Dingguo Xu

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Name: 徐定国; Xu, DingGuo
Organization: Sichuan University , China
Department: College of Chemistry
Title: Professor(PhD)
Co-reporter:Jing Xiong and Dingguo Xu
The Journal of Physical Chemistry B 2017 Volume 121(Issue 5) pp:
Publication Date(Web):January 10, 2017
DOI:10.1021/acs.jpcb.6b10501
Together with polysaccharide lyases (PLs), the unsaturated glucuronyl hydrolase of Bacillus sp., GL1, is responsible for the metabolism of glycosaminoglycans (GAGs), which plays an important role in various crucial physiological events. More importantly, the degradation mechanism of GAGs often causes extracellular bacterial infection and is thought to be one of the virulence factors. We have previously studied the first degradation step catalyzed by PLs. In this work, we focused on the degradation of the unsaturated chondroitin disaccharide, which is produced from chondroitin by chondroitin lyase. A combined quantum mechanical and molecular mechanical method was employed in all simulations. First of all, molecular dynamics simulations were performed to obtain a stable initial enzyme–substrate complex structure. Almost all interactions between the substrate and enzyme were found to be related to the d-glucuronic acid unit, whereas no recognition specificity was observed for the N-acetyl-d-galactosamine unit. Experimentally, two different pathways have been proposed on the basis of X-ray structures and kinetic isotopic effects. In our simulation, the pathway involving the formation of an epoxide intermediate has been found to be favorable rather than that involving direct hydration of the vinyl ether group around carbons 4 and 5. A metastable oxocarbenium-ion-like intermediate can be found in our simulation.
Co-reporter:Yeshuang Zhong, Cheng Chen, Chunchun Zhang, Dingguo Xu, Zhien Lin
Inorganic Chemistry Communications 2017 Volume 84(Volume 84) pp:
Publication Date(Web):1 October 2017
DOI:10.1016/j.inoche.2017.08.029
•Three indium oxalates were prepared in the presence of different amines.•A chainlike metal oxalate has a cationic skeleton.•The photoluminescent property of a metal oxalate was investigated.Three new indium oxalates, formulated as H3dpta·In(C2O4)(H2O)3·2SO4 (1), In(qd)(C2O4)1.5·1.5H2O (2), and H2bpp·In2(C2O4)4 (3) in which dpta = dipropylenetriamine, qd = quinoxaline-2,3(1H,4H)-dione, and bpp = 1,3-bis(4-piperidyl)propane, were prepared in the presence of different amines. These compounds have cationic, neutral, and anionic frameworks, respectively. Topological analyses reveal that compound 2 has an hcb net, while compound 3 has a dia net. The photoluminescent property of compound 2 was also investigated.Three indium oxalates with chainlike, layered, and framework structures were prepared in the presence of different amines. These compounds feature anionic, cationic, and neutral frameworks. The experimental and theoretical studies of the luminescence of the layered compound were also presented.Download high-res image (85KB)Download full-size image
Co-reporter:Qingyu Liu;Fang Zuo;Zhigang Zhao;Junxian Chen
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 35) pp:23924-23933
Publication Date(Web):2017/09/13
DOI:10.1039/C7CP02292A
A recently reported liquid-crystal sensor system based on the substrate competitive inclusion effects of β-cyclodextrin (β-CD) has been investigated using molecular dynamics simulations in this work. In such a system, the released indicator could induce an orientational transition of liquid-crystals from planar to homeotropic. The analyte molecule can thus be easily and efficiently detected by observing the corresponding optical image changing from bright to dark. Here, the different binding affinity of β-CD for the indicator (sodium dodecyl sulfate, SDS) and the analyte (methylene blue, MB) was identified using molecular dynamics simulations and absolute binding free energy calculations. The inclusion processes calculated using the adaptive biasing force algorithm can completely explain the competitive inclusion between MB and SDS by β-CD, and thus lead to a significant change in the liquid crystal optical properties.
