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Lectures in Enzymology
My name is Ioan LASCU
Please send me an email for any question during these [email protected]
I am Professor of Biochemistry at the University of Bordeaux (France)
Ni-men ha!
Lectures in Enzymology
My scientific interests:
• Kinetic studies of phosphotransferasesNucleoside diphosphate kinaseATP + GDP � ADP + GTP
• Folding and stability of proteins
• Amyloid fibrils
Bordeaux is the 6th town of France (about 600,000 people). It is famous for its wine and for its University.
Lectures in Enzymology
University of Bordeaux, France
Lectures in Enzymology
Sciences used for studying enzymes
“Classical” biochemistry (cell metabolism)BiophysicsOrganic Chemistry –mechanism, stereochemistryPhysical Chemistry – kinetics, thermodynamicsStructural Biology Molecular Biology Bioinformatics
But……
Studying enzymology may help understanding all that sciences
Lectures in Enzymology
I will try to explain the concepts in a simple way, so you may understand the basis of complex phenomena and may use these concepts for other situations.…..but…..
« The trouble with simple things is that one mustunderstand them very well »
(Anonymous, cited by Donald T. Haynie, Biological Thermodynamics, Cambridge University Press 2001)
Please interrupt me and ask if something is not clear (or we may discuss after the lectures)
You may have success if a carreful analysis first, instead of working first…. Our example 1
Nucleoside diphosphate kinase from red blood cellsAbout 10 mg from 3 kg of red blood cells Several isoenzymesWhat to do next?Other scientists separated the isoenzymes by complicated procedures and studied their kinetic properties
At that time (1988-89) I was working in Romania and we were very poor and no good chromatographic equipment (in fact I fabricated myself columns, ion exchangers and affinity material)We made the following theoretical analysis:The several HEXAMERIC isoforms may be just the random association of two polypeptide chains, like lactate dehydrogenaseIf this is trus, the two kind of polypeptide, unfolded in urea, may be easily separated by simple ion exchange chromatography….
Calculated abondance of isoforms
The designed experiment:
The results:
NDPK-B (basic)
NDPK-A (acidic)
How to make Sepharose using a paint blower?Agarose droplets are spherical, if you cool them rapidlyYou get Sepharose!
Simple method for the preparation of spherical agarose and composite gel particlesPRESECAN E. ; PORUMB H. ; LASCU I. ;Inst. hygiene public health, Cluj-Napoca 3400, RomaniaJournal of chromatography 1989, vol. 469, pp. 396-398
You may have success if a carreful analysis first, instead of working first…. Our example 2
While teaching protein structure, one of the most proeminent properties of the native state is COOPERATIVITY. It is stabilized by a large number of weak interactions (Fig B rather than A).
A B
Experimentally, cooperativity translates by sigmoid denaturationand renaturation curves
100
150
200
250
300
350
0 1 2 3 4 5 6
Flu
ores
cenc
ein
tens
ity(a
rbitr
ary
units
)
[ Urea ], (M)
wt, denaturation
wt, renaturation
S120G, denaturation
S120G, renaturation
NDP kinase A denaturation/renaturation followedbythe fluorescence of Trp residues
What would means a non-cooperative renaturation curve (here in red)? As we teach « native structure is cooperative », a non-cooperative curve would means that the structure is non-native!
Lectures in Enzymology an over-view
Why studying the enzymes?
“Because they exist” ….. basic knowledge
Role in metabolism
Enzymes are used in the analytical biochemistry to measure metabolite concentrations in complex misture (body fluids)
Enzymes are used in the industrial biochemistry, to prepare useful molecules
Most drugs are enzyme inhibitors
ENZYMES FOR PLEASURE AND FOR PROFIT
Lectures in Enzymology: an over-view
There are three major TOOLS for studying enzyme mechanism
Steady-state kinetics but enzymology is not a branch of the Algebra
Structure
Mutagenesis (site-directed or random)
Lectures in Enzymology: an over-view
Preparing lectures is useful for students (I hope) but for the professor, too: is the opportunity to think about the progress in enzymology since the last teaching!
Molecular biologist Biological Physicist
Your model is oversimplified and has nothing to do with biology!
Your model is too complicated and has no predictive power!
