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ISSN 1000-6818CN 11-1892/O6CODEN WHXUEU
Acta Phys Chim Sin >> 2013,Vol.29>> Issue(04)>> 843-848     doi: 10.3866/PKU.WHXB201301183         中文摘要
BIOPHYSICAL CHEMISTRY
Molecular Dynamics Simulations of the Unbinding of Phenylsulfonamide from Carbonic Anhydrase II
SUN Wei-Qi1,3, ZHANG Ji-Long2, ZHENG Qing-Chuan2, SUN Zhi-Wei1,4, ZHANG Hong-Xing2
1 School of Public Health, Jilin University, Changchun 130021, P. R. China;
2 State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China;
3 School of Public Health, Beihua University, Jilin 132013, P. R. China;
4 School of Public Health and Family Medicine, Capital Medical University, Beijing 100069, P. R. China
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Molecular dynamics (MD) simulations and free energy calculations were integrated to investigate substrate-enzyme dynamic interactions during the unbinding of phenylsulfonamide from carbonic anhydrase II (CA II). The potential of mean force (PMF) along the unbinding pathway shows that a special ligand-binding state exists, and the electrostatic interaction dominates the ligand?s binding with CA II. The analysis of trajectories reveals that, apart from the zinc ion, the key residues in the unbinding pathway, Leu198, Thr199, and Thr200, prevent the substrate?s unbinding from the enzyme by hydrogen bonding with the sulfanilamide group of the substrate. The present results are of direct significance for the in-depth understanding of the sulfonamide-CA II binding process and related drug design.



Keywords: Molecular dynamics simulation   Free energy   Phenylsulfonamide   Carbonic anhydrase II   Substrate’s binding  
Received: 2012-11-08 Accepted: 2013-01-15 Publication Date (Web): 2013-01-18
Corresponding Authors: Email: zhengqc@jlu.edu.cn; zwsun@ccmu.edu.cn

Fund: The project was supported by the National Natural Science Foundation of China (21273095, 20903045, 21203072), Specialized Research Fund for the Doctoral Program of Higher Education, China (20070183046), and Specialized Fund for the Basic Research of Jilin University, China (201003044).

Cite this article: SUN Wei-Qi, ZHANG Ji-Long, ZHENG Qing-Chuan, SUN Zhi-Wei, ZHANG Hong-Xing. Molecular Dynamics Simulations of the Unbinding of Phenylsulfonamide from Carbonic Anhydrase II[J]. Acta Phys. -Chim. Sin., 2013,29 (04): 843-848.    doi: 10.3866/PKU.WHXB201301183

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77. ZHAO Jian-Wei, LIU Hong-Mei, NI Wen-Bin, GUO Yan, YIN Xing.Electron Transfer Studied at theMolecular Level[J]. Acta Phys. -Chim. Sin., 2009,25(07): 1472-1480
78. SONG Qi-Sheng, GUO Xin-Li, YUAN Shi-Ling, LIU Cheng-Bu.Molecular Dynamics Simulation of Sodium Dodecyl Benzene Sulfonate Aggregation on Silica Surface[J]. Acta Phys. -Chim. Sin., 2009,25(06): 1053-1058
