Citation: ZHANG Jun-Wei, ZHOU Jun-Gang, Lü Hong, HUANG Qiang. Molecular Dynamics Simulation of Active-Sites of Retaining and Inverting β-Xylosidases[J]. Acta Physico-Chimica Sinica, ;2015, 31(6): 1169-1178. doi: 10.3866/PKU.WHXB201504151 shu

Molecular Dynamics Simulation of Active-Sites of Retaining and Inverting β-Xylosidases

ZHANG Jun-Wei ¹ ,
ZHOU Jun-Gang ^1, ,
Lü Hong ^1,2 ,
HUANG Qiang ^1,2,

1.
1 State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200433, P. R. China;
2 Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, P. R. China

Received Date: 16 February 2015
Available Online: 15 April 2015
Fund Project: 上海市自然科学基金(13ZR1402400) (13ZR1402400)国家自然科学基金(31200022)资助项目 (31200022)

Xylans are important as potential renewable energy sources. In recent years, there has therefore been interest in improving their degradation efficiencies. β-Xylosidases are key enzymes for xylan degradation; these enzymes are classified, based on their hydrolysis mechanisms, as retaining or inverting enzymes. Although much research has been devoted to understanding retaining and inverting mechanisms, little is known about their differences in solution. We used molecular dynamics (MD) simulations with explicit solvent representation to study the dynamic behaviors of the active-sites of four typical β-xylosidases by analyzing the distances between two catalytic amino acids and the pK_a values of proton-donor amino acids. The results show that the distance between the catalytic amino acids with inverting enzymes is about 0.8-1.0 nm, which is greater than that for retaining enzymes, i.e., 0.5-0.6 nm. This is consistent with previous results based on the crystal structures of glycosidases. We found that the pK_a of the retaining proton donors are modulated by interactions with neighboring amino acids, enabling switching between low and high values. Such a pK_a switch is needed for the double-displacement mechanism of retaining enzymes. In contrast, inverting proton donors, modulated by interactions with neighboring glutamic acids, have only high pK_a values. This may be important in proton capture from the solvent by donors, and may facilitate the single-displacement mechanism of inverting enzymes. This study provides new insights into the hydrolysis mechanisms of β-xylosidases, and will therefore be useful in improving the efficiency and applications of β-xylosidases.
- β-Xylosidase,
- Catalytic mechanism,
- Molecular modelling,
- Proton donor,
- pK_a value
1. [1]
  
