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研究生(外文):Chia-Wang Chiang
論文名稱(外文):Structural analysis of human prostacyclin synthase
指導教授(外文):Nei-Li Chan
外文關鍵詞:porstacyclin synthaseprostagladin I2P450 superfamilycrystallography
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前列環素合成酶 (prostacyclin synthase) 主要存在於血管內皮細胞中,負責前列環素 (prostacyclin) 之生合成。前列環素能以自泌性及旁泌性訊號傳遞的方式,透過與前列環素受體的結合,幫助血管內皮細胞的舒張及抑制血小板的凝集。近幾年的研究發現,前列環素也能夠啟動peroxisome proliferator-activated receptor delta,調控與脂質代謝有關的基因表現,此代謝途徑可能與胚胎的正常發育有關。
前列環素合成酶屬於含有血基質 (heme) 的cytochrome P450蛋白家族,與此龐大家族中之其他成員相較,僅有前列環素合成酶和血栓素合成酶在催化反應時不需要任何還原酶的輔助,所以二者被歸類為class III次蛋白家族。血栓素合成酶與前列環素合成酶皆能催化前列腺素H2之同分異構化,但其產物血栓素及前列環素的結構不同且功能相互拮抗。
為了解cytochrome P450 class III次蛋白家族的結構是否與其他P450不同,以及前列環素合成酶如何利用其立體結構的特異性,達成催化前列環素合成的反應專一性。本研究首先針對前列環素合成酶進行X光晶體學之結構解析。結果顯示前列環素合成酶的三級結構雖然與其他P450家族的成員類似,但仍有幾點特徵異於典型P450家族。一、扮演活化中心的血基質有異於典型P450家族,其丙酸根 (propionate group) 不傾向與周圍胺基酸形成離子鍵。二、活化中心的N287似乎能與受質之氧原子結合並幫助過氧化鍵的斷裂,此推論與in vitro實驗中,N287突變蛋白之酵素反應速率下降的結果一致。三、活化中心周圍胺基酸所形成的厭水性環境,可能與受質之辨識有關。四、I-helix的彎曲十分明顯,處於I helix中段的P290與G286、G289應是造成I helix彎曲的主因之一,此形變使活化中心的空間擴大,以容納體積較大的前列腺素H2。五、位於活化中心底部的W282除了可以藉由凡得瓦力協助前列腺素H2結合,此胺基酸亦可能作為一支撐點,幫助受質結合後血基質的位移,使血基質的丙酸根與周圍胺基酸形成離子鍵,改變鐵離子的氧化還原電位,使酵素反應得以發生。此外,我們亦成功解析前列環素合成酶與競爭型抑制劑minoxidil的複合體結構,發現minoxidil結合後,活化中心的周圍雖然有顯著的構形改變,但這些變化與受質類似物結合所引起的結構變化明顯不同,顯示酵素活化中心結構的改變與 ligand 的種類密切相關。
Prostacyclin synthase (PGIS) is mainly expressed in the endothelium cell. It catalyzes an isomerization of prostaglandin H2 to form prostacyclin (PGI2), which serves as an autocrine or paracrine to promote vasodilation and inhibit platelet aggregation. PGI2 also regulates gene expression in pre-adipocytes and adiposytes by activating the peroxisome proliferator-activated receptor delta. This pathway may participate in the normal embryo development.
PGIS belongs to the heme-contaning cytochrome P450 enzyme superfamily that participates in various crucial biological oxidation reactions. Among the numerous P450 family members, PGIS and thromboxane synthase (TXAS) are unique and classified as the class III P450s, which perform catalysis in the absence of O2 and redox partner. Interestingly, although PGIS and TXAS both catalyze PGH2 isomerization, their respective products counteract each other’s biological activity, a phenomenon thought to be important for maintain homeostasis.
To understand the unique characteristics of PGIS structural basis of stereospecific catalysis, we determined the three-dimensional PGIS structure by X-ray crystallography. PGIS structure exhibits the typical triangular prism-shaped P450 fold. However, significant structural differences were observed. 1. Different from other P450s, the propionate groups of the heme do not form salt bridges with the surrounding residues. 2. The conserved acid-alcohol pair in the I helix of P450s is replaced by residues G286 and N287 in PGIS. The side chain of N287 appears to be positioned to facilitate the peroxide bond cleavage. This hypothesis is consistence with the finding that the N287S mutation lowers catalytic activity by nearly 70%. 3. The residues around the active site form a hydrophobic environment, which is thought to relate to the substrate recognition. 4. The presence of P290 in the middle of I helix, along with helix-disrupting G286 and G289 cause the distinctive bending of I helix. A combination of I helix-bending and tilted B’ helix creates a channel extending from the heme distal pocket, which seemingly allows binding of the bulky PGH2. 5. Residue W282, placed in the active site at a distance of 8.4 Å from the iron with its indole side chain lying parallel to the porphyrin plane, may serve as an anchoring point to facilitate substrate-induced conformational change of heme, leading to formation of salt bridges between propionate and conserved R359. These interactions may influence the heme redox potential to facilitate substrate isomerization. In addition, we also obtain the inhibitor minoxidil-bound hPGIS crystal structure. The structure reveals the ligand-induced conformational changes around the active site. Interestingly, the changes are different from those observed in the substrate analog-bound PGIS structure, suggesting that the conformation change of PGIS may be ligand-specific.