79. SUN Hao, JIANG Yong-Jun, YU Qing-Sen, ZOU Jian-Wei.Molecular Dynamics Simulation of Significant Roles of Structural Water Molecules in Glycogen Synthase Kinase-3β[J]. Acta Phys. -Chim. Sin., 2009,25(04): 635-639
80. CHEN Xin-Yuan, LV Yang, LI Shen-Min.Molecular Dynamics Simulations on the Stability of (3+1) Mixed-Type Hybrid G-quadruplex in Human Telomere[J]. Acta Phys. -Chim. Sin., 2009,25(04): 783-791
81. CUI Wei, ZHANG Huai, JI Ming-Juan.Molecular Dynamics Simulations and Free Energy Calculations of a Novel Series of Protein Tyrosine Phosphatase 1B Difluoromethylenephosphonic Acid Inhibitors[J]. Acta Phys. -Chim. Sin., 2009,25(04): 668-676
82. CAI Kai-Cong, WANG Jian-Ping.Molecular Dynamical Structures of Glycolaldehyde[J]. Acta Phys. -Chim. Sin., 2009,25(04): 677-683
83. ZHAO Yong-Shan, ZHENG Qing-Chuan, ZHANG Hong-Xing, CHU Hui-Ying, SUN Chia-Chung.Homology Modeling of Human Serine Racemase and Its Molecular Docking with Peptide Inhibitors[J]. Acta Phys. -Chim. Sin., 2009,25(03): 417-422
84. CHEN Cong, LI Wei-Zhong.Molecular Dynamics Simulation of Hydrogen Bonding Characteristics in Aqueous Glycerol Solutions[J]. Acta Phys. -Chim. Sin., 2009,25(03): 507-512
85. PAN Guo-Xiang; NI Zhe-Ming; WANG Fang; WANG Jian-Guo; LI Xiao-Nian.Molecular Dynamics Simulation on Structure, Hydrogen-Bond and Hydration Properties of Diflunisal Intercalated Layered Double Hydroxides[J]. Acta Phys. -Chim. Sin., 2009,25(02): 223-228
86. FU Yi-Zheng; LIU Ya-Qing; MEI Lin-Yu; LAN Yan-Hua.Molecular Dynamics Simulation on Binding Energies and Mechanical Properties of HTPB and Different Crystal Faces of Al[J]. Acta Phys. -Chim. Sin., 2009,25(01): 187-190
87. LI Zhen-Quan; GUO Xin-Li; WANG Hong-Yan; LI Qing-Hua; YUAN Shi-Ling; XU Gui-Ying; LIU Cheng-Bu.Molecular Dynamics Simulation of Anionic Surfactant Aggregation at the Oil/Water Interface[J]. Acta Phys. -Chim. Sin., 2009,25(01): 6-12
88. CHEN Ying; WANG Xiu-Ying; ZHAO Jun-Qing.Molecular Dynamics Simulation on Melting of Metal Cluster with Small Size[J]. Acta Phys. -Chim. Sin., 2008,24(11): 2042-2046
89. HU Jian-Ping; KE Guo-Tao; CHANG Shan; CHEN Wei-Zu; WANG Cun-Xin.Conformational Change of HIV-1 Viral DNA after Binding with Integrase[J]. Acta Phys. -Chim. Sin., 2008,24(10): 1803-1810
90. ZHANG Jun; ZHAO Wei-Min; GUO Wen-Yue; WANG Yong; LI Zhong-Pu.Theoretical Evaluation of Corrosion Inhibition Performance of Benzimidazole Corrosion Inhibitors[J]. Acta Phys. -Chim. Sin., 2008,24(07): 1239-1244
91. SHEN Qiu-Chan; LIANG Wan-Chun; HU Xing-Bang; LI Hao-Ran.Molecular Dynamics Simulation for Formamide Aqueous Solution[J]. Acta Phys. -Chim. Sin., 2008,24(07): 1169-1174
92. ZHAO Xia; OU Xiu-Qin; LIANG Guang-Chuan; WANG Li; XU Sheng-Zhao.Effect of Pyrolytic Reaction Conditions on Surface Free Energy of LiFePO4/C Composite[J]. Acta Phys. -Chim. Sin., 2008,24(07): 1326-1328
