Structure and mechanism of proteases. Peptide bond hydrolysis is exergonic

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1 Structure and mechanism of proteases Serine proteases Voet + Voet, Biochemistry Enzyme catalysis, pg Chemical reaction mechanisms, pg Serine proteases, pg Aspartate proteases A. Wlodawer lecture on HIV-Protease, Biozentrum s 30th Anniversary Symposium, Peptide bond hydrolysis is exergonic R 1 O R 2 O H 3 N + C C N C C + H 2 O H H H O - exp( -2 kcal/mol/kt) = exp( -2/0.6) = exp(-3.3) = 1 : 27!! R 1 O H R 2 O H 3 N + C C + H N + C C + 2 kcal/mol H O - H H O - Stephan Grzesiek 1

2 Reaction rates The large free energy difference (G) between hydrolysed and condensed amino acids does not mean that the reaction occurs rapidly. It only predicts that the equilibrium is mostly in the hydrolysed form. The reaction rates for spontaneous peptide hydrolysis are very low. (Otherwise we would not be here.) Reaction rates can be described successfully by transition state theory. Transition state diagram for a reaction where G decreases Stephan Grzesiek 2

3 Transition state theory Transition state theory assumes that a reaction A + B P + Q occurs via an intermediate (activated) state X : A + B X P + Q The reaction occurs from this state X with a rate constant that is given by the thermal vibrational frequency : = k B T/h h = k B T State X is in rapid equilibrium with A + B, such that [X ] = K [A] [B] = exp(-g / kt) [A] [B] where G is the free energy difference between the intermediate state and the initial state. G is also called the activation or kinetic barrier. The total rate k for the reaction A + B P + Q is then simply k = (k B T/h)* [X ] = (k B T/h)*exp(-G / k B T) [A] [B] Catalysts (enzymes) increase the reaction rates by lowering the height of the activation barrier Stephan Grzesiek 3

4 Transition state theory exercise We look again at the reaction A + B P + Q with intermediate (activated) state X : A + B X P + Q. Assume that G 1 is the free energy of the original state (1) with reactants A and B, and G 2 the energy of the activated state (2), and G 3 is the energy of the final state (3) with reactants C and D, Calculate the rates for forward (k 13 ) and backward (k 31 ) reactions in terms of free energies G 1, G2, G3. Show that the ratio of forward and backward rates gives a normal chemical equilibrium equation. Proteases (proteinases, peptidases) work by lowering the activation barrier for peptide hydrolysis The activated state is usually a tetrahedral intermediate Stephan Grzesiek 4

5 Specificities of Various Endopeptidases Scissile bond Enzyme Source Specificity Comments Trypsin Bovine R n-1 = positively charged Highly specific pancreas residues: Arg, Lys; R n Pro Chymotrypsin Bovine pancreas R n-1 = bulky hydrophobic residues: Phe, Trp, Tyr; Cleaves more slowly for R n-1 = Asn, His, Met, Leu R n Pro Elastase Bovine pancreas R n-1 = small neutral residues: Ala, Gly, Ser, Val; R n Pro Thermolysin Pepsin Endopeptidase V8 Bacillus thermoproteolyticus Bovine gastric mucosa Staphylococcus aureus R n = Ile, Met, Phe, Trp, Tyr, Val; R n-1 Pro R n = Leu, Phe, Trp, Tyr; R n-1 Pro R n-1 = Glu Occasionally cleaves at R n = Ala, Asp, His, Thr; heat stable Also others; quite nonspecific; ph optimum = 2 A Selection of Serine Proteases Enzyme Source Function Trypsin Pancreas Digestion of proteins Chymotrypsin Pancreas Digestion of proteins Elastase Pancreas Digestion of proteins Thrombin Vertebrate serum Blood clotting Plasmin Vertebrate serum Dissolution of blood clots Kallikrein Blood and tissues Control of blood flow Complement C1 Serum Cell lysis in the immune response Acrosomal protease Sperm acrosome Penetration of ovum Lysosomal protease Animal cells Cell protein turnover Cocoonase Moth larvae Dissolution of cocoon after metamorphosis -Lytic protease Bacillus sorangium Possibly digestion Proteases A and B Streptomyces griseus Possibly digestion Subtilisin Bacillus subtilis Possibly digestion Source: Stroud, R.M., Sci. Am. 231(1): 86 (1974). Stephan Grzesiek 5

