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]
  Yanglin Jiang , Mingqing Chen , Min Liang , Yige Yao , Yan Zhang , Peng Wang , Jianping Zhang . Experimental and Theoretical Investigations of Solvent Polarity Effect on ESIPT Mechanism in 4′-N,N-diethylamino-3-hydroxybenzoflavone. Acta Physico-Chimica Sinica, 2025, 41(2): 100012-. doi: 10.3866/PKU.WHXB202309027
2. [2]
  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
3. [3]
  Zhi Zhou , Yu-E Lian , Yuqing Li , Hui Gao , Wei Yi . New Insights into the Molecular Mechanism Behind Clinical Tragedies of “Cephalosporin with Alcohol”. University Chemistry, 2025, 40(3): 42-51. doi: 10.12461/PKU.DXHX202403104
4. [4]
  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
5. [5]
  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
6. [6]
  Zhifang SU , Zongjie GUAN , Yu FANG . Process of electrocatalytic synthesis of small molecule substances by porous framework materials. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2373-2395. doi: 10.11862/CJIC.20240290
7. [7]
  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
8. [8]
  .
  CCS Chemistry | 超分子活化底物为自由基促进高效选择性光催化氧化
  . CCS Chemistry, 2025, 7(10.31635/ccschem.025.202405229): -.
9. [9]
  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
10. [10]
  Yaping Li , Sai An , Aiqing Cao , Shilong Li , Ming Lei . The Application of Molecular Simulation Software in Structural Chemistry Education: First-Principles Calculation of NiFe Layered Double Hydroxide. University Chemistry, 2025, 40(3): 160-170. doi: 10.12461/PKU.DXHX202405185
11. [11]
  Zhuoya WANG , Le HE , Zhiquan LIN , Yingxi WANG , Ling LI . Multifunctional nanozyme Prussian blue modified copper peroxide: Synthesis and photothermal enhanced catalytic therapy of self-provided hydrogen peroxide. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2445-2454. doi: 10.11862/CJIC.20240194
12. [12]
  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
13. [13]
  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
14. [14]
  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
15. [15]
  Yongjie ZHANG , Bintong HUANG , Yueming ZHAI . Research progress of formation mechanism and characterization techniques of protein corona on the surface of nanoparticles. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2318-2334. doi: 10.11862/CJIC.20240247
16. [16]
  Huanhuan XIE , Yingnan SONG , Lei LI . Two-dimensional single-layer BiOI nanosheets: Lattice thermal conductivity and phonon transport mechanism. Chinese Journal of Inorganic Chemistry, 2025, 41(4): 702-708. doi: 10.11862/CJIC.20240281
17. [17]
  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
18. [18]
  Jiaxuan Zuo , Kun Zhang , Jing Wang , Xifei Li . 锂离子电池Ni-Co-Mn基正极材料前驱体的形核调控及机制. Acta Physico-Chimica Sinica, 2025, 41(1): 2404042-. doi: 10.3866/PKU.WHXB202404042
19. [19]
  Jiabo Huang , Quanxin Li , Zhongyan Cao , Li Dang , Shaofei Ni . Elucidating the Mechanism of Beckmann Rearrangement Reaction Using Quantum Chemical Calculations. University Chemistry, 2025, 40(3): 153-159. doi: 10.12461/PKU.DXHX202405172
20. [20]
  Jin Tong , Shuyan Yu . Crystal Engineering for Supramolecular Chirality. University Chemistry, 2024, 39(3): 86-93. doi: 10.3866/PKU.DXHX202308113

Get Citation

PDF

XML

Metrics

PDF Downloads(289)
Abstract views(810)
HTML views(42)

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