There are different ways to teach enzymology
Lectures in Enzymology: an over-view
Not all chapters of enzymology and not all classes of enzymes will be discussed here
Examples will be from well studied pathways (glycolysis)
Detailed description of proteases and phosphotransferases
Once you have understood how the experimental data will be integrated into a theoretical model for one enzyme, it would be easy to do this for another enzyme
Lectures in Enzymology: Recommended Books
Lubert STRYER, Jeremy M. Berg, John L. Tymoczko
BIOCHISTRY (necessary but not sufficient)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books&cmd=search&term=stryer
Alan FERSHT
STRUCTURE AND MECHANISM IN PROTEIN SCIENCE: A GUIDE TO ENZYME CATALYSIS AND PROTEIN FOLDING
W. H. Freeman, New York 1999
Lectures in Enzymology: Recommended SoftwareYou can fing excellent software for free: some people spent time and energy for the colleagues
Software for fiting experimental data Kaleidagraph Costly, but the DEMO version is freeCurveExpert A very good freeware, excellent algoritm
Monte Carlo Simulation : Chemical Kinetics Simulator (CKS). Can be download at:https://www.almaden.ibm.com/st/computational_science/ck/msim/)Simulation and fitting:KINSIM et FITSIM. Developped by C. Frieden; you write the chemicalmechanism and the software will calculete the concetration in function of time http://www.biochem.wustl.edu/cflab/message.htmlProtein structure RASMOL. Coloured and easy to use (http://mc2.cchem.berkeley.edu/Rasmol/v2.6/)SwissPDBViewer Less good as graphics, but excellent for studying biomolecular interactionshttp://www.expasy.org/spdbv/text/download.htm
Lectures in Enzymology: Recommended Software
Drawing chemical structures
ISIS Draw 2.4 Very easy to use www.mdli.com/download/
Bitmap images
Irfan View (http://www.irfanview.com/) or Paint of Microsoft
A navigator (I use Firefox)
A software for reading pdf documents. Foxit Reader is fast and free!
Specificity --- the ability of enzymes to discriminate between a substrate and a competing molecule.
High specificity --- functional groups in the active site of enzyme arranged optimally to form a variety of weak interactions with a given substrate in the transition state
Logarithmic scale of kcat and knon values for some
representative reactions at 25 ° C. The length of each vertical bar
represents the rate enhancement by ADC ) arginine decarboxylase;
25 ODC ) orotidine 5¢-phosphate decarboxylase;23 STN )
staphylococcal nuclease;17 GLU ) sweet potato â-amylase;13
FUM ) fumarase;21 MAN ) mandelate racemase;22 PEP )
carboxypeptidase B;14 CDA ) E. coli cytidine deaminase;30 KSI )
ketosteroid isomerase;23 CMU ) chorismate mutase;19 CAN )
carbonic anhydrase.23
Accelération (kcat)
HN
O
CN
O
OHOH
OP-O
O-
OO
OO
HN
O
N
O
OHOH
OP-O
O-
O O
HA
HN
O
N
O
OHOH
OP-O
O-
O O-A
CO2
knon = 2.8 x 10-16 s-1 kcat = 40 s-1 kcat /knon = 1.4 x 1017
t1/2 = 78 millions d’années t 1/2 = 18 millisecondes
VERY unstable intermediate
The interesting question is NOT how large is the rate acceleration, but how can the enzyme accelerate the reaction so much
OMP Decarboxylase (kcat/knon)
Orotidine 5’Phosphate decarboxylase
Fumaric acid 1 kg 8.5 mol 17.5 $ 2 $/molNH4OH 1 L 8.57 mol 16 $ 1.8 $/molL-Aspartic acid 1 kg 5.78 mol 119 $ 20.6 $/molDL-Aspartic acid 1 kg 73 $
1 mg…100 UI µmol/min 173*100*10-6 g 17 mg/min 24.9 g/24 h
A practical application (making money with the help of an enzyme) L-aspartate ammonia-lyase (aspartase).
Another practical application (making economies)
If you needs large amounts of TDP (thymidine 5’-diphosphate)
25 mg (62 µmol)……240$, or 3.87 $/µmol
Phosphorylate the TMP which costs 0.13 $/µmol!!
Some history: The methods
1925 Briggs et Haldanestady-state
1915 Michelis-Menten (invertase)ES complex
1960 W. W. Clelandclassification of enzymatic reactionsmany useful developments od enzyme
kinetics
1915 Enzymatic kinetics (Michaelis)The physical nature of enzymes was unknown (ill-
defined “colloids”)1928 Urease – crystallization of an enzyme. This was an essential
step: enzymes are homogeneous moleculas which can be studied by chemical means
1955 Sanger: first sequence of a small protein (insuline)1968 X-ray structure of an enzyme: Blow (chymotrypsin)1950-1980 affinity labeling for identifying the active-site residues
(now in disuse)1978 Gene cloning: recombinant enzymes could be obtained1983 site-directed mutagenesis
Some history: The methods
1a. Can be used independently of enzyme structure
1b. No hint on enzyme structure
2. Can be compatible with a mechanism, but is not a proof
Formal kinetics: the black box
Substrat Produit(s)
Substrat Produit(s)
Traps of formal kinetics….
C (t): the same kinetic equationRate-limiting step�the rate of the slowest step in a sequence�the value which we measure!
