Structural basis of specific inhibition of tissue-type plasminogen activator by plasminogen activators inhibitor-1.

Thrombosis is a leading cause of death worldwide [1]. Recombinant tissue-type plasminogen activator (tPA) is the FDA-approved thrombolytic drug for ischemic strokes, myocardial infarction and pulmonary embolism. tPA is a multi-domain serine protease of the trypsin-family [2] and catalyses the critical step in fibrinolysis [3], converting the zymogen plasminogen to the active serine protease plasmin, which degrades the fibrin network of thrombi and blood clots. tPA is rapidly inactivated by endogenous plasminogen activators inhibitor-1 (PAI-1) [4] (Fig. 1). Engineering on tPA to reduce its inhibition by PAI-1 without compromising its thrombolytic effect is a continuous effort [5]. Tenecteplase (TNK-tPA) is a newer generation of tPA variant showing slower inhibition by PAI-1 [6]. Extensive studies to understand the molecular interactions between tPA and PAI-1 have been carried out [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], however, the precise details at atomic resolution remain unknown. We report the crystal structure of tPA·PAI-1 complex here. The methods required to achieve these data include: (1) recombinant expression and purification of a PAI-1 variant (14-1B) containing four mutations (N150H, K154T, Q319L, and M354I), and a tPA serine protease domain (tPA-SPD) variant with three mutations (C122A, N173Q, and S195A, in the chymotrypsin numbering) [19]; (2) formation of a tPA-SPD·PAI-1 Michaëlis complex in vitro [19]; and (3) solving the three-dimensional structure for this complex by X-ray crystallography [deposited in the PDB database as 5BRR]. The data explain the specificity of PAI-1 for tPA and uPA [19], [20], and provide structural basis to design newer generation of PAI-1-resistant tPA variants as thrombolytic agents [19].

Specifications table

Value of the data

Determines the crystal structure of the Michaëlis complex between tPA and PAI-1.

Provides insight on the specificity of PAI-1 for tPA and uPA.

Identifies key residues of tPA for binding to PAI-1.

Explains the PAI-1-resisting property of Tenecteplase.

Offers important clues to design newer generation of PAI-1-resistant tPA variants.

Data, experimental design, materials and methods

Data and experimental design

We have determined the structure of tPA·PAI-1 Michaëlis complex and identified key residues of tPA for binding to PAI-1 by X-ray crystallography, and the data are summarized in the original publication [19].

We expressed the recombinant PAI-1 variant 14-1B (N150H, K154T, Q319L, and M354I) [21], using the expression vector pT7-PL and BL21 cells as soluble protein [22]. The choice of this particular variant is to obtain PAI-1 in active form, advantageous for crystallization, because the wild type PAI-1 has a half life of only 2 h and has propensity to spontaneously convert into an inactive, so-called latent form, and to aggregate at high concentration [23], [24].

PAI-1 inhibits tPA by a suicide-substrate mechanism common to all SERPIN members [23], [25] – see Fig. 1A in the original publication [19]. In this SERPIN mechanism, a long flexible loop of PAI-1 (reaction center loop, or RCL) inserts into the active site of tPA to form a transient Michaëlis complex. The RCL is cleaved by tPA through the classical serine proteolytic mechanism. tPA forms a covalent acyl-enzyme intermediate with PAI-1 by cleaving the scissible bond of PAI-1 RCL, following the Michaëlis complex. Before the hydrolysis of this acyl-enzyme intermediate, the PAI-1 RCL undergoes major conformational changes and inserts itself into the PAI-1 β-sheet A. At the same time, the tPA in the intermediate is pulled to the other side of PAI-1, distorted, and deactivated before the hydrolysis of the acyl-enzyme intermediate can take place.

Fig. 1

A structural basis to design newer thrombolytics. Recombinant tPA (surface) is the FDA-approved thrombolytic drug. High dose of recombinant tPA is typically needed to lyse clot in stroke patients, partly due to its rapid inactivation by endogenous inhibitor (PAI-1, in ribbon). Such high dosage leads to dangerous side effects, including intracranial hemorrhage and neurotoxicity. Here, the crystal structure of tPA•PAI-1 Michaëlis complex was determined. This structure offers important clues to design newer generation of tPA thrombolytics with reduced PAI-1 inactivation.

Human tPA contains a fibronectin type II domain (amino acids 1–50), a growth factor domain (amino acids 51–91), two kringle domains (amino acids 92–261), an interdomain linker (amino acids 262–275) and a serine protease domain (SPD, amino acids 276–527) [2] – see Fig. 1B in the original publication [19]. The tPA-SPD is the catalytic domain responsible for the plasminogen activation and is inhibited by PAI-1. Thus, we used only the recombinant tPA-SPD domain to form the Michaëlis complex with PAI-1. We generated three mutations in tPA-SPD: S478A (or S195A in the chymotrypsin numbering) to render the tPA-SPD catalytically inactive, so the Michaëlis complex does not proceed to a stable, covalent complex; N448Q (or N173Q in the chymotrypsin numbering) to remove the glycosylation on tPA-SPD, increasing the homogeneity of the recombinant protein and facilitating protein crystallization; and C395A (or C122A in the chymotrypsin numbering that will be used throughout the rest of text) mutation to remove the disulfide bond linked to K2 domain – see Fig. 1B in the original publication [19]. The recombinant tPA-SPD mutant was expressed in P. pastoris and confirmed by SDS-PAGE and mass spectrometry after trypsin digestion (Table 1).

Table 1

Trypsin digested fragments of recombinant tPA-SPD SPD from MALDI-TOF-MS and the expected fragment mass.

Mr observed (Da)	Mr calculated (Da)	Peptide sequence
1387.1	1386.8004	53FPPHHLTVILGR64
1335.8	1335.6328	142HEALSPFYSER152
1179.4	1179.6157	239VTNYLDWIR247
878.8	878.4618	231DVPGVYTK238
722.4	722.3831	160LYPSSR165

The recombinant PAI-1 14-1B and tPA-SPD were respectively dialysed into a high-concentration salt (1 M NaCl) and low pH (20 mM Mes pH 6.1) buffer before the Michaëlis complex formation. This condition is required to stabilize PAI-1 at its active form. Subsequently, these two proteins in high salt concentrations and low pH buffer were mixed in a 1:1 M ratio, followed by a dialysis into a low-concentration salt (150 mM NaCl) and neutral pH (20 mM Tris–HCl pH 7.4) buffer. This dialysing step ensures the complex formation similar to that in physiologic condition. A further gel filtration chromatography purification yielded a complex of greater than 99% purity.

Materials and methods

Recombinant protein production

The recombinant PAI-1 mutant 14-1B [21] containing four point mutations (N150H, K154T, Q319L, and M354I), and a hexa-His-tag was expressed in E. coli, using the expression vector pT7-PL and BL21 cells as previously described [22]. The recombinant tPA-SPD was expressed in P. pastoris X-33. This strain facilitates the formation of five disulfide bonds (C42-C58, C50-C111, C100-C182, C136-C201, C168-C182 in chymotrypsin numbering) in tPA-SPD with a high yield about 50 mg recombinant protein per liter medium – see in the original publication [19].

The peptide mass fingerprinting of tPA-SPD by MALDI-TOF mass spectrometry

The SDS-PAGE was performed using 15% polyacrylamide gels. Following SDS-PAGE, the gels were stained with 0.1% (w/v) Coomassie brilliant blue R-250 in 25% (v/v) ethanol and 10% (v/v) acetic acid. The gel digestion was performed using a modified version of previously published protocol [26]. Briefly, the gel band containing 100 ng tPA-SPD was excised from the 15% two-dimensional SDS-PAGE gel, cut in pieces, and destained by washing with 50% (v/v) acetonitrile in 100 μl of 25 mM NH4HCO3 for 30 min at room temperature. The gel pieces were then dried in a SpeedVac Vacuum (Savant Instruments, Holbrook, NY, USA) and rehydrated at 4 °C for 15 min in 3–5 μl digestion solution (25 mM NH4HCO3 and 12.5 ng/μl modified sequence-grade trypsin). Then 3–5 μl of digestion solution without trypsin was added to keep the gel pieces wet during the digestion. After overnight incubation at 37 °C, the digestion was stopped with 5% trifluoroacetic acid (TFA) for 20 min. The peptides were extracted by 20 μl of 5% TFA for 1 h at 37 °C and then by 20 μl of 2.5% TFA/50% acetonitrile for 1 h at 37 °C. The combined supernatants were evaporated in the SpeedVac Vacuum and dissolved in 4 μl 0.5% aqueous TFA for MS analysis.

All mass spectra of MALDI-TOF-MS were obtained on a Bruker REFLEX III MALDI-TOF-MS (Bruker–Franzen, Bremen, Germany) in positive ion mode at an accelerating voltage of 20 kV with the matrix of α-cyano-4-hydroxy cinnamic acid. The spectra were internally calibrated using trypsin autolysis products. The peptide mass fingerprinting obtained was used to search through the SWISS-PROT and NCBI database by the Mascot search engine (http://mascot.proteomics.com.cn/) with a tolerance of ~+0.3 D and one missed cleavage site.

X-ray crystallography

The tPA-SPD·PAI-1 Michaëlis complex was formed by mixing tPA-SPD and PAI-1 in a 1:1 M ratio at low concentration (~ 0.5 mg/ml), followed by dialysis into 20 mM Tris–HCl pH 7.4, and 150 mM NaCl, concentration to 0.5 ml volume for a further gel filtration chromatography purification, which yielded to a complex of greater than 99% purity. The purified complex was then concentrated to 10 mg/mL before setting up crystallization trials. Crystals of the tPA-SPD·PAI-1 Michaëlis complex were grown at 20 °C with the sitting drop method by mixing equal volumes of protein solution and precipitant solution (8% PEG-6000 and 0.1 M Tris pH 7.4), and appeared quickly within one day. However, the crystals always appeared as very thin plates, and decayed rapidly in the X-ray beam, posing great difficulty for X-ray data collection. Most crystals diffracted to only 4–5 Å at Shanghai Synchrotron Radiation Facility (SSRF) BL-17U beam line, and the diffracting spots often appeared as elongated or splitted shapes. After many crystallization and data collection trials for one and half years, one 3.16 Å data set was finally obtained at SSRF beam line BL17U using 25% glycerol as cryoprotectant at a wavelength of 0.979 Å. The data were processed and scaled using the HKL2000 program package [27]. The crystal belongs to P212121 space group with one complex in the crystallographic asymmetric unit. The structure of the tPA-SPD·PAI-1 Michaëlis complex was solved by molecular replacement method using MolRep program [28], which gave very strong and unambiguous solutions. A tPA-SPD molecule was first positioned inside the crystal lattice using the structure of the tPA-SPD catalytic domain (PDB code 1A5H) [29] as a searching model and all the X-ray data up to 3.3 Å. The molecular replacement using MolRep gave a contrast of 12.33, a signal to sigma ratio for translational function of 16.02, and a correlation coefficient of 0.365. Next, the position of PAI-1 was searched using the model of active stable variant of PAI-1 (Protein Data Bank code 1DVM) [30] while fixing the already positioned tPA-SPD model, giving only one translational function with a signal to sigma ratio of 19.4, and a correlation coefficient of 0.538. The molecular replacement model was subjected to iterative refinement and manual model rebuilding using Refmac [31] and Coot [32], respectively, giving a final R factor and Rfree factor of 0.20 and 0.27, respectively. The structure was validated with PROCHECK [33] and analyzed by PyMOL [34] and PISA [35]. The final refined crystal structure of tPA-SPD·PAI-1 Michaëlis complex was deposited in PDB with the code 5BRR.

Subject area	Biology
More specific subject area	Protein structure and biochemistry
Type of data	X-ray crystal structure, Mass spectrometry
How data was acquired	X-ray diffraction data were collected at Shanghai Synchrotron Radiation Facility. Mass spectra of MALDI-TOF-MS were obtained on a Bruker REFLEX III MALDI-TOF-MS (Bruker-Franzen, Bremen, Germany).
Data format	Processed
Experimental factors	Recombinant proteins were purified to high homogeneity before use.
Experimental features	The structure of the tPA·PAI-1 complex was determined by X-ray crystallography.
Data source location	City, Country and/or Latitude & Longitude (& GPS coordinates) for collected samples/data if applicable
Data accessibility	The data is available from the related publication by Gong et al. (http://www.ncbi.nlm.nih.gov/pubmed/26324706), and the structure deposited in the Protein Data Bank (entry 5BRR).