Table of contents
1. Introduction•••••••••••••••••••••••1
1.1 Preface••••••••••••••••••••••••••1
1.2 Biosynthesis of prostanoids••••••••••••••••••2
1.3 The physiological roles of PGI2••••••••••••••••3
1.4 The discovery and earlier biochemical charaterizations•••••••5
1.5 Structural features of Cytochrome P450s and PGIS•••••••••6
1.6 The mechanism of PGIS and thromboxane synthase••••••••9
1.7 Inhibition of PGIS activity by selective COX-2 inhibitor••••••10
1.8 Specific aims of this study••••••••••••••••••11
2. Methods and Materials••••••••••••••••••13
2.1 Materials•••••••••••••••••••••••••13
2.2 Recombinant hPGIS••••••••••••••••••••13
2.3 hPGIS Purification•••••••••••••••••••••14
2.3.1 Overexpression 14
2.3.2 Lyse cell 14
2.3.3 Ni-NTA column chromatography 15
2.3.4 CM chromatography 15
2.3.5 Gel filtration chromatography 15
2.3.6 Se-hPGIS overexpression 16
2.4 Crystallization•••••••••••••••••••••••16
2.4.1 Ligand-free hPGIS protein crystallization 16
2.4.2 Minoxidil-bound hPGIS protein crystallization 17
2.5 Data collection and processing••••••••••••••••17
2.6 Structure determination, model building and refinements••••••18
2.6.1 Ligand-free hPGIS structure 18
2.6.2 Minoxidil-bound hPGIS structure 18
2.7 Ligand docking to PGIS•••••••••••••••••••19
3. Results••••••••••••••••••••••••21
3.1 Purification and crystallization of ligand-free hPGIS••••••••21
3.2 Structural determination and refinements of ligand-free hPGIS••••22
3.3 Crystallization and structure determination of minoxidil-bound hPGIS
3.4 Overall hPGIS structure•••••••••••••••••••24
3.5 Characteristics on the heme binding pocket of hPGIS•••••••25
3.6 The active site of hPGIS•••••••••••••••••••26
3.7 The channel exist from the active site to the surface••••••••29
3.8 Minoxdil-bound hPGIS structure•••••••••••••••30
3.9 Rofecoxib docking to hPGIS•••••••••••••••••31
4. Discussion•••••••••••••••••••••••32
4.1 The entrance channel of PGIS•••••••••••••••••32
4.2 The active site of PGIS•••••••••••••••••••34
4.2.1 The structural features of PGIS as a P450 enzyme 34
4.2.2 The bending of I helix and the role of P290 35
4.2.3 The role of heme propionate and the role of W282 37
4.2.4 The role of N287 and the O-O scission 40
4.3 Selective COX-2 inhibitor••••••••••••••••••41
5. Conclusion•••••••••••••••••••••••43
6. Figures ••••••••••••••••••••••••44
Figure 1. The cascade and biological consequences of prostanoids metabolism•••••••••••••••••••••44
Figure 2. The secondary and tertiary structure of typical P450•••••45
Figure 3. The mechanism of PGI2 synthesis•••••••••••••46
Figure 4. The mechanism of TXA2 synthesis••••••••••••47
Figure 5. hPGIS purification and crystallization•••••••••••48
Figure 6. The unbiased electron density map of bound minoxidil••••49
Figure 7. Overall hPGIS crystal structure••••••••••••••50
Figure 8. The active site of hPGIS structure•••••••••••••51
Figure 9. Superposition and alignments of I helix of hPGIS with other P450s••••••••••••••••••••••••52
Figure 10. The H-bond network observed in the central region of hPGIS I helix•••••••••••••••••••••••53
Figure 11. Stereo model of the PGIS-PGH2 complex•••••••••54
Figure 12. The substrate entrance channel in hPGIS structure••••••55
Figure 13. Stereoview of the hPGIS cysteine ligand loop•••••••56
Figure 14. The 2Fo-Fc electron denstity map in the heme binding pocket•57
Figure 15. Stereoview showing the superposition between minoxidil-bound and ligand-free hPGIS structures•••••••••••••58
Figure 16. Structural changes around the active site, Cys ligand loop, and B’ helix upon minoxidil binding••••••••••••••59
Figure 17. Docking of rofecoxib onto the ligand-free hPGIS structure••60
Figure 18. Docking of rofecoxib onto the minoxidil-bound hPGIS structure61
Figure 19. Structure of the U51605-bound zebrafish PGIS•••••••62
Figure 20. Superposition of the ligand-free hPGIS and zPGIS structures•63
Figure 21. The opening of the substrate entrance channel is close to the prediction peripheral membrane-binding region of PGIS••••64
Figure 22. Channels observed in the U51605-bound zPGIS structure•••65
Figure 23. Heme-ligated U51605 in the active site of zPGIS••••••66
Figure 24. Comparing the active sites of W282F mutant and native hPGIS67
Figure 25 The leading roles for PGH2 binding in the active site of PGIS. •68
7. Tables••••••••••••••••••••••••69
Table 1. Summary of crystallographic analysis••••••••••••69
Table 2. Alignment of PGIS primary sequences from different species••70
Table 3. Comparing the sequences of the bent region of I helices••••71
Table 4. The dissociation constants of the recombinant hPGIS for ligands•72
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