Co-reporter:Yeshuang Zhong, Wei Zhang, Daichuan Ma, Dingguo Xu, Zhien Lin
Inorganic Chemistry Communications 2017 Volume 86(Volume 86) pp:
Publication Date(Web):1 December 2017
DOI:10.1016/j.inoche.2017.10.002
•A three-dimensional lead borate was prepared under solvothermal conditions.•A fluorite network is constructed from two different cluster building units.•The band structure and density of states of a lead borate were calculated.Presented here is a new three-dimensional lead borate, namely, PbB2O4 (denoted as SCU-8). This compound has a fluorite net constructed from two different cyclic building units: 4-connected Pb3O6 cluster and 8-connected B12O24 cluster. It is a wide-gap semiconductor with the band gap of 4.0 eV. The band structure and density of states of the compound were also calculated based on density functional theory.A new three-dimensional lead borate was prepared under solvothermal conditions. This compound has a fluorite net constructed from two different cyclic building units: Pb3O6 and B12O24 clusters. It is an indirect-gap material with the band gap of 4.0 eV.Download high-res image (95KB)Download full-size image
Co-reporter:Kangcai Wang, Yixuan Bian, Jing Li, Dingguo Xu, and Zhien Lin
Inorganic Chemistry 2016 Volume 55(Issue 8) pp:3727-3729
Publication Date(Web):April 1, 2016
DOI:10.1021/acs.inorgchem.6b00589
Presented here are two open-framework zinc phosphites, namely, Zn(dabco)0.5(HPO3) (SCU-18) and Zn4(Hdabco)2(CH3COO)2(HPO3)4 (SCU-20), where dabco = 1,4-diazabicyclo[2.2.2]octane. SCU-18 features a rare 3-connected inorganic skeleton with a chiral qtz-h topology. It contains 18-membered-ring (18 MR) channels displaying porosity and second-harmonic-generation response. SCU-20 has a bnn topology containing large 20 MR channels that shows a strong blue emission as a result of excitation at 375 nm.
Co-reporter:Hong Wu, Dingguo Xu, Mingli Yang, and Xingdong Zhang
Langmuir 2016 Volume 32(Issue 18) pp:4643-4652
Publication Date(Web):April 20, 2016
DOI:10.1021/acs.langmuir.5b04667
The surface structure of hydroxyapatite (HAP) is crucial for its bioactivity. Using a molecular dynamics simulated annealing method, we studied the structure and its variation with annealing temperature of the HAP (100) surface. In contrast to the commonly used HAP surface model, which is sliced from HAP crystal and then relaxed at 0 K with first-principles or force-field calculations, a new surface structure with gradual changes from ordered inside to disordered on the surface was revealed. The disordering is dependent on the annealing temperature, Tmax. When Tmax increases up to the melting point, which was usually adopted in experiments, the disordering increases, as reflected by its radial distribution functions, structural factors, and atomic coordination numbers. The disordering of annealed structures does not show significant changes when Tmax is above the melting point. The thickness of disordered layers is about 10 Å. The surface energy of the annealed structures at high temperature is significantly less than that of the crystal structure relaxed at room temperature. A three-layer model of interior, middle, and surface was then proposed to describe the surface structure of HAP. The interior layer retains the atomic configurations in crystal. The middle layer has its atoms moved and its groups rotated about their original locations. In the surface layer, the atomic arrangements are totally different from those in crystal. In particular for the hydroxyl groups, they move outward and cover the Ca2+ ions, leaving holes occupied by the phosphate groups. Our study suggested a new model with disordered surface structures for studying the interaction of HAP-based biomaterials with other molecules.
Co-reporter:Kangcai Wang, Jing Li, Dingguo Xu, Daibing Luo and Zhien Lin  
CrystEngComm 2015 vol. 17(Issue 10) pp:2162-2167
Publication Date(Web):03 Feb 2015
DOI:10.1039/C4CE02226B
Two new open-framework beryllium phosphates, formulated as MV·Be2(HPO4)2(H2PO4)2 (1) and EV·Be2(HPO4)2(H2PO4)2 (2), have been synthesized under solvothermal conditions, where MV = methylviologen and EV = ethylviologen. The two compounds have large 16-membered ring (16 MR) channels with a zeolitic CrB4 topology. They contain in situ generated viologen dications from the alkylation of 4,4′-bipyridine (4,4′-bpy) molecules as the structure-directing agents (SDAs). In comparison, the use of 4,4′-bpy and 2,2′-bpy as the SDAs results in the formation of two different open-framework compounds, (4,4′-H2bpy)2·Be5(HPO4)7 (3) and (2,2′-H2bpy)0.5·Be3(OH)(HPO4)3 (4). Compounds 3 and 4 have different framework structures with 12 MR channels. The presence of large 41084124 cages in the structure of 3 is worth noting.
Co-reporter:Kangcai Wang, Na Yang, Dingguo Xu, Daibing Luo, Zhien Lin
Inorganic Chemistry Communications 2015 Volume 58() pp:95-98
Publication Date(Web):August 2015
DOI:10.1016/j.inoche.2015.06.020
•New beryllium phosphates were prepared under solvothermal conditions.•Open-framework structures are constructed from different cluster-like building blocks.•Beryllium phosphates display hcb, sql, and bnn topologies.Three new beryllium phosphates, namely, H3aep·Be2(PO4)2(H2PO4)·H2O (1), H2tmdp·Be3(HPO4)3(PO4CH3)·2.25H2O (2), and H2dmpda·Be3(PO4)(HPO4)2(H2PO4) (3), were prepared under solvothermal conditions. These compounds display different open-framework structures with hcb (for 1), sql (for 2), and bnn (for 3) topologies, respectively. The formation of phosphate ester from in situ esterification reaction of phosphoric acid and methanol is noteworthy.Three open-framework beryllium phosphates were synthesized under solvothermal conditions. These compounds display hcb, sql, and bnn topologies. The coexistence of phosphate and methylphosphate in the same crystalline structure is noteworthy.
Co-reporter:Kangcai Wang, Daibing Luo, Dingguo Xu, Furong Guo, Lin Liu and Zhien Lin  
Dalton Transactions 2014 vol. 43(Issue 36) pp:13476-13479
Publication Date(Web):29 Jul 2014
DOI:10.1039/C4DT01503G
Presented here are two novel open-framework cobalt sulfate-oxalates constructed from molecular and chain-like building blocks. The two compounds have different structures: an hcb-type layer with 20-ring windows and a mog-type framework with 12-ring channels. Amine molecules play dual roles in the two structures: as a chelating ligand and a charge-balancing agent.
Co-reporter:Kangcai Wang;Daibing Luo;Lin Liu;Zhien Lin
European Journal of Inorganic Chemistry 2014 Volume 2014( Issue 12) pp:2025-2028
Publication Date(Web):
DOI:10.1002/ejic.201400113

Abstract

Four beryllium hydrogen phosphates, Be2(Hea)(PO4)(HPO4) (1), Him·Be3(OH)(HPO4)3 (2a), Hpy·Be3(OH)(HPO4)3 (2b), and Hma·Be1.5(HPO4)2·0.5H2O (3) in which ea = ethanolamine, im = imidazole, py = pyridine, and ma = methylamine, were synthesized under solvothermal conditions. All compounds have open-framework structures with (3,4)-connected networks. Compound 1 features a neutral inorganic–organic hybrid framework with an interrupted zeolitic GIS topology. The dual role of the amine molecules as charge-balancing agents and coordinating agents to the beryllium atoms is noteworthy. Compounds 2a and 2b are isostructural, and they have an AFI-related framework with elliptical 12-ring channels. Compound 3 has a 3D structure with 4.82 layers pillared by corner-sharing four-ring chains. It represents the first example of an open-framework beryllium hydrogen phosphate with 16-ring channels.

Co-reporter:Tingzhi Liu, Daibing Luo, Dingguo Xu, Kangcai Wang, Zhien Lin
Inorganic Chemistry Communications 2014 Volume 48() pp:136-139
Publication Date(Web):October 2014
DOI:10.1016/j.inoche.2014.08.034
•Three magnesium-base coordination polymers were prepared and characterized.•A luminescent magnesium-base coordination polymer has square-shape channels.•Coordination polymers display anatase, and tfz-d topologies.Three magnesium-based coordination polymers, formulated as Mg(3,4-pyb)2 (1), Mg(4,3-pyb)2 (2), and Mg2.5(4,4-pyb)2(HCOO)2(OH) (3), have been synthesized under solvothermal conditions, where 3,4-pyb = 3-(pyridin-4-yl)benzoate, 4,3-pyb = 4-(pyridin-3-yl)benzoate, and 4,4-pyb = 4-(pyridin-4-yl)benzoate. Compounds 1 and 2 have (3,6)-connected frameworks with an anatase topology. Compound 3 has a (3,8)-connected framework with an unusual tfz-d topology by regarding Mg5(HCOO)4(OH)2 clusters as 8-connected nodes and bridging 4,4-pyb ligands as 3-connected nodes.Three new magnesium-base coordination polymers with anatase and tfz-d topologies have been synthesized and characterized. The presence of square-shape channels in the photoluminescent anatase-type network is noteworthy.
Co-reporter:Youzhou He;Min Xu;Rongzhao Gao;Xiaowei Li;Fengxue Li;Xuedan Wu; Dingguo Xu;Dr. Huaqiang Zeng; Lihua Yuan
Angewandte Chemie International Edition 2014 Volume 53( Issue 44) pp:11834-11839
Publication Date(Web):
DOI:10.1002/anie.201407092

Abstract

A unique supramolecular two-component gelation system was constructed from amphiphilic shape-persistent cyclo[6]aramides and diethylammonium chloride (or triethylammonium chloride). This system has the ability to discriminate native arginine from 19 other amino acids in a specific fashion. Cyclo[6]aramides show preferential binding for the guanidinium residue over ammonium groups. This specificity was confirmed by both experimental results and theoretical simulations. These results demonstrated a new modular displacement strategy, exploring the use of species-binding hydrogen-bonded macrocyclic foldamers for the construction of two-component gelation systems for selective recognition of native amino acids by competitive host–guest interactions. This strategy may be amenable to developing a variety of functional two-component gelators for specific recognition of various targeted organic molecular species.

Co-reporter:Ling Dang, Libo Liang, Cheng Qian, Meiqin Fu, Tongmei Ma, Dingguo Xu, Huanfeng Jiang, and Wei Zeng
The Journal of Organic Chemistry 2014 Volume 79(Issue 2) pp:769-776
Publication Date(Web):December 31, 2013
DOI:10.1021/jo402705w
A Cu(OAc)2-promoted cascade carboamination/oxidative cyclization of alkenes with α-imino esters has been explored. This transformation provides a concise approach to rapid assembly of 2-oxo-3-iminopyrrole derivatives in moderate to good yields.
Co-reporter:Tingzhi Liu, Daibing Luo, Dingguo Xu, Hongmei Zeng and Zhien Lin  
Dalton Transactions 2013 vol. 42(Issue 2) pp:368-371
Publication Date(Web):07 Nov 2012
DOI:10.1039/C2DT31394D
Two new photoluminescent magnesium-based coordination polymers, Mg(int)2·H2O (1) and Mg(nt)2 (2), were synthesized under solvothermal conditions. Structural analyses reveal that they have different 3,6-connected frameworks with rutile- and anatase-type topologies, respectively. Compound 1 remains stable after the removal of its guest molecules and it exhibits weak ferroelectric behavior.
Co-reporter:Kangcai Wang, Yu Wang, Dingguo Xu, Daibing Luo, Zhien Lin
Inorganic Chemistry Communications 2013 Volume 36() pp:146-149
Publication Date(Web):October 2013
DOI:10.1016/j.inoche.2013.08.040
•Three lanthanide sulfate–oxalate hybrid solids were synthesized and characterized.•An open-framework structure was synthesized under solvent-free conditions.•These compounds display different ladder-like and framework structures.Three new lanthanide sulfate–oxalate hybrid solids, Er2(SO4)(C2O4)2(H2O)6·0.5H2O (1), Nd3(SO4)(C2O4)3.5(H2O)7·H2O (2), and [C4H14N2]0.5·Nd2(SO4)2(C2O4)1.5(H2O)4 (3), have been synthesized and structurally characterized. Compound 1 has a rare ladder-like structure, while compounds 2 and 3 have different three-dimensional structures. The presence of large 12-ring channels in the structure of 3 is noteworthy. The powder X-ray diffraction, IR spectra, thermogravimetric analyses, and magnetic susceptibility measurements of compounds 1 and 2 have also been investigated.Three new lanthanide sulfate–oxalate hybrid solids have been synthesized and characterized. These compounds display different structures containing isolate ErO8 polyhedra, Nd2O16 dimers and inorganic chains of NdO9 polyhedra, respectively.
Co-reporter:Min Zheng and Dingguo Xu
The Journal of Physical Chemistry B 2013 Volume 117(Issue 35) pp:10161-10172
Publication Date(Web):August 14, 2013
DOI:10.1021/jp406206s
Hyaluronate lyase from Spectrococcus pneumonia can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. The major functions of hyaluronan are to regulate water balance and osmotic pressure and act as an ion-exchange resin. It has been suggested in our previous molecular dynamics simulation that the binding of the substrate molecule could lead to the ionization of Y408 and protonation of H399. Followed by our recent molecular dynamics simulation of the enzyme–substrate complex, a unified proton abstraction and donation mechanism for this enzyme can be established using a combined quantum mechanical and molecular mechanical approach and density functional theory method. Y408 is shown to serve as the general base in the proton abstraction, while general acid is the next proton donation step. Overall, this reaction can be classified into syn-elimination reaction mechanism. The neutralization effects of C5 carboxylate group by several polar residues such as N349 and H399 were also examined. Finally, in combination of our previous molecular dynamics simulations, a complete catalytic cycle for the degradation of hyaluronan tetrasaccharide catalyzed by the hyaluronate lyase from Spectrococcus pneumonia is proposed.
