522 Chapter 16 ● Mechanisms of Enzyme Action
The AIDS Virus HIV-1 Protease Is an Aspartic Protease
Recent research on acquired immune deficiency syndrome (AIDS) and its causative viral agent, the human immunodeficiency virus (HIV-1), has brought a new aspartic protease to light. HIV-1 protease cleaves the polyprotein products of the HIV-1 genome, producing several proteins necessary for viral growth and cellular infection. HIV-1 protease cleaves several different peptide linkages in the HIV-1 polyproteins, including those shown in Figure 16.28. For example, the protease cleaves between the Tyr and Pro residues of the sequence Ser- Gln-Asn-Tyr-Pro-Ile-Val, which joins the p17 and p24 HIV-1 proteins.
The HIV-1 protease is a remarkable viral imitation of mammalian aspartic proteases: It is a dimer of identical subunits that mimics the two-lobed monomeric structure of pepsin and other aspartic proteases. The HIV-1 protease subunits are 99-residue polypeptides that are homologous with the individual domains of the monomeric proteases. Structures determined by X-ray diffraction studies reveal that the active site of HIV-1 protease is formed at the interface of the homodimer and consists of two aspartate residues, designated Asp25 and Asp25 , one contributed by each subunit (Figure 16.29). In the homodimer, the active site is covered by two identical “flaps,” one from each subunit, in contrast to the monomeric aspartic proteases, which possess only a single active-site flap.
Enzyme kinetic measurements by Thomas Meek and his collaborators at SmithKline Beecham Pharmaceuticals have shown that the mechanism of HIV-1 protease is very similar to those of other aspartic proteases (Figure 16.30). Two concerted proton transfers by the aspartate carboxyls facilitate nucleophilic attack by water on the carbonyl carbon of the peptide substrate. If the protease-substrate complex is incubated with H218O, incorporation of 18O into the peptide carbonyl group can be measured. Thus, not only is the formation of the amide dihydrate reversible, and the two hydroxyl groups of the dihydrate equivalent, but the protonation states of the active-site carboxyl groups must interchange (Figure 16.30). The simplest model would involve direct proton exchange across the Asp-Asp dyad as shown. The symmetrical nature of the active-site aspartyl groups is consistent with the idea of facile exchange of the proton between the two Asp residues.
The observation that 18O can accumulate in the substrate from H218O also implies that formation and reversal of the amide dihydrate must be faster than
FIGURE 16.28 ● HIV mRNA provides the genetic information for synthesis of a polyprotein. Proteolytic cleavage of this polyprotein by HIV protease produces the individual proteins required for viral growth and cellular infection.
gag |
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pol |
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(gag–pol polyprotein) |
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Protease |
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p11(protease) |
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Proteins |
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p24 |
p66/51 (reverse transcriptase) |
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p15 |
p32(integrase) |
(Adapted
FIGURE 16.30
FIGURE 16.29
16.12 ● The Aspartic Proteases |
523 |
● (left) HIV-1 protease complexed with the inhibitor Crixivan® (red) made by Merck. The flaps (residues 46–55 from each subunit) covering the active site are shown in green and the active site aspartate residues involved in catalysis are shown in white.
(right) The close-up of the active site shows the interaction of Crixivan® with the carboxyl groups of the essential aspartate residues.
its breakdown to form product. Kinetic studies by Meek and his coworkers are consistent with a model in which breakdown of the dihydrate intermediate is the rate-determining step for the protease reaction. These studies also show that the transition state of this step involves two proton transfers—with one aspartate acting as a general acid to donate a proton to the departing proline and the other aspartate acting as a general base to abstract a proton from one of the hydroxyl groups, facilitating collapse of the dihydrate to a carboxyl group. Note that the events of the breakdown to form product are simply the reversal of the steps that formed the intermediate.
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dihydrate |
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● A mechanism for the incorporation of 18O from H218O into peptide substrates in the HIV protease reaction.
from Hyland, L., et al., 1991. Biochemistry 30:8441– 8453.)
