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
1. [1]
  Guangming YIN , Huaiyao WANG , Jianhua ZHENG , Xinyue DONG , Jian LI , Yi'nan SUN , Yiming GAO , Bingbing WANG . Preparation and photocatalytic degradation performance of Ag/protonated g-C₃N₄ nanorod materials. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1491-1500. doi: 10.11862/CJIC.20240086
2. [2]
  Zhao Lu , Hu Lv , Qinzhuang Liu , Zhongliao Wang . Modulating NH₂ Lewis Basicity in CTF-NH₂ through Donor-Acceptor Groups for Optimizing Photocatalytic Water Splitting. Acta Physico-Chimica Sinica, 2024, 40(12): 2405005-. doi: 10.3866/PKU.WHXB202405005
3. [3]
  Jingzhao Cheng , Shiyu Gao , Bei Cheng , Kai Yang , Wang Wang , Shaowen Cao . 4-氨基-1H-咪唑-5-甲腈修饰供体-受体型氮化碳光催化剂的构建及其高效光催化产氢研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2406026-. doi: 10.3866/PKU.WHXB202406026
4. [4]
  Heng Zhang . Determination of All Rate Constants in the Enzyme Catalyzed Reactions Based on Michaelis-Menten Mechanism. University Chemistry, 2024, 39(4): 395-400. doi: 10.3866/PKU.DXHX202310047
5. [5]
  Zhonghua Xi , Xuanfeng Kong , Jinyue Yang , Bin Liu , Tingyu Zhu , Hui Zhang , Wenwei Zhang . Construction of Public Teaching Instrument Platform and Exploration of Opening Mechanism. University Chemistry, 2024, 39(7): 200-206. doi: 10.12461/PKU.DXHX202405123
6. [6]
  Yufang GAO , Nan HOU , Yaning LIANG , Ning LI , Yanting ZHANG , Zelong LI , Xiaofeng LI . Nano-thin layer MCM-22 zeolite: Synthesis and catalytic properties of trimethylbenzene isomerization reaction. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1079-1087. doi: 10.11862/CJIC.20240036
7. [7]
  Tingyu Zhu , Hui Zhang , Wenwei Zhang . Exploration and Practice of Ideological and Political Education in the Course of Experiments on Chemical Functional Molecules: Synthesis and Catalytic Performance Study of Chiral Mn(III)Cl-Salen Complex. University Chemistry, 2024, 39(4): 75-80. doi: 10.3866/PKU.DXHX202311011
8. [8]
  Huan LI , Shengyan WANG , Long Zhang , Yue CAO , Xiaohan YANG , Ziliang WANG , Wenjuan ZHU , Wenlei ZHU , Yang ZHOU . Growth mechanisms and application potentials of magic-size clusters of groups Ⅱ-Ⅵ semiconductors. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1425-1441. doi: 10.11862/CJIC.20240088
9. [9]
  Xuan Zhou , Yi Fan , Zhuoqi Jiang , Zhipeng Li , Guowen Yuan , Laiying Zhang , Xu Hou . Liquid Gating Mechanism and Basic Properties Characterization: a New Experimental Design for Interface and Surface Properties in the Chemistry “101 Plan”. University Chemistry, 2024, 39(10): 113-120. doi: 10.12461/PKU.DXHX202407111
10. [10]
  Jin Tong , Shuyan Yu . Crystal Engineering for Supramolecular Chirality. University Chemistry, 2024, 39(3): 86-93. doi: 10.3866/PKU.DXHX202308113
11. [11]
  Yong Shu , Xing Chen , Sai Duan , Rongzhen Liao . How to Determine the Equilibrium Bond Distance of Homonuclear Diatomic Molecules: A Case Study of H₂. University Chemistry, 2024, 39(7): 386-393. doi: 10.3866/PKU.DXHX202310102
12. [12]
  Quanliang Chen , Zhaohui Zhou . Research on the Active Site of Nitrogenase over Fifty Years. University Chemistry, 2024, 39(7): 287-293. doi: 10.3866/PKU.DXHX202310133
13. [13]
  Laiying Zhang , Yinghuan Wu , Yazi Yu , Yecheng Xu , Haojie Zhang , Weitai Wu . Innovation and Practice of Polymer Chemistry Experiment Teaching for Non-Polymer Major Students of Chemistry: Taking the Synthesis, Solution Property, Optical Performance and Application of Thermo-Sensitive Polymers as an Example. University Chemistry, 2024, 39(4): 213-220. doi: 10.3866/PKU.DXHX202310126
14. [14]
  Yang YANG , Pengcheng LI , Zhan SHU , Nengrong TU , Zonghua WANG . Plasmon-enhanced upconversion luminescence and application of molecular detection. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 877-884. doi: 10.11862/CJIC.20230440
15. [15]
  Yuhao SUN , Qingzhe DONG , Lei ZHAO , Xiaodan JIANG , Hailing GUO , Xianglong MENG , Yongmei GUO . Synthesis and antibacterial properties of silver-loaded sod-based zeolite. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 761-770. doi: 10.11862/CJIC.20230169
16. [16]
  Wenyan Dan , Weijie Li , Xiaogang Wang . The Technical Analysis of Visual Software ShelXle for Refinement of Small Molecular Crystal Structure. University Chemistry, 2024, 39(3): 63-69. doi: 10.3866/PKU.DXHX202302060
17. [17]
  Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
18. [18]
  Rui Gao , Ying Zhou , Yifan Hu , Siyuan Chen , Shouhong Xu , Qianfu Luo , Wenqing Zhang . Design, Synthesis and Performance Experiment of Novel Photoswitchable Hybrid Tetraarylethenes. University Chemistry, 2024, 39(5): 125-133. doi: 10.3866/PKU.DXHX202310050
19. [19]
  Wenbing Hu , Jin Zhu . Flipped Classroom Approach in Teaching Professional English Reading and Writing to Polymer Graduates. University Chemistry, 2024, 39(6): 128-131. doi: 10.3866/PKU.DXHX202310015
20. [20]
  Shicheng Yan . Experimental Teaching Design for the Integration of Scientific Research and Teaching: A Case Study on Organic Electrooxidation. University Chemistry, 2024, 39(11): 350-358. doi: 10.12461/PKU.DXHX202408036

Get Citation

PDF

XML

Metrics

PDF Downloads(289)
Abstract views(719)
HTML views(33)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142