surrounded by a hydration layer; hence, for coordination to occur
Water molecules must be displaced by the metal and the ligandStability depends on
Attractive forces between the metal and ligandAttractive and repulsive interaction between adjacent lignadsWater is itself a ligand that stabilizes the ionized state
MLLM K⎯→←+
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Mechanisms that elevate cytosol CaMechanisms that elevate cytosol Ca2+2+ concentrationconcentration
EvolutionDevelopment of switchable membrane channels
Action of phospholipase CCalcium mobilizing receptorsLigand gated channels in membranes
Electrically excitable Ca2+ cellsInositol triphosphate receptors (IP3R) and Ryanodine receptors (RyR)
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Analysis of the feedback motifAnalysis of the feedback motif
Real time analysisLaplace transforms & Laplace domain analysisOpen‐loop and closed‐loop systemsFrequency response analysis
),( uxfkxdtdx
+=
Gene
Gene1 Gene N
)(xgu =
ux
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Calcium RegulationCalcium Regulation
The regulation of calcium in the blood is regulated against disturbances in calcium utilization and uptakeParathyroid hormone (PTH) and Vitamin D, control how much Ca is introduced into the blood from the intestine
Σ Control Σ ∫Vol1
⎯
VT - VcL
[Ca]
Set point
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Example Example –– Insulin Insulin signalingsignaling pathway
pathway
Dynamics of insulin signaling pathway with negative and positive
feedback loops. Downstream kinases
are JNK, mTOR, S6K1 and
ERK dependent or independent of Akt
Insulin
IRS11-P13K
Akt
GLUT4 Kinase
K1 = 0.3 nM; K2 =5*10-6 nM; k1 = 10-6 nM/s; k2 = 10-3 nM/s; k3 =1.16*10-4 /s; k4 =0.06 /skd1 = 0.05 /s; kd2 = 0.05 /s;
Equations and Conditions for the Equations and Conditions for the ProblemProblem
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Patterns of cytosol CaPatterns of cytosol Ca2+2+ changeschanges
Temporal aspectsSpatial detailCa2+ release eventsSignals in electrically excitable cellsLocalization of second messengers
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Effects of elevated calciumEffects of elevated calcium
Calmodulin and Troponin CCa2+ ‐ calmodulin dependent kinases
Multifunctional Ca2+/calmodulin protein kinasesPhosphorylase kinase, CaM‐kinases I‐IVMyosin light chain kinase (MLCK)Ca2+/calmodulin sensitive adenylyl cyclaseCalcineurinNOS (nitric oxide synthase)
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Paradigms of Calcium Paradigms of Calcium signallingsignalling
Neurotransmitter secretionContraction of striated muscleSmooth muscle contractionAdrenergic control of heart contraction
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Failure Condition AnalysisFailure Condition Analysis
Material flow failure – robust response – safeElevated blood glucoseElevated blood glutamine
Signaling Failure Changes in binding affinity – robust response – safeChanges in CICR (Ca induced Ca release) – sensitive – can cause a disorder
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CICR Failure AnalysisCICR Failure Analysis
0
5
10
15
20
25
30
0 600 1200 1800 2400 3000 3600
Time (s)
Cal
cium
sig
nal (
uM)
0.0E+00
2.0E-05
4.0E-05
6.0E-05
8.0E-05
1.0E-04
1.2E-04
Dep
hosp
hory
late
d B
AD
(uM
)
CaC2BAD
0
0.2
0.4
0.6
0.8
1
1.2
1.4
1.6
1.8
2
0 600 1200 1800 2400 3000 3600
Time (s)
Cal
cium
sig
nal (
uM)
0.0E+00
2.0E-05
4.0E-05
6.0E-05
8.0E-05
1.0E-04
1.2E-04
Dep
hosp
hory
late
d su
gnal
(uM
)
CaC2BAD
0
0.1
0.2
0.3
0.4
0.5
0.6
100 120 140 160 180 200
Time (s)
Cal
cium
sig
nal (
uM)
A sustained Ca2+ signal triggers dephosphorylation of BAD. The level of the signal influences the time it takes to trigger. Once BAD is triggered apoptosis sets in.
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Using NeuroDNet we created the disease
network for ALS Presenilin‐1 (PSEN1) is associated with calcium signallingThe androgen receptor (AR) ANG is associated with ribonucleolytic activity
PSEN1
AR – associate with sporadic ALS
ANG
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PSEN1
AR – associate with sporadic ALS
ANG
ALS Protein Interaction NetworkALS Protein Interaction NetworkUsing NeuroDNet
‐
create
the disease network for ALS
Presenilin‐1 (PSEN1) is associated with calcium signallingThe androgen receptor (AR) ANG is associated with ribonucleolytic activity
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PSEN1 and Ca PSEN1 and Ca SignallingSignalling
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Network StructureNetwork StructureWhat are the properties that describe the structure of a
network ?Connectedness
expresses the existence of a path between the information conveyed by a signalling molecule and the its receptor
Navigabilityquantified by the difficulty of finding a connecting path; usually, related to terms such as observability and controllability used in control theory terminology
Efficiencylatency of each utilized path; usually a function of the number of hops; related to the concept of time threshold that arises as a consequences of the kinetic relationship along each path
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Availability of network dataAvailability of network data
The quantity and quality of network data has rapidly increased in the last few years; understanding the state of existing data and methods is important in order to further what can be done with this dataDatabases in existence which contain information on biological networks; these resources vary in their focus, size, availability and popularityA number of databases have been expanding their focus to encompass a larger variety of data
Metabolic pathwaysSignalling pathwaysTranscription regulatory networksProtein‐protein interactions
MetaCyc, KEGG, BioPAX, SBML, CellML, RegulonDB, PDB, Brenda, STRING, BioGRID
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Visualization of networksVisualization of networks
A.
