CHAPTER 9: CATALYTIC STRATEGIES. Chess vs Enzymes King vs Substrate

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1 CHAPTER 9: CATALYTIC STRATEGIES Chess vs Enzymes King vs Substrate

2 INTRODUCTION CHAPTER 9 What are the sources of the catalytic power and specificity of enzymes? Problems in reactions in cells Neutral ph, water as a solvent and 37 C Hard to achieve optimal reaction rate at these conditions Need a special strategy to achieve specificity Enzyme classes discussed in this chapter Serine proteases Carbonic anhydrases Restriction endonucleases Myosins

3 INTRODUCTION CHAPTER 9 Comparison between class members reveals how enzyme active sites have evolved and been refined Our knowledge of catalytic strategies has been used to develop practical applications Potential drugs Enzyme inhibitors Other catalytic molecules (catalytic RNA)

4 A FEW BASIC CATALYTIC PRINCIPLES CHAPTER 9 Substrate binding Establishes substrate specificity Stabilizes the transition state (lowers the activation E) Increases effective concentration Induced fit : the binding promotes structural changes that facilitate catalysis Covalent catalysis The active site contains a reactive group (nucleophile) The nucleophile becomes temporarily attached to a part of the substrate in the course of catalysis Proteolytic enzymes

5 A FEW BASIC CATALYTIC PRINCIPLES CHAPTER 9 General Acid-Base Catalysis A molecule other than water plays the role of a proton donor or acceptor Histidines in chymotrypsin and carbonic anhydrase, phosphate group of ATP in myosins Catalysis by Approximation Reaction rate enhancement by proximity effect Metal Ion Catalysis Nucleophile activation (carbonic anhydrase) Stabilizing reaction intermediate (EcoRV) Increasing binding affinity of substrates (myosin)

6 9.1 CATALYSIS OF PROTEASES CHAPTER 9 Proteases facilitate a fundamentally difficult reaction Involved in protein turnover Important in regulating the activity of enzymes and proteins Perform a hydrolysis reaction The addition of a water molecule to a peptide bond Thermodynamically favored reaction Half-life ~ yrs at physiological condition Peptide bonds need to be hydrolyzed within miliseconds in some biochemical processes

7 9.1 CATALYSIS OF PROTEASES Kinetic stability of peptide bonds The resonance structure of a peptide bond - Planar conformation - Partial double bond character CHAPTER 9 - The amide carbon is less electrophilic than the ester carbon These properties make the peptide bond stable

8 CHYMOTRYPSIN POSSESSES A HIGHLY REACTIVE SERINE RESIDUE Chymotrypsin cleaves peptide bonds selectively on the carboxyl side of the large hydrophobic AA C-term of Trp, Phe, Tyr and Met A good example of the use of covalent catalysis - A powerful Nu: attacks the unreactive carbonyl carbon of the substrate CHAPTER 9.1 PROTEASES - The Nu: becomes covalently attached to the substrate Fig 9.1 Specificity of chymotrypsin Chymotrypsin cleaves the amide bond of the carboxyl side of hydrophobic amino acid.

9 CHYMOTRYPSIN POSSESSES A HIGHLY REACTIVE SERINE RESIDUE Identification of the reactive Nu: in chymotrypsin Treatment of chymotrypsin with diisopropylphospho-fluoridate (DIPF) makes the enzyme irreversibly inactive Only a single residue, Ser195 was modified - The residue plays a central role in the catalytic mechanism of chymotrypsin CHAPTER 9.1 PROTEASES Fig 9.2 An unusually reactive serine residue in chymotrypsin. Chymotrypsin is inactivated by treatment with DIPF, which reacts only with Ser195 among 28 possible serine residues

10 CHAPTER 9.1 PROTEASES TWO-STEP ACTION OF CHYMOTRYPSIN Kinetic study of chymotrypsin N-acetyl-L-phenylalanine p-nitrophenyl ester was used to monitor the reaction by a colored product. Fig 9.3 Chromogenic substrate. N-acetyl-L-phenylalanine p-nitrophenyl ester yields a yellow product, p-nitrophenolate, on cleavage by chymotrypsin.

11 CHAPTER 9.1 PROTEASES TWO-STEP ACTION OF CHYMOTRYPSIN Kinetic study of chymotrypsin Michealis-Menten kinetics with a K M of 20 mm and a k cat of 77 s -1. Hydrolysis proceeds in two steps: an initial rapid burst followed by a steady-state Fig 9.4 Kinetics of chymotrypsin catalysis. Two phases are evident in the cleaving of N-acetyl-L-phenylalanine p-nitrophenyl ester by chymotrypsin.