A B C110
[C] = [A]0 [1 + 1/(10-1)*(1*e-10*t – 10*e-1*t)]
A B C101
[C] = [A]0 [1 + 1/(1-10)*(10*e-1*t – 1*e-10*t)]
Enzymes are very EFFICIENT catalysts
Wild Type yeast: Yeast Trp94→AlaHighly active towards ethanol Activity 350-fold reducedWeakly active towards hexanol Activity 5-fold increased
HB HA
CH3O
Zn
Ser 48 (Yeast: Thr 48)
Nicotinamide
A’
C’
Leu 57
(Yeast: Trp 57)
Phe 93
(Yeast: Trp 94) B’
Enzymes are very SPECIFIC catalysts
alcohol dehydrogenase (EC 1.1.1.1)
HAHC
Pro-chiral
Méthodes d’étude du mécanisme catalytique de la chymotrypsine1. cinétique à l’état stationnaire
E + S � ES ES’ E + P2
P2INTERMEDIARE rapide
lente
rapide
lente
Méthodes d’étude du mécanisme catalytique de la chymotrypsine2. modification d’affinité
Modification chimique SERINE ACTIVE1950-1960
Di-isopropyl-fluorophosphate
Méthodes d’étude du mécanisme catalytique de la chymotrypsine3. Resolution de la structure 3D
D. Blow 1968
1. TRIADE CATALYTIQUE2. LA POCHE OXYANIONIQUE
Méthodes d’étude du mécanisme catalytique de la chymotrypsine4. La mutagenèse dirigée
Classification des enzymes
La nomenclature EC (EC est le sigle de Enzyme Commission numbers, la Commission des enzymes) est une classification numérique des enzymes, basée sur la réaction chimique qu'elles catalysent. En tant que système de nomenclature des enzymes, chaque numéro EC est associé à un nom recommandé pour l'enzyme correspondante.
Chaque code d'enzyme consiste en les lettres majuscules « EC » suivies de quatre nombres séparés par des points. Ces nombres représentent chacun une étape dans la précision de la classification de l'enzyme. Par exemple, l'enzyme tripeptide aminopeptidase a le code EC 3.4.11.4 qui est construit comme suit : 3 signifie une hydrolase (enzymes qui utilisent l'eau pour détruire une autre molécule), 3.4 signifie hydrolases agissant sur des liens peptidiques, 3.4.11 implique celles qui détachent un acide aminé amino-terminal d'un polypeptide et 3.4.11.4 implique celles qui détachent cet acide aminé amino-terminal d'un tripeptide.
Classification des enzymes
Le niveau supérieur de cette classification est
* EC 1 Oxydoréductases : catalysent les réactions d'oxydo-réduction* EC 2 Transférases : transfèrent un groupement fonctionnel (par exemple un groupe méthyle
ou phosphate)* EC 3 Hydrolases : catalysent l'hydrolyse de diverses liaisons* EC 4 Lyases : brisent diverses liaisons par d'autres procédés que l'hydrolyse et l'oxydation* EC 5 Isomérases : catalysent les réactions d'isomérisation dans une simple molécule* EC 6 Ligases : joignent deux molécules par des liaisons covalentes
La nomenclature complète peut être vue à l'adresse http://www.chem.qmul.ac.uk/iubmb/enzyme/
EC 1 OxidoreductasesEC 1.1 Acting on the CH-OH group of donorsEC 1.2 Acting on the aldehyde or oxo group of donorsEC 1.3 Acting on the CH-CH group of donorsEC 1.4 Acting on the CH-NH2 group of donorsEC 1.5 Acting on the CH-NH group of donors
EC 1.6 Acting on NADH or NADPH
EC 1.1.1 With NAD or NADP as acceptor
EC 1.1.2 With a cytochrome as acceptor
EC 1.1.3 With oxygen as acceptor
EC 1.1.4 With a disulfide as acceptor
EC 1.1.5 With a quinone or similar compound as acceptor
EC 1.1.99 With other acceptors
EC 1.1.1.1 alcohol dehydrogenaseEC 1.1.1.2 alcohol dehydrogenase (NADP+)EC 1.1.1.3 homoserine dehydrogenaseEC 1.1.1.4 (R,R)-butanediol dehydrogenaseEC 1.1.1.5 acetoin dehydrogenaseEC 1.1.1.6 glycerol dehydrogenaseEC 1.1.1.7 propanediol-phosphate dehydrogenaseEC 1.1.1.8 glycerol-3-phosphate dehydrogenase(NAD+)EC 1.1.1.9 D-xylulose reductase
EC 1.1.1.287 D-arabinitol dehydrogenase (NADP+)EC 1.1.1.288 xanthoxin dehydrogenaseEC 1.1.1.289 sorbose reductaseEC 1.1.1.290 4-phosphoerythronate dehydogenase
Classification des enzymes
Définitions, utilité
Enzymes = biocatalyseurs
protéines; (qq exemples d’ARN catalytiques = ribozymes )
Co-facteurs ions métaliques, Co-enzymesGroupement prostétiques
Avantages de la catalyse enzymatique(par rapport à la catalyse chimique)
Spécificité
Efficacité
Glucose oxydase
Etudes fondamentales "parce'qu-elles existent"= relation structure-activité
Biologie - métabolisme
Biochimie analytique (glucose, anomers)
Biochimie industrielle (glucose isomérase) 60° C, Co2+
Médecine (médicaments = inhibiteurs) « drug design »
Pourqui étudier les enzymes ?
1. Ecrire la réaction catalysée par la cholinestérase (formules chimiques obligatoires!)
3a. Déduire l'équation de Michaelis qui décrit ce méc anisme. De quel type d’inhibition s’agît-il ?
L'enzymologie n'est pas une branche de l’algèbre !
Noté zéro si les passages n’ont pas été expliqués, même sil’équation finale est correcte !
Exemple de questions d’examen: