Allosteric signaling
• Biochemistry
• Direct negative feedback
• Indirect feedback
• Cyclic processes
Allosteric mechanisms
• Regulation by binding to a site other (άλλος allos) than the catalytic site
• Multiple chemical states in complex molecules– Concerted, 2 state model– Sequential, multi-state model
• Product – mediated feedback control
• Oxygen-hemoglobin binding
Ligand induced conformation
Deoxy-hemoglobin Oxy-hemoglobin
Globin
Heme Heme-O2
O2 allows pocket closureSmall shift in helixOne added AA interaction
Sequential model
• Equilibrium among multiple affinity states• Multi-subunit molecules undergo sequential
conformational changes as each subunit binds ligand• Allows “Negative” cooperativity• Koshlind et al., 1966
Low affinitystate
High affinitystate
-2 -1 0 1 20
0.2
0.4
0.6
0.8
1
Log (ligand)
Bou
nd L
igan
d
Apparent affinity of H/L mix
Ligand
Concerted model
• Equilibrium between distinct high and low affinity states• Multi-subunit molecules make a concerted or unified
conformational change • Ligand binding increases the high affinity enzyme
cooperative binding• Monod et al., 1965
Low affinitystate
High affinitystate -2 -1 0 1 2
0
0.2
0.4
0.6
0.8
1
Log (ligand)
Bou
nd L
igan
d
Apparent affinity of H/L mix
Ligand
Glucose metabolism
• Sequential phosphorylation of glocose
• Symmetric cleavage to PEP & on to citric acid cycle
• PFK is rate limiting
Phospho-fructo-kinasePFK
PFK
• Activated by ADP, F1P
• Inhibited by PEP (prokaryots) or citrate (eukaryots)
PDB:4PFKPDB:3PFK
Allosteric ADP binding site
Active siteNo reactants With reactants
PEP inhibits PFKPEP bound ADP bound
PEP binding causes a large scale reorganization of four monomers (Concerted model)
Allosteric cofactor interacts with its own peptide chain and other subunit (green chain a; aqua chain b)
PDB:6PFK PDB:4PFK
Allosteric homeostasis loop (PFK)
• Homeostasis: stable feedback control
Controller
Sensor
Plant
PFK(catalytic)
PFK(allosteric)
Glycolysis
PFK (catalytic)
PFK(allosteric)
Glycolysis
General model
PFK increases F1,6P, glycolysis converts this to PEP, which inhibits PFK
PFK increases F1,6P, glycolysis converts ADP to ATP, reducing ADP, which is an activator of PFK
OutputState
IndicatorState
PEP
ADP
ATP
ATP
Glucose storage
• Extracellular glucose uptake
• Phosphorylation by hexose kinase
• Conversion to fructose 1,6,-bisphosphate
• Storage in glyogen polymers– Conversion to UDP-glucose– Ligation by glycogen synthase
Glucose Glucose-6P
Phospho-fructose
Fructosebisphosphate
UDP-glucose
Glycogen
GlycolysisHK isomerase
UDP glucosephosphorylase
GS
PFK
Glycogen synthase
• Adds UDP-glucose to glycogen
• Glucose-dependent
• ATP-dependent
GlycogenSynthase
(allosteric)
GlycogenSynthase(catalytic)
Glycogen
Rothman-Denes & Cabib, 1971
Controller
Sensor
Plant
G-6-P
G6P regulation of GS
• Allosteric conformational change
Without G6P With G6P
Baskaran et al. 2010
Cytoskeletal remodeling
• Polymerizaton of actin filaments
• Regulation of myosin contractility– Myosin Light Chain Kinase– Myosin Light Chain Phosphatase
Focaladhesion
RhoA ROCK MLP Cell motility
Small GTPases
• GTP is not usually a Pi donor
• GTPases can be allosterically regulated allosteric regulators– GTPase timer– GAP switch
• Guanine Activating Proteins (GAPs)– Facilitators of GTPase– Active of themselves– ie: GAPs may be
allosterically regulated by GTP-GTPase EF-Tu, the eEF1 homolog
Rho kinase, cytoskeletal remodeling
• GTP holds RhoA domains close
• Residues of now adjacent domains bind ROCK1
PDB:1S1CPDB:1FTN
GDP-RhoA GTP-RhoA+ROCK1
ROCK1
GTPase cycle
• GTP hydrolysis limits time of activation• Many GTPase effectors are GAPs
– eg: ribosome– Autoinhibitory, self-sensing controller
• Many GTPases require GEFs– Less a sensor of [GTP]– More a communication method
GEFGAP
GDP-GTPaseInactive
GTP-GTPaseActive
GTP ExchangeGTP hydrolysis