12 CHAPTER 9.1 PROTEASES TWO-STEP ACTION OF CHYMOTRYPSIN Explanation of the two-step hydrolysis The first step: acyl-enzyme intermediate formation - Ser195 attacks the carbonyl carbon of the substrate - p-nitrophenolate is released The second step: Hydrolysis of the acyl-enzyme intermediate Fig 9.5 Covalent Catalysis. Hydrolysis by chymotrypsin takes place in two steps: (A) acylation to form the acyl-enzyme intermediate followed by (B) deacylation to regenerate the free enzyme.

13 CHAPTER 9.1 PROTEASES CATALYTIC TRIAD The 3-D structure of chymotrypsin was solved in 1967 Comprises three polypeptide chains linked by disulfide bonds Synthesized as a single polypeptide (chymotrypsinogen), which is activated by the proteolytic cleavage to yield the three chains Fig 9.6 The 3-D structure of chymotrypsin.

14 CATALYTIC TRIAD CHAPTER 9.1 PROTEASES The active site lies in a left on the surface of the enzyme Two hydrogen bonds in the active site Between Ser195 and His57 Between His57 and Asp102 These three residues are referred to as the catalytic triad Fig 9.7 The catalytic triad. The catalytic triad, shown on the left, converts serine 195 into a potent nucleophile, as illustrated on the right

15 CATALYTIC TRIAD Activate the Nu: CHAPTER 9.1 PROTEASES Stabilizes the (-) charge of the intermediate Cleavage of the amide bond Nucleophilic attack Substrate binding Release of the amino component Release of the carboxylic acid component Nucleophilic attack Water binding Cleavage of the ester bond Fig 9.8 Peptide hydrolysis by chymotrypsin.

16 CATALYTIC TRIAD CHAPTER 9.1 PROTEASES Positioning of Ser195 Hydrophobic environment Fig 9.9 The oxyanion hole. Fig 9.10 Specificity pocket of chymotrypsin Fig 9.11 Specificity nomenclature for protease-substrate interactions.

17 CHAPTER 9.1 PROTEASES CATALYTIC TRIADS FOUND IN OTHER ENZYMES Catalytic triads are found in other hydrolytic enzymes Trypsin and elastase are obvious homologs of chymotrypsin - 40% identical sequence - overall structures are quite similar - remarkable difference in substrate specificity: aromatic/hydrophobic, long/(+) charged, and small (Fig 9.13) Fig 9.12 Structural similarity of trypsin and chymotrypsin. Chymotrypsin (red); trypsin (blue)

18 CHAPTER 9.1 PROTEASES CATALYTIC TRIADS FOUND IN OTHER ENZYMES Fig 9.13 The S1 pockets of chymotrypsin, trypsin, and elastase.

19 CHAPTER 9.1 PROTEASES CATALYTIC TRIADS FOUND IN OTHER ENZYMES Catalytic triads are found in many other hydrolytic enzymes This catalytic strategy must be an especially effective approach to the hydrolysis of peptides and related bonds Fig 9.14 The catalytic triad and oxyanion hole of subtilisin.

20 CHAPTER 9.1 PROTEASES SITE-DIRECTED MUTAGENESIS STUDY How can we prove that the proposed mechanism is correct? One way is to test the contribution of individual AA Each residues within the catalytic triad in subtilisin are individually converted into Ala Asp32, His64, and Ser221 By site-directed mutagenesis Oxyanion hole Asn155 to Gly k cat reduces to 0.2% Shows the significant role of the amide proton Fig 9.15 Site-directed mutagenesis of subtilisin.

21 OTHER PEPTIDE-CLEAVING ENZYMES CHAPTER 9.1 PROTEASES Three alternative approaches to peptide-bond hydrolysis Fig 9.16 Three classes of proteases and their active sites.

22 CHAPTER 9.1 PROTEASES OTHER PEPTIDE-CLEAVING ENZYMES Cysteine proteases Their catalytic strategy is similar to the chymotrypsin family Cysteine plays the role of serine in chymotrypsin The cysteine is activated by a histidine residue Asp in the catalytic triad does not exist. (better nucleophilicity of Cys) Fig 9.17A The activation strategy for cysteine proteases.

23 CHAPTER 9.1 PROTEASES OTHER PEPTIDE-CLEAVING ENZYMES Aspartyl proteases There are two aspartic acid residues in the active site One Asp activates the attacking water molecule The other polarizes the peptide carbonyl group Examples are renin and pepsin Fig 9.17B The activation strategy for aspartyl proteases.

24 CHAPTER 9.1 PROTEASES OTHER PEPTIDE-CLEAVING ENZYMES Metalloproteases The active site contains a metal ion (zinc in most cases) The metal ion activates the attacking water molecule and polarizes the peptide carbonyl group Examples are thermolysin and carboxylpeptidase A Fig 9.17C The activation strategy for metalloproteases.

25 CHAPTER 9.1 PROTEASES PROTEASE INHIBITORS Captopril The first angiotensin-converting enzyme inhibitor (ACE inhibitor) Developed in 1975 by three researchers at the U.S. drug company Squibb (now Bristol-Myers Squibb) Used for the treatment of hypertension and some types of congestive heart failure ( ) Figure Structures of captopril

26 CHAPTER 9.1 PROTEASES PROTEASE INHIBITORS Indinavir A protease inhibitor used to treat HIV infection and AIDS FDA-approved in 1996 Aspartyl protease Non-peptidic substrate analog Fig 9.18 HIV protease, a dimeric aspartyl protease. Fig 9.19 Indinavir, an HIV protease inhibitor.

27 9.2 CATALYSIS OF CARBONIC ANHYDRASES Hydration of carbon dioxide (CO 2 ) CO 2 is a major end product of aerobic metabolism and released into the blood and transported to the lungs In the red blood cells, it reacts with water. k 1 = M -1 s -1 CHAPTER 9 k -1 = 50 s -1 K 1 = 5.4 X 10-5 pk a = 3.5 Carbonic anhydrases (CAs) accelerate CO 2 hydration The most active CAs hydrate CO 2 at k cat = 10 6 M -1 s -1.

28 9.2 CATALYSIS OF CARBONIC ANHYDRASES ZINC ION IN CARBONIC ANHYDRASE (CA) CA was discovered in 1932 In 10 years after the discovery, the enzyme was found to contain a bound zinc ion Appeared to be necessary for catalytic activity It made CA the first known zinc-containing enzyme Hundreds of enzymes are known to contain zinc. One-third of all enzymes contain or require metal ions for activity Metal ions have several properties that increase chemical reactivity: (+) charges, strong yet kinetically labile bonds, and several oxidation states The chemical properties explain why they are important for enzyme activity

29 9.2 CATALYSIS OF CARBONIC ANHYDRASES ZINC ION IN CARBONIC ANHYDRASE (CA) At least seven CAs are present in human beings They are all clearly homologous CA II is a major protein component of red blood cells and one of the most active CAs Fig 9.21 The structure of human CA II and its zinc site.

30 9.2 CATALYSIS OF CARBONIC ANHYDRASES CATALYSIS ENTAILS ZINC ACTIVATION OF A WATER MOLECULE ph dependence of enzymatic CO 2 hydration k cat increases with increasing ph The midpoint is near ph 7 Fig 9.22 Effect of ph on CA activity. Fig 9.23 The pk a of zinc-bound water. Binding to zinc lowers the pk a of water form 15.7 to 7.

31 9.2 CATALYSIS OF CARBONIC ANHYDRASES CATALYSIS ENTAILS ZINC ACTIVATION OF A WATER MOLECULE Zinc ion acts as a Lewis acid and lowers the pk a of the bound water The zinc-bound OH - is a potent nucleophile CA also possesses a hydrophobic patch Serves as a binding site for carbon dioxide Fig 9.24 Carbon dioxide binding site.

32 9.2 CATALYSIS OF CARBONIC ANHYDRASES CATALYSIS ENTAILS ZINC ACTIVATION OF A WATER MOLECULE Mechanism of CA Water deprotonation CO 2 binding Nucleophilic attack by HO - Displacement of HCO 3- by water Fig 9.25 Mechanism of CA.

33 9.2 CATALYSIS OF CARBONIC ANHYDRASES CATALYSIS ENTAILS ZINC ACTIVATION OF A WATER MOLECULE Studies of a synthetic analog model system Provide evidence for the mechanism s plausibility The pk a of the bound water is 8.7 At ph 9.2, this complex accelerates the hydration of CO 2 more than 100-fold This experiment supports the proposed mechanism is correct Fig 9.26 A synthetic analog model system for carbonic anhydrase.

