catalytic strategies. basic catalytic principles what is meant by the binding energy as it relates...
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Catalytic Strategies
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Basic Catalytic Principles
• What is meant by the binding energy as it relates to enzyme substrate interactions?– free energy released by formation of weak interactions
between enzyme and substrate
• How is binding energy used in catalysis?– establishes substrate specificity
– increases catalytic efficiency
– promotes structural changes in enzyme and substrate
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Basic Catalytic Principles
• What are the four strategies used by enzymes to carry out catalysis?– covalent catalysis
• functional groups in enzyme act as nucleophile– OH groups of serine
– SH groups of cysteine
– Imidazole group of histidine
• example - chymotrypsin
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Basic Catalytic Principles
– general acid-base catalysis• enzymes provide functional groups that act as
proton donors or acceptors– amino groups
– carboxyl groups
– sulfhydryl groups
• Example – lysozyme (donates proton)
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Basic Catalytic Principles
– metal ion catalysis• metal ion acts as electrophilic catalyst
– stabilizes negative charge on intermediate
• metal ion may generate a nucleophile by increasing acidity of nearby molecule
– example – carbonic anhydrase
• metal ion may bind to substrate and increase binding energy
– example – NMP kinases
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Basic Catalytic Principles
– catalysis by approximation• binding to enzyme brings two substrates together
– example – NMP kinases
• binding to enzyme orients substrate– susceptible bond is close to catalytic groups of active site
– orbital steering (Koshland and Storm)
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Proteases
• What are proteases?– protein degrading enzymes
• Why are proteases important in biological systems?– recycling of amino acids– digestion of proteins in diet– Enzyme regulation
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Proteases
• Describe the reaction catalyzed by proteases.
• Why is it so difficult to break a peptide bond?
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Chymotrypsin
• What is the nature of the reaction is catalyzed by chymotrypsin?
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Chymotrypsin
• What catalytic strategy does chymotrypsin use?– covalent catalysis
• nucleophilic group in enzyme attacks unreactive carbonyl group of substrate forming covalent bond
• Which group of enzyme acts as the nucleophile?– serine 195
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Chymotrypsin
• How was it possible to identify the specific functional group involved in catalysis?
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Chymotrypsin
• What are the two steps involved in the action of chymotrypsin?
O2 N OCCH3
O
O2 N O-
CH3 CO-O
p-Nitrophenylacetate
p-Nitrophenolate
Step 1 E +
E-OCH3
O
+
Step 2 E-OCH3
O+ H2 O E +
Enzyme
An acyl-enzymeintermediate
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Chymostrypsin
• Can see two stages of chymotrypsin catalysis
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Chymotrypsin
• Three-dimensional structure of enzyme has helped to reveal its catalytic mechanism
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Chymotrypsin
• Three amino acid residues are involved in catalysis: serine 195, histidine 57, aspartate 102
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Chymotrypsinmechanism of action
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Chymotrypsinmechanism of action
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Chymotrypsinmechanism of action
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Chymotrypsinmechanism of action
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Chymotrypsinmechanism of action
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Chymotrypsinmechanism of action
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Chymotrypsinmechanism of action
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Chymotrypsinmechanism of action
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Chymotrypsinmechanism of action
• Unstable tetrahydral intermediate is stabilized by interactions with NH groups from protein at oxyanion hole
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Chymotrypsin
• What accounts for the preference of this enzyme cleaving peptide bonds adjacent to residues with large hydrophobic side chains?
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Serine Proteases
• Other proteases use same catalytic triad– trypsin
• cleaves at peptide bond after residue with long, positively charged side chain
– elastase• cleaves at peptide bond after residue with small side
chains
• Specificity depends upon residues in pocket
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Serine Proteases
• Subtilisin from Bacillus amyloliquefaciens also uses catalytic triad and oxyanion hole
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Serine Proteases
• Carboxypeptidase II which has a very different structure also uses catalytic triad and oxyanion hole
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Serine Proteases
• Presence of similar active sites in different protein families is a result of convergent evolution.
• What does this tell us about this mechanism for the hydrolysis of peptides?
• What is site-directed mutagenesis and how is it used?
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Other Proteases
• What are cysteine, aspartyl and metalloproteases?– Cysteine proteases – cysteine residue acts as
nucleophile• Papain
– Aspartyl proteases – pair of aspartate residues act to enable water molecule to attack peptide bond• renin
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Other Proteases
– Metalloproteases – active site contains a metal ion that activates water to act as a nucleophile• metal is usually zinc
• Carboxypeptidase A
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Protease Inhibitors
• Several useful drugs– Catopril – ACE inhibitor
• regulator of blood pressure
– Crixivan – HIV protease• AIDS treatment
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Carbonic Anhydrases
• What is the reaction catalyzed by these enzymes?
– CO2 + H2O H2CO3 HCO3- + H+
• Where does this reaction take place?
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Carbonic Anhydrases
• What metal ion is associated with these enzymes and where is it bound to the enzyme?
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Carbonic Anhydrases
• How does the zinc complex facilitate the hydration of carbon dioxide?– Binding of water to zinc reduces pKa of water from 15.7 to 7 and
creates a hydroxide ion that can act as a nucleophile
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Carbonic Anhydrases
• Mechanism of action
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Carbonic Anhydrases
• What enables these enzymes to be extremely effective catalysts?– Proton shuttle mechanism
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Restriction Enzymes
• What are restriction endonucleases and how have they been used by bacterial cells?– Enzymes that cleave DNA– Protection against invading viruses
• What is cognate DNA?– DNA containing recognition sites
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Restriction Enzymes
• How do bacteria protect their own DNA from cleavage?
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Restriction Enzymes
• What bond is cleaved by these enzymes?– Bond between 3! oxygen atom an phosphorous atom
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Restriction Enzymes
• What is the mechanism of this reaction?– direct attack of water as a nucleophile on
phosphorous
• Why is Mg+2 needed for activity?– Mg+2 helps position water molecule to attack
phosphate– Mg+2 along with aspartate residue helps to
deprotinate water molecule
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Restriction Enzymes
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• What ensures specificity of the EcoRV reaction?– Inverted repeats of recognition site creates a twofold
rotational symmetry
Restriction Enzymes
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Restriction Enzymes
• G and A bases at 5! End form hydrogen bonds with residues from two loops of enzyme causing distortion of DNA and bonding with Mg+2
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Restriction Enzymes
• How does methylation protect host DNA from restriction enzymes?
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Restriction Enzymes
• What is horizontal gene transfer and how do this relate to the presence of restriction enzymes in bacteria?
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Restriction Enzymes
• Different bacteria share common gene sequences and a similar active site conformation
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NMP Kinases
• What reaction do nucleoside monophosphate kinases catalyze?– transfer of phosphate group from a nucleoside
triphosphate to a nucleoside monophosphate
• Example of NMP kinase?– adenylate kinase
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NMP Kinases
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NMP Kinases
• What structural features does this family of enzymes have in common?
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NMP Kinases
• What role does Mg+2 or Mn+2 play in the catalytic mechanism of these enzymes?
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NMP Kinases
• How do we know that binding between enzyme and substrate involves an induced fit mechanism?
• What catalytic strategy is used by this enzyme?
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NMP Kinases
• Many important proteins contain P-loop NTPase domains.