6 Serine Protease Kinetics Chymotrypsin can act as an esterase as well as a protease. This is not so surprising because ester and amide hydrolysis are almost identical. The esterase activity on p-nitrophenylacetate can be easily followed because the product p-nitrophenolate is strongly colored. The time course of the reaction reveals two phases: 1. A "burst phase", in which p-nitrophenolate is rapidly formed in amounts that are stoichiometric with the quantity of the active enzyme present. 2. A "steady state phase", in which p-nitrophenolate is generated at reduced but constant rate that is independent of substrate concentration, but proportional to the enzyme concentration. Stephan Grzesiek 6

7 Ester hydrolysis as a Kinetic Model for Chymotrypsin (strongly colored) Time course of p-nitrophenylacetate hydrolysis by chymotrypsin [chymotrypsin] Stephan Grzesiek 7

8 These observations can be interpreted in terms of a two-stage reaction sequence in which the enzyme (1) rapidly reacts with the p- nitrophenylacetate to release the nitrophenolate ion forming a covalent acylenzyme intermediate that (2) is slowly hydrolysed to release acetate. Chymotrypsin-catalyzed amide hydrolysis has been shown to follow a reaction pathway similar to that of ester hydrolysis but with the first step of the reaction, enzyme acylation, being rate determining rather than the deacylation step. Time course of p-nitrophenylacetate hydrolysis by chymotrypsin Rate limiting Stephan Grzesiek 8

9 Identification of active site residues Chymotrypsin's catalytically important residues have been identified by a number of experiments including chemical labeling studies, site-directed mutagenesis, and structural evidences. Ser195: The active Ser can be identified from a reaction with Diisopropylphosphofluoridate (DIPF) that irreveribly inactivates the enzyme. Other serine residues of the enzyme do not react with DIPF. His57: Chymotrypsin specifically binds tosyl-l-phenylalanine chloromethyl ketone (TPCK), because of its resemblance to a Phe residue (one of chymotrypsin's preferred residues, see table). Active-site bound TPCK's chloromethyl ketone group is a strong alkylating agent; it reacts only with His57, thereby inactivating the enzyme. Asp102: In all structures of chymotrypsin and homologues such as bovine trypsin and porcine elastase, His57 and Ser195 are located at the substrate binding site together with the invariant (in all serine proteases) Asp102, which is buried in a solvent-inaccessible pocket. These three residues form a hydrogen-bonded constallation referred to as the catalytic triad. Stephan Grzesiek 9

10 Identification of Catalytic Residue Ser195 Inactive!!! Identification of Catalytic Residue His57 Inactive!!! Tosyl-L-phenylalanine chloromethyl ketone Stephan Grzesiek 10

11 Serine protease structure X-ray structure of bovine trypsin Stephan Grzesiek 11

12 X-ray structure of bovine trypsin The active site residues of chymotrypsin Stephan Grzesiek 12

13 Structural superposition of 5 homologous proteases Sequence identity ~40% Sequence and structural homologies A large number of sequence homologues exist for chymotrypsin. The sequence homologies correspond to very similar structures. In general, sequence identities of more than 30-40% lead to identical folds and very similar structures. It is nowadays possible to generate very reasonable predictions of such homologous structures from modeling. One such program (swiss model server) can be accessed from the Swiss-Model website (under Biozentrum's home page, group Schwede) and returns within few minutes a modeled structure from the input of an aminoacid sequence and a homologous known structure. Stephan Grzesiek 13

14 An example of convergent evolution Subtilisin, chymotrypsin, and serine carboxypeptidase II have low sequence identity Divergent and convergent evolution The great similarities among chymotrypsin, trypsin, and elastase indicate that these proteins evolved through gene duplications of an ancestral serine protease followed by the divergent evolution of the resulting enzymes. In contrast, there a two known serine proteases (Subtilisin and Serine carboxypeptidase II) whose primary and tertiary structures bear no discernable relationship to each other or to chymotrypsin but which, nevertheless, contain catalytic triads at their active sites whose structures closely resemble that of chymotrypsin. Since the order of the active site residues in the three types of serine proteases are quite different, it seems highly improbable that they could have evolved from the same ancestral protease. These proteins apparently constitute a remarkable example of convergent evolution: Nature seems to have independently discovered the same catalytic mechanism at least three times. Stephan Grzesiek 14