34 9.2 CATALYSIS OF CARBONIC ANHYDRASES PROTON TRANSFER IN CA CATALYSIS (pk a of the bound water is 7) Fig 9.27 Kinetics of water deprotonation. Protons diffuse very rapidly with 2 nd order rate constants near M -1 s -1. k M -1 s -1 and K = 10-7 M, then k s -1 If CO 2 is hydrated at a rate of 10 6 s -1, then every step in the mechanism must take place at least this fast!!

35 9.2 CATALYSIS OF CARBONIC ANHYDRASES PROTON TRANSFER IN CA CATALYSIS Fig 9.28 The effect of buffer on deprotonation. K = k 1 /k -1 1 if pk a of BH + is 7. The highest rates of carbon dioxide hydration require the presence of buffer. k 1 and k -1 will be limited by buffer diffusion, 10 9 M -1 s -1 At [B] = 1 mm, the rate of proton abstraction becomes 10 6 M -1 s -1

36 9.2 CATALYSIS OF CARBONIC ANHYDRASES PROTON TRANSFER IN CA CATALYSIS Fig 9.29 Histidine proton shuttle. His64 in CA II functions as the buffer His64 abstracts a proton from the zinc-bound water and then transfer the proton to the buffer In many enzymatic reactions, the proton transfer is crucial to the function

37 9.3 CATALYSIS OF RESTRICTION ENZYMES Bacteria and archaea have mechanisms to protect themselves from viral infections A major protective strategy for the host is to use restriction endonucleases (REs) REs recognize particular base sequences REs must show tremendous specificity at two levels They must not degrade host DNA containing the recognition sequences They must cleave only DNA molecules containing recognition sites For example, a recognition site, 5 -GATATC-3, requires more than 4 6 (4096) times more efficient activity How do REs achieve these specificity? CHAPTER 9

38 CLEAVAGE MECHANISM 9.3 CATALYSIS OF RESTRICTION ENZYMES REs catalyze the hydrolysis of the phosphodiester backbone of DNA Generate a free 3 -hydroxyl group and a 5 -phosphoryl group Fig 9.32 Hydrolysis of a phosphodiester bond.

39 TWO PROPOSED MECHANISMS Mechanism 1 (covalent intermediate) 9.3 CATALYSIS OF RESTRICTION ENZYMES Mechanism 2 (direct hydrolysis)

40 TWO PROPOSED MECHANISMS 9.3 CATALYSIS OF RESTRICTION ENZYMES How can we figure out which mechanism is correct? In-line displacement (S N 2) Interconversion of the R and S configurations Comparison of the two mechanisms In both cases, the reaction takes place by in-line displacement Two conversions occur in mechanism 1 Only one conversion occurs in mechanism 2

41 TWO PROPOSED MECHANISMS 9.3 CATALYSIS OF RESTRICTION ENZYMES How can we figure out which mechanism is correct? Analysis of the product configuration A problem is that the product is not chiral! Designing a special substrate Phosphorothioate Water containing 18 O Fig 9.33 Labeling with phosphorothioates.

42 TWO PROPOSED MECHANISMS 9.3 CATALYSIS OF RESTRICTION ENZYMES Fig 9.34 Stereochemistry of cleaved DNA. The analysis revealed that the stereochemical configuration at the phosphorus atom was inverted only once with cleavage Mechanism 2

43 9.3 CATALYSIS OF RESTRICTION ENZYMES MAGNESIUM FOR CATALYTIC ACTIVITY One or more Mg 2+ are essential to the function of RE As many as three metal ions have been found to be present per active site The roles of the multiple metal ions is still under investigation One ion-binding site appears in all RE structures In the EcoRV structure, the Mg 2+ activates and positions a water molecule to attack the phosphorus atom Fig 9.35 A magnesium ion-binding site in EcoRV.

44 9.3 CATALYSIS OF RESTRICTION ENZYMES THE ORIGIN OF THE SEQUENCE-SPECIFICITY The recognition sequences for most REs are inverted repeats Palindromic sequence / twofold rotational symmetry Most REs functions as a dimer Fig 9.36 Structure of the recognition site of EcoRV.

45 9.3 CATALYSIS OF RESTRICTION ENZYMES THE ORIGIN OF THE SEQUENCE-SPECIFICITY The binding affinity of EcoRV to the cognate DNA The enzyme can bind DNA in the absence of Mg 2+ Almost no affinity difference between the cognate and noncognate! Fig 9.37 Structure of EcoRV embracing a cognate DNA molecule.

46 9.3 CATALYSIS OF RESTRICTION ENZYMES THE ORIGIN OF THE SEQUENCE-SPECIFICITY A unique set of interactions between the enzyme and the cognate DNA Direct interaction of GA in 5 -GATATC-3 with the enzyme Fig 9.37 Structure of EcoRV embracing a cognate DNA molecule.

