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Fan F, Zheng YC, Fu Y, Zhang Y, Zheng H, Lyu C, Chen L, Huang J, Cao Z. QM/MM and MM MD simulations on decontamination of the V-type nerve agent VX by phosphotriesterase: Toward a comprehensive understanding of steroselectivity and activity. Phys Chem Chem Phys 2022; 24:10933-10943. [DOI: 10.1039/d2cp00773h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to deadly toxicity and high environmental stability of the nerve agent VX, an efficient decontamination approach is desperately needed in tackling its severe threat to human secu-rity. The enzymatic...
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Zhang X, Liu X, Zhang Z, Zhao Y, Wang C. Atomic-Level Investigation of Reactant Recognition Mechanism and Thermodynamic Property in Glucosamine 6-Phosphate Deaminase Catalysis. Front Chem 2021; 9:737492. [PMID: 34414167 PMCID: PMC8369159 DOI: 10.3389/fchem.2021.737492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Glucosamine 6-phosphate deaminase (NagB) influences the direction of N-acetylglucosamine (GlcNAc) metabolism, facilitating the conversion of D-glucosamine 6-phosphate (GlcN6P) to D-fructose 6-phosphate (Fru6P) with the release of ammonia. Here, extensive molecular dynamics simulations combined with various techniques were performed to study the recognition and delivery process of GlcN6P by SmuNagB, due to its guidance of subsequent enzymatic reaction. The key residues Lys194, His130, Arg127, Thr38, and Ser37 stabilize GlcN6P in the active site by hydrogen bond interactions, therein electrostatic and polar solvent effects provide the primary traction. Four delivery channels were identified, with GlcN6P most likely to enter the active site of NagB through a “door” comprising residues 6–10, 122–136, and 222–233. The corresponding mechanism and thermodynamic properties were investigated. An exothermic recognition and delivery process were detected, accompanied by the flipping of GlcN6P and changes in key direct and indirect hydrogen bond interactions, which provide the driving force for the chemical reaction to occur. Furthermore, “the lid motif” was identified that remain open in alkaline condition with different extent of opening at each stage of transfer that induced GlcN6P to move the active site of NagB. The work will assist in the elucidation of the catalytic mechanism of action of NagB, allowing inhibitors to be designed with superior dynamic behavior.
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Affiliation(s)
- Xiao Zhang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
| | - Xiaoyuan Liu
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
| | - Zhiyang Zhang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
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Fan F, Zhao Y, Cao Z. Insight into the delivery channel and selectivity of multiple binding sites in bovine serum albumin towards naphthalimide-polyamine derivatives. Phys Chem Chem Phys 2019; 21:7429-7439. [PMID: 30892331 DOI: 10.1039/c9cp00527g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naphthalimide derivatives are types of small-molecule anticancer drug candidates; however, their negative factors and potential side effects make their application limited. The pharmacophores select a direct access into the tumor cells as the first choice; this can reduce the side effect of the anti-cancer drugs on the normal cells. Herein, the delivery and binding of the naphthalimide-polyamine complex assisted by the bovine serum albumin (BSA) protein have been studied by combining several molecular dynamic simulations. The plausible transportation channels and the most favorable pathways for the delivery of the naphthalimide-polyamine complex to two drug sites (DSI and DSII), their thermodynamic and dynamic properties and the mechanisms have been discussed in detail. The residues His287 and Phe394 acted as guards in the DSI and DSII, respectively, which played a gating-switch role by flipping the ring from open to close during the compound delivery. The binding mode, binding energy and substituent effects have been also identified. The two drug sites have different preferences towards the compound with the electron-withdrawing and electron-donating substituents, and their strong interactions are more sensitive to the number of the substituent groups. The naphthalimide-polyamine complexes are more likely to choose DSI, both thermodynamically and dynamically, as compared to DSII. This selective specificity of these two drug sites manipulated by the electron-withdrawing and electron-donating substituents is quite promising for the design of new naphthalimide drugs.