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524 Chapter 16 ● Mechanisms of Enzyme Action
H U M A N B I O C H E M I S T R Y
Protease Inhibitors Give Life to AIDS Patients
Infection by HIV was once considered a death sentence, but the emergence of a new family of drugs called protease inhibitors has made it possible for some AIDS patients to improve their overall health and extend their lives. These drugs are all specific inhibitors of the HIV protease. By inhibiting the protease, they prevent the development of new virus particles in the cells of infected patients. Clinical testing has shown that a combination of drugs—including a protease inhibitor together with a reverse transcriptase inhibitor like AZT—can reduce the human immunodeficiency virus (HIV) to undetectable levels in about 40 to 50% of infected individuals. Patients who respond successfully to this combination therapy have experienced dramatic improvement in their overall health and a substantially lengthened lifespan.
Four of the protease inhibitors approved for use in humans by the U.S. Food and Drug Administration are shown below: Crixivan® by Merck, Invirase® by Hoffman-LaRoche, Norvir® by Abbott, and Viracept® by Agouron. These drugs were all developed from a “structure-based” design strategy; that is, the drug molecules were designed to bind tightly to the active site of the HIV-1 protease. The backbone OH-group in all these substances inserts between the two active-site carboxyl groups of the protease.
In the development of an effective drug, it is not sufficient merely to show that a candidate compound can cause the desired
biochemical effect. It must also be demonstrated that the drug can be effectively delivered in sufficient quantities to the desired site(s) of action in the organism, and that the drug does not cause undesirable side effects. The HIV-1 protease inhibitors shown here fulfill all of these criteria. Other drug candidates have been found that are even better inhibitors of HIV-1 protease in cell cultures, but many of these fail the test of bioavailability—the ability of a drug to be delivered to the desired site of action in the organism.
Candidate protease inhibitor drugs must be relatively specific for the HIV-1 protease. Many other aspartic proteases exist in the human body and are essential to a variety of body functions, including digestion of food and processing of hormones. An ideal drug thus must strongly inhibit the HIV-1 protease, must be delivered effectively to the lymphocytes where the protease must be blocked, and should not adversely affect the activities of the essential human aspartic proteases.
A final but important consideration is viral mutation. Certain mutant HIV strains are resistant to one or more of the protease inhibitors, and even for patients who respond initially to protease inhibitors it is possible that mutant viral forms may eventually thrive in the infected individual. The search for new and more effective protease inhibitors is ongoing.
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C R I T I C A L D E V E L O P M E N T S I N B I O C H E M I S T R Y
The pH Dependence of Aspartic Proteases and HIV-1 Protease
The first hint that two active-site carboxyl groups—one protonated and one ionized—might be involved in the catalytic activity of the aspartic proteases came from studies of the pH dependence of enzymatic activity. If an ionizable group in an enzyme active site is essential for activity, a plot of enzyme activity versus pH may look like one of the plots at right.
If activity increases dramatically as pH is increased, catalysis may depend on a deprotonated group that may normally act as a general base, accepting a proton from the substrate or a water molecule, for example (a). Protonation of this group at lower pH prevents it from accepting another proton (from the substrate or water, for example).
On the other hand, if activity decreases sharply as pH is raised, activity may depend on a protonated group, which may act as a general acid, donating a proton to the substrate or a catalytic water molecule (b). At high pH, the proton dissociates and is not available in the catalytic events.
The bell-shaped curve in part (c) of the figure combines both of these behaviors, so that activity first increases, then decreases, as pH is increased. This is consistent with the involvement of two ionizable groups—one with a low pK a that acts as a base above its pK a, and a second group with a higher pK a that acts as an acid below its pK a.
Kinetic studies with pepsin have produced bell-shaped curves for a variety of substrate peptides; see below, (a).
As such data are fitted to calculated curves, dissociation constants can be estimated for the ionizable groups at the active site. In pepsin, the general base exhibits a pK a of approximately 1.4, whereas the general acid displays a pK a of about 4.3. Compare these values with the expected pK a for an aspartate carboxyl group in a protein of 4.2 to 4.6. The value for the aspartyl group acting as a general acid in pepsin is typical, but that for the aspartyl group acting as a general base is unusually low.
The pH dependence of HIV-1 protease has been assessed by measuring the apparent inhibition constant for a synthetic substrate analog (b). The data are consistent with the catalytic involvement of ionizable groups with pK a values of 3.3 and 5.3. Maximal enzymatic activity occurs in the pH range between these two values. On the basis of the accumulated kinetic and structural data on HIV-1 protease, these pK a values have been ascribed to the
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Bell-shaped activity versus pH profiles arise from two separate active-site ionizations. (a) Enzyme activity increases upon deprotonation of B -H.