93. CUI Bao-Qiu; GONG Li-Dong; ZHAO Dong-Xia.Molecular Dynamics Simulation of Microperoxidase in Aqueous Solution in Terms of the ABEEM/MM Method[J]. Acta Phys. -Chim. Sin., 2008,24(06): 1035-1040
94. ZHANG Rong; TAN Zai-You; ZHENG Dun-Sheng; LUO San-Lai; LI Hao-Ran.Molecular Dynamics Simulations on the Special System of TFE Aqueous Solution[J]. Acta Phys. -Chim. Sin., 2008,24(03): 428-432
95. LI Shu; LIU Lei; CAO Zhen; WANG Ji-Qiang; YAN Tian-Ying.Molecular Dynamics Simulation on a Eutectic Systemof LiTFSI/Urea[J]. Acta Phys. -Chim. Sin., 2007,23(07): 983-986
96. PENG Chuan-Xiao; WANG Li; ZHANG Yan-Ning.Amorphization of Ni Nanowires Induced by Strain Rate[J]. Acta Phys. -Chim. Sin., 2007,23(04): 517-520
97. GE Su-Hong;DONG Guang-Xing;CHENG Xin-Lu;YANG Xiang-Dong.Reaction of H2 and N+ Ion under Titan′s Atmosphere[J]. Acta Phys. -Chim. Sin., 2006,22(10): 1217-1221
98. ZHOU Zhen;YAN Tian-Ying;GAO Xue-Ping.Simulation and Design for Energy Storage Materials[J]. Acta Phys. -Chim. Sin., 2006,22(09): 1168-1174
99. HOU Huai-Yu;CHEN Guo-Liang;CHEN Guang.Molecular Dynamics Simulation of the Structure Transformation before and after Ni Melting[J]. Acta Phys. -Chim. Sin., 2006,22(07): 771-776
100. LIU Chun-li; LI Chun-hua; CHEN Wei-zu; WANG Cun-xin.Study on Interaction between HIV-1 Integrase and Its Dicaffeoyl Inhibitors through Molecular Modeling Approach[J]. Acta Phys. -Chim. Sin., 2005,21(11): 1229-1234
101. WU Xiao-ping; LIU Zhi-ping; WANG Wen-chuan.Molecular Dynamics Simulation of Gas Solubility in Room Temperature Ionic Liquids[J]. Acta Phys. -Chim. Sin., 2005,21(10): 1138-1142
102. WU Xiao-ping; LIU Zhi-ping.Computer Simulation Study of the Mixtures of Room Temperature Ionic Liquid [bmim][BF4] and Water[J]. Acta Phys. -Chim. Sin., 2005,21(09): 1036-1041
103. FANG Mei-juan; LUO Shu-na; WANG He-qing; LIU Wan-yun; ZHAO Yu-fen.The Effect of Phosphoryl Oxygen on the Intermolecular Action of Alanine and Lysozyme[J]. Acta Phys. -Chim. Sin., 2005,21(09): 1042-1045
104. LI Xu-Dong; HOU Ting-Jun; Xu Xiao-Jie.Comparative Studies of 14 Binding Free Energies Scoring Functions[J]. Acta Phys. -Chim. Sin., 2005,21(05): 504-507
105. ZHANG Ai-Long; LIU Rang-Su; LIANG Jia; ZHENG Cai-Xing.A Simulation Study for Effects of Cooling Rate on Evolution of Microstructures during Solidification Process of Liquid Metal Ni[J]. Acta Phys. -Chim. Sin., 2005,21(04): 347-353
106. ZHANG Tao;GU Ting-Kun;QI Yuan-Hua.Evolvement on the Microstructure of Molten Compound AuCu3 in Rapid Cooling[J]. Acta Phys. -Chim. Sin., 2005,21(02): 173-176
107. LIU Ying-Chun;WANG Qi;LÜ Ling-Hong;ZHANG Lian-Zhong.Structural and Diffusion Properties of Water in Hydrophobic Micropores by Molecular Simulation[J]. Acta Phys. -Chim. Sin., 2005,21(01): 63-68
108. Yin Kai-Liang;Xu Duan-Jun;Xia Qing;Ye Ya-Jing;Wu Guo-Ying;Chen Cheng-Lung.Molecular Dynamics Simulation on Solidification Process of n-hexadecane Systems[J]. Acta Phys. -Chim. Sin., 2004,20(03): 302-305
109. Liu Xin;Meng Chang-Gong;Liu Chang-Hou.Melting and Superheating of Ag at High Heating Rate[J]. Acta Phys. -Chim. Sin., 2004,20(03): 280-284
110. Shao Jun;Xu Hua;Lu Wen-Cong;Chen Nian-Yi.Transport Property Anomalies under High Pressure in Molten Na2O-SiO2 Binary System Studied by Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 2004,20(03): 237-239
111. Qin Xu-Bo;Zhang Yan-Ning;Lu Jian-Lin.The Ability of Glass Formation Dominated by the Mismatch in Atomic Size[J]. Acta Phys. -Chim. Sin., 2003,19(12): 1163-1166
112. Hou Ting-Jun;Zhang Wei;Huang Qin;Qiao Xue-Bin;Xu Xiao-Jie.Empirical Aqueous Solvation Model for Protein Based on Accessible Surface Areas[J]. Acta Phys. -Chim. Sin., 2003,19(08): 723-726
113. Zhang Tao;Zhang Xiao-Ru;Wu Ai-Ling;Guan Li;Xu Chang-Ye.Molecular Dynamics Simulations of the Heating and Melting Processes of Metal Cu[J]. Acta Phys. -Chim. Sin., 2003,19(08): 709-713
114. Liu Xin;Meng Chang-Gong;Liu Chang-Hou.Heating Rate Induced Melting and Superheating of Pb[J]. Acta Phys. -Chim. Sin., 2003,19(08): 681-685
115. Zhang Wei;Hou Ting-Jun;Qiao Xue-Bin;Xu Xiao-Jie.Parameters of GB/SA Solvation Model Consistent with AMBER Force Field[J]. Acta Phys. -Chim. Sin., 2003,19(04): 289-292
116. Dong Wen-Ju;Feng Jiu-Ju;Wang Jian-Ji.Standard Gibbs Energies of Transfer of In(Ⅲ) Ion[J]. Acta Phys. -Chim. Sin., 2003,19(03): 230-232
117. Zhou Guo-Rong;Wu You-Shi;Zhang Chuan-Jiang;Zhao Fang.Molecular Dynamics Simulations of the Effect of Icosahedral Quasicrystal on the Formation of Amorphous[J]. Acta Phys. -Chim. Sin., 2003,19(01): 13-16
118. Zhang Yan-Ning;Wang Li;Bian Xiu-Fang.Melting of Au Nanoclusters by Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 2003,19(01): 35-39
119. Hou Ting-Jun;Xu Xiao-Jie.Aqueous Solvation Models Based on Accessible Surface Area Calculations[J]. Acta Phys. -Chim. Sin., 2002,18(11): 1052-1056
120. Gu Guo-Tuan;Zhang Zhi-Jun;Dang Hong-Xin.Preparation and Tribological Behavior of Perfluoroctanoxamidepropyltrioxylmethyl Silane SAM[J]. Acta Phys. -Chim. Sin., 2002,18(07): 669-672
121. Wang Li;Yi Su;Bian XiuFang.Atom Clusters in Liquid and Amorphous of Ni3Al Alloy[J]. Acta Phys. -Chim. Sin., 2002,18(04): 297-301
122. Cong Hong-Ri;Bian Xiu-Fang;Li Hui;Wang Li.Mediumrange Order Structure in Liquid Al80Fe20Alloy[J]. Acta Phys. -Chim. Sin., 2002,18(01): 39-44
123. Xu Hua;Shao Jun.Molecular Dynamics Simulation of Fast Li Conduction in Fluoroborate Glasses[J]. Acta Phys. -Chim. Sin., 2002,18(01): 10-13
124. Cao Li-Xin;Zhou Bao-Xue;Shi Peng-Fei;Zhou Li-Zhuang.Systematic Study of the Standard Transfer Gibbs Energy of Potassium Tetrophenylb orate from Water to Water and Alcohol Mixtures[J]. Acta Phys. -Chim. Sin., 2001,17(06): 565-569
125. Zou Li-Chun, Wang Xiao-Ling, Zhang Pi-Jian, Wang Feng-Ge, Zhou Bao-Xue, Jiang Hui-Min, Qu Song-Sheng.Standard Gibbs Energies of Transfer of Ammonium Tetraphenylborate from Water to Water-t-butyl Alcohol Mixed Solvents and the Primary Medium Effect[J]. Acta Phys. -Chim. Sin., 2000,16(12): 1119-1124