47 9.3 CATALYSIS OF RESTRICTION ENZYMES THE ORIGIN OF THE SEQUENCE-SPECIFICITY The most striking feature is the distortion of the DNA The central TA in 5 -GATATC-3 is distorted to be positioned for cleavage, which results in the specificity Catalytic activity difference is > fold Fig 9.38 Distortion of the recognition site. Fig 9.39 Nonspecific and cognate DNA within EcoRV.

48 9.3 CATALYSIS OF RESTRICTION ENZYMES PROTECTION OF THE HOST-CELL DNA Restriction-modification system The host DNA is methylated by methylases for protection REs cannot cleave methylated DNA For each RE, the host cell produces a corresponding methylase to methylate the cognate sequence Fig 9.41 Protection by methylation.

49 9.4 ATP HYDROLYSIS OF MYOSINS Myosins comprise a family of ATP-dependent motor proteins Involved in muscle contraction and a wide range of other eukaryotic motility processes Found in all eukaryotes and the human genome encodes more than 40 different myosins Catalyze the hydrolysis of ATP Produce ADP and inorganic phosphate Thermodynamically favorable reaction Use the energy to drive the motion of molecules CHAPTER 9

50 MYOSIN-ATP COMPLEX STRUCTURE 9.4 ATP HYDROLYSIS OF MYOSINS The ATPase domain structure of the myosin from the soil-living amoeba Dictyostelium discoideum Approximately 750 amino acids No significant structural change between the apo form and complexed form No hydrolysis observed in the complexed structure Mg 2+ is not present in the enzyme All NTPs are present as NTP-Mg 2+ complex Fig 9.45 Myosin-ATP complex structure. blue, no ligands bound; purple, complexed with ATP.

51 9.4 ATP HYDROLYSIS OF MYOSINS MYOSIN-ATP COMPLEX STRUCTURE How does the hydrolysis occur? Water needs to be activated Requires a basic residue or activation by a metal ion The enzyme-atp complex is stable No basic residue and nucleophilic water observed Conformational change required for catalysis Fig 9.45 Myosin-ATP complex structure. blue, no ligands bound; purple, complexed with ATP.

52 9.4 ATP HYDROLYSIS OF MYOSINS THE COMPLEX STRUCTURE WITH A TS-ANALOG For catalysis, ATPase must stabilize the TS of the reaction Expected that ATP hydrolysis includes a pentacoordinate TS The complex structure of the ATPase with VO 4 3-, ADP and Mg 2+ The vanadium atom is coordinated to five oxygen atoms Ser236 is positioned to play a role in catalysis Pentacoordinated transition state of ATP Fig 9.46 Myosin ATPase transition state analog.

53 9.4 ATP HYDROLYSIS OF MYOSINS THE COMPLEX STRUCTURE WITH A TS-ANALOG The proposed mechanism of ATP hydrolysis The water molecule attacks the γ-phosphoryl group The hydroxyl group of Ser236 mediates the proton transfer from the water molecule to γ-phosphoryl group The ATP serves as a base to promote its own hydrolysis Fig 9.47 Facilitating water attack.

54 9.4 ATP HYDROLYSIS OF MYOSINS THE COMPLEX STRUCTURE WITH A TS-ANALOG Conformational change of myosin Some residues in the active site moves by ~2 Å - This helps facilitating the hydrolysis by stabilizing the TS 60 amino acids at the C- terminus moves by ~25 Å - This motion is amplified even more as the C-terminal domain is connected to other structures. Fig 9.48 Myosin conformational changes. red, ATP-bound; blue, TS analog-bound.

55 9.4 ATP HYDROLYSIS OF MYOSINS THE RATE LIMITING STEP Slow turnover rate of myosin Once per second What steps limit the rate of turnover? Experiment with H 18 2 O

56 9.4 ATP HYDROLYSIS OF MYOSINS THE RATE LIMITING STEP Experiment with H 18 2 O Two or three 18 O were observed the hydrolysis reaction is reversible the release of the products (P i ) is rate limiting Fig 9.48 Reversible hydrolysis of ATP within the myosin active site.

57 9.4 ATP HYDROLYSIS OF MYOSINS THE RATE LIMITING STEP Myosins are examples of P-loop NTPase enzymes P-loop is named because it interacts with phosphoryl groups P-loop is found in many enzymes involved in ATP-mediated conformation change Fig 9.51 Three proteins containing P-loop NTPase domains.

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