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Affiliation(s)
- Fangfang Fan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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Zhao Y, She N, Ma Y, Wang C, Cao Z. A Description of Enzymatic Catalysis in N-Acetylhexosamine 1-Kinase: Concerted Mechanism of Two-Magnesium-Ion-Assisted GlcNAc Phosphorylation, Flexibility Behavior of Lid Motif upon Substrate Recognition, and Water-Assisted GlcNAc-1-P Release. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Nai She
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Yiming Ma
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of China
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Tian G, Liu Y. Mechanistic insights into the catalytic reaction of ferulic acid decarboxylase from Aspergillus niger: a QM/MM study. Phys Chem Chem Phys 2018; 19:7733-7742. [PMID: 28262890 DOI: 10.1039/c6cp08811b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ubiquinone plays a pivotal role in the aerobic cellular respiratory electron transport chain, whereas ferulic acid decarboxylase (FDC) is involved in the biosynthesis of ubiquinone precursor. Recently, the complete crystal structure of FDC (based on the co-expression of the A. niger fdc1 gene in E. coli with the associated ubix gene from E. coli) at high resolution was reported. Herein, the detailed catalytic non-oxidative decarboxylation mechanism of FDC has been investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Calculation results indicate that, after the 1,3-dipolar cycloaddition of the substrate and cofactor, the carboxylic group can readily split off from the adduct, and the overall energy barrier of the whole catalytic reaction is 23.5 kcal mol-1. According to the energy barrier analysis, the protonation step is rate-limiting. The conserved protonated Glu282 is suggested to be the proton donor through a "water bridge". Besides, two cases, that is, the generated CO2 escapes from the active site or remains in the active site, were considered. It was found that the prolonged leaving of CO2 can facilitate the protonation of the intermediate. In particular, our calculations shed light on the detailed function of both cofactors prFMNiminium and prFMNketamine in the decarboxylation step. The cofactor prFMNiminium is the catalytically relevant species compared with prFMNketamine.
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Affiliation(s)
- Ge Tian
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
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Fan F, Chen N, Wang Y, Wu R, Cao Z. QM/MM and MM MD Simulations on the Pyrimidine-Specific Nucleoside Hydrolase: A Comprehensive Understanding of Enzymatic Hydrolysis of Uridine. J Phys Chem B 2018; 122:1121-1131. [PMID: 29285933 DOI: 10.1021/acs.jpcb.7b10524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The pyrimidine-specific nucleoside hydrolase Yeik (CU-NH) from Escherichia coli cleaves the N-glycosidic bond of uridine and cytidine with a 102-104-fold faster rate than that of purine nucleoside substrates, such as inosine. Such a remarkable substrate specificity and the plausible hydrolytic mechanisms of uridine have been explored by using QM/MM and MM MD simulations. The present calculations show that the relatively stronger hydrogen-bond interactions between uridine and the active-site residues Gln227 and Tyr231 in CU-NH play an important role in enhancing the substrate binding and thus promoting the N-glycosidic bond cleavage, in comparison with inosine. The estimated energy barrier of 30 kcal/mol for the hydrolysis of inosine is much higher than 22 kcal/mol for uridine. Extensive MM MD simulations on the transportation of substrates to the active site of CU-NH indicate that the uridine binding is exothermic by ∼23 kcal/mol, more remarkable than inosine (∼12 kcal/mol). All of these arise from the noncovalent interactions between the substrate and the active site featured in CU-NH, which account for the substrate specificity. Quite differing from other nucleoside hydrolases, here the enzymatic N-glycosidic bond cleavage of uridine is less influenced by its protonation.