  (1) Himmel, M. E.; Ding, S. Y.; Johnson, D. K.; Adney, W. S.; Nimlos, M. R.; Brady, J.W.; Foust, T. D. Science 2007, 315 (5813), 804. doi: 10.1126/science.1137016
2. [2]
  (2) Dionisi, D.; Anderson, J. A.; Aulenta, F.; McCue, A.; Paton, G. J. Chem. Technol. Biotechol. 2014, 90 (3), 366. doi: 10.1002/jctb.4544
3. [3]
  (3) Shallom, D.; Shoham, Y. Curr. Opin. Microbiol. 2003, 6 (3), 219. doi: 10.1016/s1369-5274(03)00056-0
4. [4]
  (4) Lorenz, W.W.; Wiegel, J. J. Bacteriol. 1997, 179 (17), 5436.
5. [5]
  (5) Minic, Z.; Rihouey, C.; Do, C. T.; Lerouge, P.; Jouanin, L. Plant. Physiol. 2004, 135 (2), 867. doi: 10.1104/pp.104.041269
6. [6]
  (6) Sunna, A.; Antranikian, G. Crit. Rev. Biotechnol. 1997, 17 (1), 39. doi: 10.3109/07388559709146606
7. [7]
  (7) Knob, A.; Terrasan, C. R. F.; Carmona, E. C. World. J. Microb. Biot. 2010, 26 (3), 389. doi: 10.1007/s11274-009-0190-4
8. [8]
  (8) Davies, G.; Henrissat, B. Structure 1995, 3 (9), 853. doi: 10.1016/S0969-2126(01)00220-9
9. [9]
  (9) Rye, C. S.; Withers, S. G. Curr. Opin. Chem. Biol. 2000, 4 (5), 573. doi: 10.1016/S1367-5931(00)00135-6
10. [10]
  (10) White, A.; Rose, D. R. Curr. Opin. Struc. Biol. 1997, 7 (5), 645. doi: 10.1016/s0959-440x(97)80073-5
11. [11]
  (11) Barker, I. J.; Petersen, L.; Reilly, P. J. J. Phys. Chem. B 2010, 114 (46), 15389. doi: 10.1021/jp107886e
12. [12]
  (12) Jordan, D. B.; Wagschal, K.; Gri rescu, A. A.; Braker, J. D. Appl. Microbiol. Biotechnol. 2013, 97 (10), 4415. doi: 10.1007/s00253-012-4475-4
13. [13]
  (13) Vasella, A.; Davies, G. J.; Bohm, M. Curr. Opin. Chem. Biol. 2002, 6 (5), 619. doi: 10.1016/s1367-5931(02)00380-0
14. [14]
  (14) Mccarter, J. D.; Withers, S. G. Curr. Opin. Struc. Biol. 1994, 4 (6), 885. doi: 10.1016/0959-440x(94)90271-2
15. [15]
  (15) Zechel, D. L.; Withers, S. G. Curr. Opin. Chem. Biol. 2001, 5 (6), 643. doi: 10.1016/s1367-5931(01)00260-5
16. [16]
  (16) Ludwiczek, M. L.; D'Angelo, I.; Yalloway, G. N.; Brockerman, J. A.; Okon, M.; Nielsen, J. E.; Strynadka, N. C. J.; Withers, S. G.; McIntosh, L. P. Biochemistry 2013, 52 (18), 3138. doi: 10.1021/bi400034m
17. [17]
  (17) Dong, X. Y.; Du, W. J.; Liu, F. F. Acta Phys. -Chim. Sin. 2012, 28, 2735. [董晓燕, 都文婕, 刘夫锋. 物理化学学报, 2012, 28, 2735.] doi: 10.3866/pku.whxb201207162
18. [18]
  (18) Dror, R. O.; Dirks, R. M.; Grossman, J. P.; Xu, H. F.; Shaw, D. E. Ann. Rev. Biophys. 2012, 41, 429. doi: 10.1146/annurevbiophys-042910-155245
19. [19]
  (19) Yang, J. K.; Yoon, H. J.; Ahn, H. J.; Lee, B. I.; Pedelacq, J. D.; Liong, E. C.; Berendzen, J.; Laivenieks, M.; Vieille, C.; Zeikus, G. J.; Vocadlo, D. J.; Withers, S. G.; Suh, S.W. J. Mol. Biol. 2004, 335 (1), 155. doi: 10.1016/j.jmb.2003.10.026
20. [20]
  (20) Santos, C. R.; Polo, C. C.; Correa, J. M.; Simao, R. D. G.; Seixas, F. A. V.; Murakami, M. T. Acta Crystallogra. D-Biol. Crystallogr. 2012, 68 (Suppl. 10), 1339. doi: 10.1107/s0907444912028491
21. [21]
  (21) Brux, C.; Ben-David, A.; Shallom-Shezifi, D.; Leon, M.; Niefind, K.; Shoham, G.; Shoham, Y.; Schomburg, D. J. Mol. Biol. 2006, 359 (1), 97. doi: 10.1016/j.jmb.2006.03.005
22. [22]
  (22) Brunzelle, J. S.; Jordan, D. B.; McCaslin, D. R.; Olczak, A.; Wawrzak, Z. Arch. Biochem. Biophys. 2008, 474 (1), 157. doi: 10.1016/j.abb.2008.03.007
23. [23]
  (23) Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4 (3), 435. doi: 10.1021/ct700301q
24. [24]
  (24) Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65 (3), 712. doi: 10.1002/prot.21123
25. [25]
  (25) Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79 (2), 926. doi: 10.1063/1.445869
26. [26]
  (26) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98 (12), 10089. doi: 10.1063/1.464397
27. [27]
  (27) Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81 (8), 3684. doi: 10.1063/1.448118
28. [28]
  (28) Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graph. Model. 1996, 14 (1), 33. doi: 10.1016/0263-7855(96)00018-5
29. [29]
  (29) Delano, W. L. The PyMOL Molecular Graphics System; Delano Scientific: San Carlos, CA, 2002.
30. [30]
  (30) Mhlon , N. N.; Skelton, A. A.; Kruger, G.; Soliman, M. E. S.; Williams, I. H. Proteins 2014, 82 (9), 1747. doi: 10.1002/prot.24528
31. [31]
  (31) Mohamed, I. P. K.; Subramani, K. Acta Phys. -Chim. Sin. 2009, 25, 2357. [Mohamed, I. P. K., Subramani, K. 物理化学学报, 2009, 25, 2357.] doi: 10.3866/PKU.WHXB20091131
32. [32]
  (32) Huang, Q.; Opitz, R.; Knapp, E.W.; Herrmann, A. Biophys. J. 2002, 82 (2), 1050.
33. [33]
  (33) Sondergaard, C. R.; Olsson, M. H. M.; Rostkowski, M.; Jensen, J. H. J. Chem. Theory Comput. 2011, 7 (7), 2284. doi: 10.1021/ct200133y
34. [34]
  (34) Seeber, M.; Cecchini, M.; Rao, F.; Settanni, G.; Caflisch, A. Bioinformatics 2007, 23 (19), 2625. doi: 10.1093/bioinformatics/btm378
35. [35]
  (35) Saha, B. C. J. Ind. Microbiol. Biot. 2001, 27 (4), 241. doi: 10.1038/sj.jim.7000184
36. [36]
  (36) Chavez, R.; Bull, P.; Eyzaguirre, J. J. Biotechnol. 2006, 123 (4), 413. doi: 10.1016/j.jbiotec.2005.12.036
37. [37]
  (37) Eswar, N.; Eramian, D.; Webb, B.; Shen, M. Y.; Sali, A. Protein Structure Modeling with MODELLER; Humana Press: New York, 2008.
38. [38]
  (38) Kirschner, K. N.; Yongye, A. B.; Tschampel, S. M.; nzalez- Outeirino, J.; Daniels, C. R.; Foley, B. L.; Woods, R. J. J. Comput. Chem. 2008, 29 (4), 622. doi: 10.1002/jcc.20820
39. [39]
  (39) Shallom, D.; Leon, M.; Bravman, T.; Ben-David, A.; Zaide, G.; Belakhov, V.; Shoham, G.; Schomburg, D.; Baasov, T.; Shoham, Y. Biochemistry 2005, 44 (1), 387. doi: 10.1021/bi048059w
40. [40]
  (40) Yu, H. B.; Griffiths, T. M. Phys. Chem. Chem. Phys. 2014, 16 (12), 5785. doi: 10.1039/c4cp00351a
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