(b) Enzyme activity decreases upon deprotonation of A-H. (c) Enzyme activity is maximal in the pH range where one ionizable group is deprotonated (as B:) and the other group is protonated (as A-H).
two active-site aspartate carboxyl groups. Note that the value of 3.3 is somewhat low for an aspartate side chain in a protein, whereas the value of 5.3 is somewhat high.
(a) |
(b) |
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Protease |
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pH-rate profiles for (a) pepsin and (b) HIV protease. (Adapted from Denburg, J., et al., 1968. Journal of the American Chemical Society
90:479–486, and Hyland, J., et al., 1991. Biochemistry
30:8454–8463.)
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525
526Chapter 16 ● Mechanisms of Enzyme Action
16.13● Lysozyme
Lysozyme is an enzyme that hydrolyzes polysaccharide chains. It ruptures certain bacterial cells by cleaving the polysaccharide chains that make up their cell wall. Lysozyme is found in many body fluids, but the most thoroughly studied form is from hen egg whites. The Russian scientist P. Laschtchenko first described the bacteriolytic properties of hen egg white lysozyme in 1909. In 1922, Alexander Fleming, the London bacteriologist who later discovered penicillin, gave the name lysozyme to the agent in mucus and tears that destroyed certain bacteria, because it was an enzyme that caused bacterial lysis.
As seen in Chapter 9, bacterial cells are surrounded by a rigid, strong wall of peptidoglycan, a copolymer of two sugar units, N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG). Both of these sugars are N-acetylated analogs of glucosamine, and in bacterial cell wall polysaccharides, they are joined in(1 n 4) glycosidic linkages (Figure 16.31). Lysozyme hydrolyzes the glycosidic bond between C-1 of NAM and C-4 of NAG, as shown in Figure 16.31, but does not act on the (1 n 4) linkages between NAG and NAM.
Lysozyme is a small globular protein composed of 129 amino acids (14 kD) in a single polypeptide chain. It has eight cysteine residues linked in four disulfide bonds. The structure of this very stable protein was determined by X-ray crystallographic methods in 1965 by David Phillips (Figure 16.32). Although X-ray structures had previously been reported for proteins (hemoglobin and myoglobin), lysozyme was the first enzyme structure to be solved by crystallographic (or any other) methods. Although the location of the active site was not obvious from the X-ray structure of the protein alone, X-ray studies of lysozyme-inhibitor complexes soon revealed the location and nature of the active site. Since it is an enzyme, lysozyme cannot form stable ES complexes for structural studies, because the substrate is rapidly transformed into products. On the other hand, several substrate analogs have proven to be good com-
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FIGURE 16.31 ● The lysozyme reaction.
528 Chapter 16 ● Mechanisms of Enzyme Action
tions the
Lysozyme |
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Trp62 |
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Substrate-binding cleft |
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O |
NH2 |
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N |
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C |
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CH3 ...... |
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H |
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CH3 |
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NH2 |
CH3 |
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Asn59 |
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H3C |
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H3C |
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OH |
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..... |
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...... |
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OH |
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....... |
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CH2 |
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H O |
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.....NAM O |
NAG CH2OH |
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NAG |
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CH2OH |
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NAG |
H2N |
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CH3 |
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NH |
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H |
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101 |
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NH2 |
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... |
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O |
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Asp |
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Arg114 |
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Asn37 |
C |
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Lysozyme |
C |
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C |
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Ala107 |
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Phe or Trp34 |
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cuts |
Gln57 |
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Trp63 |
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FIGURE 16.36
E site
O
H218O
HO
+ 4C
● The C1–O bond, not the O–C4 bond, is cleaved in the lysozyme reaction. 18O from H218O is thus incorporated at the C1 position.
The Lysozyme Mechanism Involves General Acid–Base Catalysis
The mechanism of the lysozyme reaction is shown in Figures 16.36 and 16.37. Studies using 18O-enriched water showed that the C1OO bond is cleaved on the substrate between the D and E sites. Hydrolysis under these conditions incorporates 18O into the C1 position of the sugar at the D site, not into the oxygen at C4 at the E site (Figure 16.36). Model building studies place the cleaved bond approximately between protein residues Glu35 and Asp52. Glu35 is in a nonpolar or hydrophobic region of the protein, whereas Asp52 is located in a much more polar environment. Glu35 is protonated, but Asp52 is ionized (Figure 16.37). Glu35 may thus act as a general acid, donating a proton to the oxygen atom of the glycosidic bond and accelerating the reaction. Asp52, on the other hand, probably stabilizes the carbonium ion generated at the D site upon bond cleavage. Formation of the carbonium ion may also be enhanced by the strain on the ring at the D site. Following bond cleavage, the product formed at the E site diffuses away, and the carbonium ion intermediate can then react with H2O from the solution. Glu35 can now act as a general base, accepting a proton from the attacking water. The tetramer of NAG thus formed at sites A through D can now be dissociated from the enzyme.
On the basis of the above, the rate acceleration afforded by lysozyme appears to be due to (a) general acid catalysis by Glu35; (b) distortion of the sugar ring at the D site, which may stabilize the carbonium ion (and the transition state); and (c) electrostatic stabilization of the carbonium ion by nearby Asp52. The overall kcat for lysozyme is about 0.5/sec, which is quite slow (Table
Asp32 |
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Asp32 |
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C |
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O H |
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C |
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– |
H |
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O |
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O |
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.. |
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... |
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O |
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O |
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HO |
OH |
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... |
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NHR' |
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NHR' |
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O |
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– |
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C |
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C |
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Asp215 |
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Asp215 |
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(a) |
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(b) |
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FIGURE 16.37 ● A mechanism for the lysozyme reaction.
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Asp32 |
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... H |
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OH |
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O |
..NHR' |
R |
C O
Asp215
(c)
Asp32
C O
O O OH
C
H
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NH2R' |
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Asp215 |
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(d) |
530 Chapter 16 ● Mechanisms of Enzyme Action
14.4) compared with that for other enzymes. On the other hand, the destruction of a bacterial cell wall may only require hydrolysis of a few polysaccharide chains. The high osmotic pressure of the cell ensures that cell rupture will follow rapidly. Thus, lysozyme can accomplish cell lysis without a particularly high kcat.
PROBLEMS
1. Tosyl-L-phenylalanine chloromethyl ketone (TPCK) specifically inhibits chymotrypsin by covalently labeling His57.
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O |
CH2 |
O |
CH3 |
B |
A |
B |
SONHOCHOCOCH2Cl |
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O
Tosyl-L-phenylalanine chloromethyl ketone (TPCK)
a.Propose a mechanism for the inactivation reaction, indicating the structure of the product(s).
b.State why this inhibitor is specific for chymotrypsin.
c.Propose a reagent based on the structure of TPCK that might be an effective inhibitor of trypsin.
2. In this chapter, the experiment in which Craik and Rutter replaced Asp102 with Asn in trypsin (reducing activity 10,000-fold) was discussed.
a.On the basis of your knowledge of the catalytic triad structure in trypsin, suggest a structure for the “uncatalytic triad” of Asn- His-Ser in this mutant enzyme.
b.Explain why the structure you have proposed explains the reduced activity of the mutant trypsin.
c.See the original journal articles (Sprang, et al., 1987. Science 237:905–909 and Craik, et al., 1987. Science 237:909–913) to see what Craik and Rutter’s answer to this question was.
3.Pepstatin (see page 531) is an extremely potent inhibitor of the monomeric aspartic proteases, with KI values of less than 1 nM. a. On the basis of the structure of pepstatin, suggest an explanation for the strongly inhibitory properties of this peptide.
b. Would pepstatin be expected to also inhibit the HIV-1 protease? Explain your answer.
4.The kcat for alkaline phosphatase–catalyzed hydrolysis of methylphosphate is approximately 14/sec at pH 8 and 25°C. The rate constant for the uncatalyzed hydrolysis of methylphosphate
under the same conditions is approximately 1 10 15/sec. What is the difference in the free energies of activation of these two reactions?
Chymotrypsinogen (inactive)
1
S
π -Chymotrypsin
S
S
α -Chymotrypsin (active)
1
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Ser Arg |
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14 |
15 |
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S |
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146 |
149 |
Tyr |
Ala |