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Affiliation(s)
- Fangfang Fan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 360015, China
| | - Nanhao Chen
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Yongheng Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 360015, China
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A water-assisted nucleophilic mechanism utilized by BphD, the meta-cleavage product hydrolase in biphenyl degradation. J Mol Graph Model 2017; 76:448-455. [DOI: 10.1016/j.jmgm.2017.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 11/22/2022]
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Zhang X, Zhao Y, Duan X, Zhang HN, Cao Z, Mo Y. Mechanisms for the deamination reaction of 8-oxoguanine catalyzed by 8-oxoguanine deaminase: A combined QM/MM molecular dynamics study. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The deamination reaction of 8-oxoguanine (8-oxoG) catalyzed by 8-oxoguanine deaminase (8-oxoGD) plays a critically important role in the DNA repair activity for oxidative damage. In order to elucidate the complete enzymatic catalysis mechanism at the stages of 8-oxoguanine binding, departure of 2-hydroxy-1H-purine-6,8(7H,9H)-dione from the active site, and formation of 8-oxoxanthine, extensive combined QM(PM3)/MM molecular dynamics simulations have been performed. Computations show that the rate-limiting step corresponds to the nucleophilic attack from zinc-coordinate hydroxide group to free 8-oxoguanine. Through conformational analyses, we demonstrate that Trp115, Trp123 and Leu119 connect to O8@8-oxoguanine with hydrogen bonds, and we suggest that mutations of tryptophan (115 and 123) to histidine or phenylalanine and mutation of leucine (119) to alanine could potentially lead to a mutant with enhanced activity. On this ground, a proton transfer mechanism for the formation of 8-oxoxanthine was further discussed. Both Glu218 and water molecule could be used as proton shuttles, and water molecule plays a major role in proton transfer in substrate. On the other hand, comparative simulations on the deamination of guanine and isocytosine reveal that, for the helping of hydrogen bonds between O8@8-oxoguanine and enzyme, O8@8-oxoguanine is the fastest to be deaminated among the three substrates which are also supported by the experimental kinetic constants.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing 100029, P. R. China
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - Yuan Zhao
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, USA
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, 475004, P. R. China
| | - Xinli Duan
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Hui N. Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, USA
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Zhang F, Chen N, Zhou J, Wu R. Protonation-Dependent Diphosphate Cleavage in FPP Cyclases and Synthases. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02096] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fan Zhang
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Nanhao Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Jingwei Zhou
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
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Zhao Y, Chen N, Wang C, Cao Z. A Comprehensive Understanding of Enzymatic Catalysis by Hydroxynitrile Lyases with S Stereoselectivity from the α/β-Hydrolase Superfamily: Revised Role of the Active-Site Lysine and Kinetic Behavior of Substrate Delivery and Sequential Product Release. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02855] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuan Zhao
- The Key Laboratory of Natural Medicine
and Immuno-Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Nanhao Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine
and Immuno-Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and
Fujian Provincial Key Laboratory of Theoretical and Computational
Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of China
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Zhang X, Zhao Y, Yan H, Cao Z, Mo Y. Combined QM(DFT)/MM molecular dynamics simulations of the deamination of cytosine by yeast cytosine deaminase (yCD). J Comput Chem 2016; 37:1163-74. [DOI: 10.1002/jcc.24306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Xin Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology; Beijing 100029 China
- Department of Chemistry; Western Michigan University; Kalamazoo Michigan 49008
| | - Yuan Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University; Xiamen 360015 China
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University; Kaifeng 475004 China
| | - Honggao Yan
- Department of Biochemistry; The Center for Biological Modeling, Michigan State University; East Lansing Michigan 48824
- Department of Chemistry; The Center for Biological Modeling, Michigan State University; East Lansing Michigan 48824
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University; Xiamen 360015 China
| | - Yirong Mo
- Department of Chemistry; Western Michigan University; Kalamazoo Michigan 49008
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Abstract
A proton transfer process is usually dominant in several biological phenomena such as the energy relaxation of photo-excited DNA base pairs and a charge relay process in Ser-His-Glu.
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Affiliation(s)
- Hiroto Tachikawa
- Division of Materials Chemistry
- Graduate School of Engineering
- Hokkaido University
- Sapporo 060-8628
- Japan
| | - Tomoya Takada
- Department of Material Chemistry
- Asahikawa National College of Technology
- Asahikawa 071-8142
- Japan
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