126. Cao Li-Xin, Zhou Bao-Xue, Shi Peng-Fei, Zou Li-Zhuang.Standard Tansfer Gibbs Energy of Potassium Tetraphenylborate from Pure Solvents to Solvent Mixtures[J]. Acta Phys. -Chim. Sin., 2000,16(11): 1053-1056
127. Wang Li, Bian Xiu-Fang, Li Hui.Liquid-Solid Transition and Crystal Growth of Metal Cu by Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 2000,16(09): 825-829
128. Xu Hua, Shao Jun.Molecular Dynamics Simulation of the Phase Transition of α-berlinite under High Pressure[J]. Acta Phys. -Chim. Sin., 2000,16(06): 512-516
129. Ji Ming-Juan, Ye Xue-Qi, Yang Peng-Cheng.Molecular Dynamics Simulations for Met-enkephalin[J]. Acta Phys. -Chim. Sin., 1999,15(11): 1011-1016
130. Liu Sheng-Feng, Lin Jian-Hua, Su Mian-Zeng.Thermodynamics of Deoxidation of High Purity Niobium[J]. Acta Phys. -Chim. Sin., 1999,15(03): 228-233
131. Guo Rong, Shen Ming, Liu Tian-Qing.Thermodynamical and Electrochemical Properties of CTAB/CnH2n+1OH/H2O[J]. Acta Phys. -Chim. Sin., 1999,15(03): 269-273
132. Yang Yi-Yun, Sun Shi-Gang.Kinetics of Irreversible Reactions on Platinum Single Crystal Electrodes(III)[J]. Acta Phys. -Chim. Sin., 1998,14(10): 919-926
133. Li Lin-Wei, Chu De-Ying, Liu Rui-Lin.Determination of Activity Coefficients of RbCl in (H2O-DMF) Mixed Solvents at 283.15 to 318.15K[J]. Acta Phys. -Chim. Sin., 1998,14(08): 691-697
134. Li Hui, Bian Xiu-Fang, Li Yu-Chen, Liu Hong-Bo, Chen Kui-Ying.The Molecular Dynamics Simulation of Liquid Noble Metal Au[J]. Acta Phys. -Chim. Sin., 1998,14(07): 630-634
135. Yang Yang-Yi,Zheng Kang-Cheng,Che Guan-Quan.Solid-Liquid Phase Equilibria and Excess Gibbs Free Energies of Binary Mixtures of 1-Hexanol+o-,m-,p-Xylene[J]. Acta Phys. -Chim. Sin., 1997,13(11): 1040-1043
136. Zhu Xiao-Lei,Zhou Zhi-Hua,Lu Wen-Qing,Huang Jin-Fan,Peng Pan-Ying.A Possible New Solid Phase Observed from Molecular Dynamics Study of CBr4[J]. Acta Phys. -Chim. Sin., 1997,13(09): 815-821
137. Huang Yao-Xiong.Effect of Salt on the Phase Separation of C8-Lecithin Micellar Solutions[J]. Acta Phys. -Chim. Sin., 1997,13(02): 134-139
138. Feng Wan-Yong.The Correlation between Thermochemistry and Kinetics in the Proton Transfer Reactions of Small Proton Bound Clusters[J]. Acta Phys. -Chim. Sin., 1996,12(10): 892-899
139. Lei Yu,Cheng Zhao-Nian,Tang Ding-Yuan.A Study of Structure in β-BAB2O4 Melt by Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 1996,12(06): 481-484
140. Cheng Zhao-Nian,Ding Hong,Lei Yu,Xu Li.A Study of Molecular Dynamics Simulation for Rubidium Chloride Melting[J]. Acta Phys. -Chim. Sin., 1995,11(10): 890-895
141. Liu Rang-Su,Zhou Qun-Yi,Li Ji-Yong.A Molecular Dynamics Simulartion Study on the Structural Transitions in Liquid Metals[J]. Acta Phys. -Chim. Sin., 1995,11(08): 755-757
