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