chemistry 2100 lecture 11. protein functions + pl p l binding catalysis structure

Chemistry 2100

Lecture 11

Protein Functions

+

PLPL

Binding

Catalysis

Structure

Why Enzymes?• Higher reaction rates• Greater reaction specificity• Milder reaction conditions• Capacity for regulation

COO

OH

O COO

COO

O COO

NH2

OOCCOO

O

OH

OH

COO

NH2

COO

-

-

-

-

-

-

--

Chorismate mutase

• Metabolites have many potential pathways of decomposition

• Enzymes make the desired one most favorable

Specificity: Lock-and-Key Model

• Proteins typically have high specificity: only certain substrates bind

• High specificity can be explained by the complementary of the binding site and the ligand.

•Complementarity in

– size,

– shape,

– charge,

– or hydrophobic / hydrophilic character

•“Lock and Key” model by Emil Fisher (1894) assumes that complementary surfaces are preformed.

+

Specificity: Induced Fit

• Conformational changes may occur upon ligand binding (Daniel Koshland in 1958). – This adaptation is called the induced fit. – Induced fit allows for tighter binding of the

ligand– Induced fit can increase the affinity of the

protein for a second ligand

• Both the ligand and the protein can change their conformations

+

Apoenzyme + Coenzyme = Holoenzyme

Apoenzyme + Coenzyme = Holoenzyme

Apoenzyme + Coenzyme = Holoenzyme

Apoenzyme + Coenzyme = Holoenzyme

• increase [reactant]

• increase temperature

• add catalyst

Pote

nti

al Energ

y

Reaction

Reactants

Products

Enzymatic Activity

• increase [reactant]

• increase temperature

• add catalyst

Pote

nti

al Energ

y

Reaction

Reactants

Products

TS

• increase [reactant]

• increase temperature

• add catalyst

Pote

nti

al Energ

y

Reaction

Reactants

Products

Ea

TS

• increase [reactant]

• increase temperature

• add catalyst

Pote

nti

al Energ

y

Reaction

TS

Reactants

Products

Ea

• increase [reactant]

• increase temperature

• add catalyst

Pote

nti

al Energ

y

Reaction

Reactants

Products

Ea

TS

• increase [reactant]

• increase temperature

• add catalyst

Pote

nti

al Energ

y

Reaction

Reactants

Products

Ea

TS

Ea'

• increase [reactant]

• increase temperature

• add catalyst

Reactants

Products

Pote

nti

al Energ

y

Reaction

Ea

TS

How to Lower G?Enzymes organizes reactive groups into

proximity

How to Lower G?Enzymes bind transition states best

Pote

nti

al Energ

y

Reaction

O C OH2O +

HO C O– + H+

O

H2O + CO2 HOCO2– + H+

Pote

nti

al Energ

y

Reaction

H2O + CO2 HOCO2– + H+

H2O + O C O

Pote

nti

al Energ

y

Reaction

H2O + CO2 HOCO2– + H+

H2O + O C O

HO C O– + H+

O

Pote

nti

al Energ

y

Reaction

H2O + CO2 HOCO2– + H+

H2O + O C O

HO C O– + H+

O

Pote

nti

al Energ

y

Reaction

H2O + CO2 HOCO2– + H+

O C O

O

H

H

H2O + O C O

HO C O– + H+

O

Pote

nti

al Energ

y

Reaction

H2O + CO2 HOCO2– + H+

O C O

O

H

H

H2O + O C O

HO C O– + H+

O

Ea

H2O + CO2 HOCO2– + H+

Pote

nti

al Energ

y

Reaction

Ea

Ea'

O C O

O

H

H

H2O + O C O

HO C O– + H+

O

[ sucrose-sucrase complex ] H2O

sucrase

sucrose glucose

fructose

sucrase

++

+

[ sucrose-sucrase complex ] H2O

sucrase

sucrose glucose

fructose

sucrase

++

+

[ sucrose-sucrase complex ] H2O

sucrase

sucrose glucose

fructose

sucrase

++

+

[ sucrose-sucrase complex ] H2O

sucrase

sucrose glucose

fructose

sucrase

++

+

[ sucrose-sucrase complex ] H2O

sucrase

sucrose glucose

fructose

sucrase

++

+

[ sucrose-sucrase complex ] H2O

sucrase

sucrose glucose

fructose

sucrase

++

+

[ sucrose-sucrase complex ] H2O

sucrase

sucrose glucose

fructose

sucrase

++

+

[ sucrose-sucrase complex ] H2O

sucrase

sucrose glucose

fructose

sucrase

++

+

How to Do Kinetic Measurements

Enzyme ActivityFigure 23.3 The effect of enzyme concentration on the rate of an enzyme-catalyzed reaction. Substrate concentration, temperature, and pH are constant.