142. Gu Jian-De,Tian An-Min,Yan Guo-Sen.Molecular Dynamics Simulations for the Spectra of N2 and O2 Aqueous Solutions[J]. Acta Phys. -Chim. Sin., 1995,11(08): 719-723
143. Zou Li-Zhuang,Wang Xiao-Ling,Xu Gui-Duan,Qu Song-Sheng.Standard Transfer Free Energies of KBPh4 from Water to Straight Chain Monohydric Alcohols[J]. Acta Phys. -Chim. Sin., 1995,11(04): 369-374
144. Huang Shi-Ping, Liu Hong-Lin, Ma Yan-Hui, Tang Bo, Chen Nian-Yi.Molecular Dynamics Simulation of ZnCl2 Melts[J]. Acta Phys. -Chim. Sin., 1995,11(01): 71-73
145. Huang Shi-Ping, Ma Yan-Hui, Tang Bo, Xu Hua, Chen Nian-Yi.Molecular Dynamics Study of NaCl-NaBr Melt[J]. Acta Phys. -Chim. Sin., 1994,10(11): 1045-1048
146. Xian Jing-Chun, Zhu Shou-Rong, Lin Hua-Kuan, Chen Rong-Ti.Linear Free Energy Relationships of Complexes(XIX)[J]. Acta Phys. -Chim. Sin., 1994,10(09): 841-846
147. Cheng Zhao-Nian, Jia Zheng-Ming, Xu Li, Chen Nian-Yi.Molecular Dynamics Simulations of Molten Salt Solutions NaCaF3, Na2CaF4 and Na3CaF5[J]. Acta Phys. -Chim. Sin., 1994,10(08): 676-679
148. Huang Shu-Kun, Chen Lin-Sheng, Xie Nai-Xian, Wang Feng-Zhen, Liu Guo-Gen.Electrochemical-ESR Study of Electroreduction Process of p-toluene Sulfonamide[J]. Acta Phys. -Chim. Sin., 1994,10(07): 662-665
149. Wu Xiong-Wu; Shi Jun.A New Simulation Approach to the Entropy-related Properties of Fluids[J]. Acta Phys. -Chim. Sin., 1993,9(06): 740-745
150. Cheng Zhao-Nian; Jia Zheng-Ming; Zhang Jing; Chen Nian-Yi.Radial Distribution Functions of Molten CaF2[J]. Acta Phys. -Chim. Sin., 1993,9(04): 438-441
151. Lin Hua-Kuan; Liu Zai-Jun; Tang Xiang-Hai; Chen Rong-Ti.Further Study of Linear Free Energy Relationships in Complex Compounds[J]. Acta Phys. -Chim. Sin., 1993,9(04): 565-568
152. Wang Yi-Xuan; Zhao Jian-Ping; Dai Ming.Vapor-Liquid Equilibrium for Some Polar Aprotic Solvents with Methanol or 1,2-Dichloroethane[J]. Acta Phys. -Chim. Sin., 1992,8(05): 636-641
153. Shao Jun; Tang Zheng-Quan.A Computer Simulation on Local Structure in LiCl Quenching Process——The Computation of the Voronoi Polyhedron for the Simuiation Unit Cell Extended with Periodic Boundary Condition[J]. Acta Phys. -Chim. Sin., 1991,7(05): 571-576
154. Zhu Bu-Yao; Zhao Guo-Xi.FREE Energy of Symmetric Catanionic Surfactants in Micellization and Surface Adsorption[J]. Acta Phys. -Chim. Sin., 1991,7(04): 385-389
155. Cheng Zhao-Nian; Zhang Jing; Jia Zheng-Ming; Chen Nian-Yi.Ca2+ Sublattice and F- Sublattice in Superionic Conductor CaF2[J]. Acta Phys. -Chim. Sin., 1991,7(04): 390-393
156. JIANG Tao, TIAN Jie, WANG Ning, PENG Shu-Ming, LI Mei, HAN Wei, ZHANG Mi-Lin.Electrochemical Behavior of La (III) in Molten LiCl-KCl-LaCl3[J]. Acta Phys. -Chim. Sin., 0,(): 0-0
157. SHEN Hong-Chen, DING Ji-Yong, LI Li, LIU Fu-Feng.Effect of Y220C Mutant on the Conformational Transition of p53C Probed by Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 0,(): 0-0
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