Visualization of the metabolic network of Escherichia coli obtained from KEGG. The magenta nodes represent enzymatic
reactions and the green nodes are chemical compounds. The network
contains 2570 nodes and 5238 edges.B.
Visualization of the PPIs
within two steps away from the epidermal growth
factor receptor (EGFR) in humans extracted from the Human Protein Reference Database. The nodes are proteins and the edges represent
interactions between them. There are 2331 proteins and 5255 interactions.
EGFR is in magenta, proteins directly interacting with EGFR are in yellow and
proteins two steps away are in green. The size of the node is proportional to its
degree.
A
B
Comp Sci Rev 3 (2009), 1 – 17
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Topological Structure of Biological Topological Structure of Biological NetworksNetworksThe availability of data on biological networks has led tonew questions such as:
Are they random? Does the structure of the network have implications for its functions?
There is strong evidence that they are not fully random, but theexact nature of their structure is still not completely answered. Biological networks fit nicely into the general study of complexnetworks and so the analysis of their properties both draws upon network and graph theory.
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Graph theoretic motifsGraph theoretic motifs
the elements in the networks, whether they be proteins, chemicals, genes or other biological entities, are usually the vertices of the graph and the edges represent some sort of interactions between them.Graph theory can be used to understand the behavior of the networksThe exact graph representation can vary depending on the data and in turn this can affect the choice of algorithms and conclusions reached about the structure of the networks.
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Scale free and small worldScale free and small world
DefinitionDefinitionScale free:A scale‐free network is one whose degree distribution is characterized by a power law of the form P(k) ~ k ‐γSmall world: A small‐world network is one where any two vertices in the network can be connected by a relatively short path.
These properties of networks are of interest because a number ofreal‐world networks, such as the Internet and citation networks, appear to have similar propertiesStructure of metabolic pathways organizes the arguments against biological networks being scale‐free into four major categories
the quality of the datathe methodology used to determine scale‐freenessthe graph representation of biological networks whether scale‐free is a meaningful property.
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Identifying Network MotifsIdentifying Network Motifs
Network motifs are subgraphs which occur in significantly higher numbers than expected by random chance
These subgraphs are identified by their topology; any biological information is ignored and just the structure of the graph is analyzed.Finding motifs in the networks helps to provide a better understanding of the structural elements of biological networks beyond just looking at global properties. For example, motifs have been used to predict PPIs. The existence of different motifs may also help understand the role of modularity in biological networks and how it relates to the evolution of biological networks
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Biological network Biological network modellingmodelling and and
simulationsimulationBoolean NetworksPetri NetsDifferential EquationsStochastic SimulationHybrid Models
Signal TransductionThe meaning of transductionWhat drove the evolution of signal transductionWhich came first – hormones or receptors?Which came first – hormones or receptors?ProtoendocrinologistsNeurotransmittersReceptors and LigandsSignal TransductionPhysical transport of materialOrganization of the Phosphotransferase systemsTransmission of signalReaction Pathway for Androstenedione SynthesisReceptor Tyrosine Kinase RTKGTP binding proteinsG-Protein StructureGTPase cycleYeast signal transduction: examplesSlide Number 19Function of signaling pathwaysTransmission of Information in Biological NetworksBlock RepresentationIdeas from Linear Control TheoryResponse AnalysisTime domain equationsBehavior of Nonlinear SystemsState Space RepresentationExample 1 – Linear Second Order SystemState Space Representation of a cells growing in a reactorGeneral State Space RepresentationsSlide Number 31Exercise Problem – 1 Construction of Phase PortraitThe trp Operon of E. coli. The Mechanism of Attenuation – 1The Mechanism of Attenuation – 2The Mechanism of Attenuation – 3Ca2+ as a secondary messengerFree, bound and trapped Ca2+Distinguishing Between Mg & CaMechanisms that elevate cytosol Ca2+ concentrationAnalysis of the feedback motifCalcium RegulationExample – Insulin signaling pathwaySlide Number 45Patterns of cytosol Ca2+ changesEffects of elevated calciumParadigms of Calcium signallingSlide Number 49Slide Number 50Slide Number 51Failure Condition AnalysisCICR Failure AnalysisSlide Number 54ALS Protein Interaction NetworkPSEN1 and Ca SignallingSlide Number 57Network StructureAvailability of network dataVisualization of networksTopological Structure of Biological NetworksGraph theoretic motifsScale free and small worldIdentifying Network MotifsBiological network modelling and simulation