Enzyme ActivityFigure 23.4 The effect of substrate concentration on the rate of an enzyme-catalyzed reaction. Enzyme concentration, temperature, and pH are constant.

Enzyme ActivityFigure 23.5 The effect of temperature on the rate of an enzyme-catalyzed reaction. Substrate and enzyme concentrations and pH are constant.

Enzyme ActivityFigure 23.6 The effect of pH on the rate of an enzyme-catalyzed reaction. Substrate and enzyme concentrations and temperature are constant.

What equation models this behavior?

Michaelis-Menten Equation

H2 O

acetic acidcholine (Ch)

acetylcholine (ACh)

OHCH2(CH3 )3 N CH2

CH3CCH2(CH3 )3 N CH2 O

O

CH3CHO

O

+

+

AChE

H2 O

acetic acidcholine (Ch)

acetylcholine (ACh)

OHCH2(CH3 )3 N CH2

CH3CCH2(CH3 )3 N CH2 O

O

CH3CHO

O

+

+

AChE

H2 O

acetic acidcholine (Ch)

acetylcholine (ACh)

OHCH2(CH3 )3 N CH2

CH3CCH2(CH3 )3 N CH2 O

O

CH3CHO

O

+

+

AChE

H2 O

acetic acidcholine (Ch)

acetylcholine (ACh)

OHCH2(CH3 )3 N CH2

CH3CCH2(CH3 )3 N CH2 O

O

CH3CHO

O

+

+

AChE

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

H

H O

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

H

H O

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

H

H O

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

H

H O

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

H

H O

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

H

H O

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

H

H O

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

H

H O

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

H

Asp

COOH

His

Ser

NHN

HO

CH2

COO

H

CH3

OCH2(CH3)3N CH2 C O

Glu

••

H

H2 O

acetic acidcholine (Ch)

acetylcholine (ACh)

OHCH2(CH3 )3 N CH2

CH3CCH2(CH3 )3 N CH2 O

O

CH3CHO

O

+

+

AChE

Inhibitors

• Reversible inhibitors– Temporarily bind enzyme and prevent

activity

• Irreversible inhibitors– Permanently bind or degrade enzyme

Reversible Inhibition

Irreversible Inhibition

••

Glu

COOH

O

CH2

NHN

Ser

His

COOH

Asp

Acetylcholinesterase

••

Glu

COOH

O

CH2

NHN

Ser

His

COOH

Asp

OP

CH3

OCH

CH3

CH3

F

••

Glu

COOH

O

CH2

NHN

Ser

His

COOH

Asp

OP

CH3

OCH

CH3

CH3

F

••

Glu

COOH

O

CH2

NHN

Ser

His

COOH

Asp

OP

CH3

OCH

CH3

CH3

F

••

Glu

COOH

O

CH2

NHN

Ser

His

COOH

Asp

OP

CH3

OCH

CH3

CH3

F

••

Glu

COOH

O

CH2

NHN

Ser

His

COOH

Asp

OP

CH3

OCH

CH3

CH3

F

BrBr

succinylcholine

decamethonium bromide

(CH3 )3 N–CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2–N(CH 3 )3

CH2CH2OCCH2CH2COCH2CH2 N(CH 3 )3(CH3 )3 N

O O

Pyridine aldoxime methiodide (PAM)

IN

CH3

CH N OH

• lactase

• rennin

• papain

• high-fructose corn syrup

• pectinase

• clinical assays

Commercial Enzymes

• lactase

• rennin

• papain

• high-fructose corn syrup

• pectinase

• clinical assays

• lactase

• rennin

• papain

• high-fructose corn syrup

• pectinase

• clinical assays

• lactase

• rennin

• papain

• high-fructose corn syrup

• pectinase

• clinical assays

starch dextrins glucose fructose α-amylase glucoamylase glucose

isomerase

starch dextrins glucose fructose α-amylase glucoamylase glucose

isomerase

starch dextrins glucose fructose α-amylase glucoamylase glucose

isomerase

• lactase

• rennin

• papain

• high-fructose corn syrup

• pectinase

• clinical assays

• lactase

• rennin

• papain

• high-fructose corn syrup

• pectinase

• clinical assays

• lactase

• rennin

• papain

• high-fructose corn syrup

• pectinase

• clinical assays