15 Serine protease mechanism The catalytic mechanism I II Stephan Grzesiek 15

16 The catalytic mechanism IV III The catalytic mechanism V VI Stephan Grzesiek 16

17 The preceding model of the catalytic mechanism of serin proteases has been formulated on the basis of a large number of chemical and structural data. In the following, it is shown that the complex of trypsin with its inhibitor (bovine pancreatic trypsin inhibitor) BPTI can serve as a model for the tetrahedral intermediate, i.e. the transition state. BPTI binds to and inactivates trypsin that is prematurely activated in the pancreas from digesting that organ. The portion of BPTI in contact with the trypsin active site resembles bound substrate. The side chain of BPTI Lys15 occupies the trypsin specificity pocket and the peptide bond between BPTI Lys15 and Ala16 is positioned as if were the scissile peptide bond. What is most remarkable is that the active site complex assumes a conformation that is well along the reaction coordinate towards the tetrahedral intermediate: the side chain oxygen of trypsin Ser195 is in closer-than-van der Waals contact with the pyramidally distorted carbonyl carbon (Lys15) of BPTI's "scissile" peptide bond. However, the reaction is stopped at this point and cannot proceed because of the rigidity of the active site complex and because it is so tightly sealed that the leaving group cannot leave and water cannot enter the active site (another example that flexibility is necessary for function). Bovine pancreatic trypsin inhibitor (BPTI) Trypsin BPTI BPTI is a natural inhibitor for prematurely activated trypsin Stephan Grzesiek 17

18 Inhibiton by BPTI BPTI binds very tightly to trypsin (k = M) BPTI binding resembles the substrate binding The scissile bond of BPTI would be Lys15I- A16I The tetrahedral intermediate is almost formed Ser195-sidechain-O is closer to Lys15Icarbonyl-carbon than the van der Waals distance The reaction cannot proceed because of the rigidity of active site and because water cannot enter Trypsin BPTI The BPTI-Trypsin complex is a model for the transition state The tetrahedral intermediate is stabilized by the oxyanion hole Stephan Grzesiek 18

19 The oxyanion hole Detailed comparison of structures of several serine protease-inhibitor complexes reveal a further structural basis for the catalysis in these enzymes: 1. the conformational distortion that occurs with the formation of the tetrahedral intermediate causes the carbonyl oxygen of the scissile peptide to move deeper into the active site and to occupy a previously unoccupied position the oxyanion hole. 2. There it forms two hydrogen bonds with the enzyme that cannot form when the carbonyl is in its normal trigonal conformation. 3. The tetrahedral distortion, moreover, permits the formation of an otherwise unsatisfied hydrogen bond between the enzyme and the backbone NH group of the residue preceding the scissile bond. Consequently, the enzyme binds the tetrahedral intermediate in preference to either the Michaelis complex or the acyl-enzyme intermediate. It is this phenomenon that is responsible for the catalytic efficiency of the serine protease, i.e. the lowering of the free energy (activation barrier) of the activated intermediate. Zymogens Proteolytic enzymes are usually bionsynthesized as larger inactive precursors called zymogens The proteolytic enzymes are only activated at the appropriate location in the body by cleavage of the zymogen precursor This cleavage is started by another enzyme (e.g. enteropeptidase) and then proceeds further autolytically Stephan Grzesiek 19

20 Activation of trypsinogen by cleavage Serine protease summary Transition state theory is a successful model for the description of chemical reaction rates. Proteolytic enzymes increase the rate of peptide hydrolysis by stabilizing the transition state (lowering the activation barrier). Serine proteases contain a catalytic triad of Asp, His, and Ser at their active site. The transition state in serine proteases is a tetrahedral hybridization of the carbonyl carbon. This tetrahedral intermediate is formed by complexation to the serine and histidine sidechains. The tetrahedral intermediate is stabilized by hydrogen bonds to sited in the oxyanion hole. BPTI is a natural inhibitor for trypsin. Its binding ressembles the binding of the normal substrate, but the reaction is arrested in the transition state. This makes the conformation of the transition state observable. Zymogens are the inactive precursors of proteolytic enzymes. They are activated by external and autolytic cleavage of small fragments from their polypeptide chain. Stephan Grzesiek 20