Co-reporter:Chunchun Zhang, Shanshan Wu, and Dingguo Xu
The Journal of Physical Chemistry B 2013 Volume 117(Issue 22) pp:6635-6645
Publication Date(Web):May 15, 2013
DOI:10.1021/jp400974n
The angiotensin-converting enzyme (ACE) exhibits critical functions in the conversion of angiotensin I to angiotensin II and the degradation of bradykinin and other vasoactive peptides. As a result, the ACE inhibition has become a promising approach in the treatment of hypertension, heart failure, and diabetic nephropathy. Extending our recent molecular dynamics simulation of the testis ACE in complex with a bona fide substrate molecule, hippuryl-histidyl-leucine, we presented here a detailed investigation of the hydrolytic process and possible influences of the chloride ion on the reaction using a combined quantum mechanical and molecule mechanical method. Similar to carboxypeptidase A and thermolysin, the promoted water mechanism is established for the catalysis of ACE. The E384 residue was found to have the dual function of a general base for activating the water nucleophile and a general acid for facilitating the cleavage of amide C–N bond. Consistent with experimental observations, the chloride ion at the second binding position is found to accelerate the reaction rate presumably due to the long-range electrostatic interactions but has little influence on the overall substrate binding characteristics.
Co-reporter:Jingli Liu, Min Zheng, Chunchun Zhang, and Dingguo Xu
The Journal of Physical Chemistry B 2013 Volume 117(Issue 35) pp:10080-10092
Publication Date(Web):August 16, 2013
DOI:10.1021/jp402110j
Bifidobacterium is a genus of Gram-positive bacteria, which is important in the absorption of nourishment from the human milk oligosaccharides (HMO). We present here the detailed simulation of the enzymatic hydrolysis of 2′-fucosyllactose catalyzed by 1,2-α-l-fucosidase from Bifidobacterium bifidum using the combined quantum mechanical and molecular mechanical approach. Molecular dynamics simulations and free energy profiles support that the overall reaction is a stepwise mechanism. The first step is the proton transfer from N423 to D766, and the second step involves the hydrolysis reaction via the inversion mechanism catalyzed by the amide group of N423. Assisted by D766, N423 serves as the general base to activate the water molecule to attack the anomeric carbon center. E566 is the general acid to facilitate the cleavage of glycosidic bond between l-fucose and galactose units. The intrinsic resonance structure for the side chain amide group of the asparagine residue is shown to be the origin to the catalytic activity, which is also confirmed by the mutagenesis simulation of N423G.
Co-reporter:Min Zheng and Dingguo Xu
The Journal of Physical Chemistry B 2013 Volume 117(Issue 39) pp:11596-11607
Publication Date(Web):August 27, 2013
DOI:10.1021/jp4065906
Metallo-β-lactamases can hydrolyze and deactivate lactam-containing antibiotics, which is the major mechanism for causing drug resistance in the treatment of bacterial infections. This has become a global concern because of the lack of clinically approved inhibitors so far. The emergence of New Delhi metallo-β-lactamase I (NDM-1) makes the situation even more serious. In this work, first, the structure of NDM-1 in complex with the inhibitor molecule l-captopril is investigated by both density functional theory (DFT) and hybrid quantum mechanical/molecular mechanical (QM/MM) methods, and the theoretical results are in good agreement with the X-ray structure. The Michaelis structure with an antibiotic compound (ampicillin) bound in the active site is constructed from a recent X-ray structure of the NDM-1 enzyme with hydrolyzed ampicillin. It is further simulated using a QM/MM molecular dynamics method. One of the interesting binding features of ampicillin in the NDM-1 active site is that the conserved C3 carboxylate group is not ligated with Zn2 but rather is only hydrogen-bonded with N220 and K211. A bridging hydroxide ion is suggested to connect two zinc cofactors. This hydroxide ion is also hydrogen-bonded with D124. Subsequent reaction path calculations indicate that the initial step of lactam ring-opening occurs through a concerted step in which the cleavage of the C–N bond and the transfer of the hydrogen bond to D124 are nearly concerted. The ligand bond between Zn2 and the C3 carboxylate group forms after the first step of nucleophilic addition. The calculated activation energy barrier height is about 19.4 kcal/mol for the hydrolysis of ampicillin, which can be compared with the experimental value of 15.8 kcal/mol derived from kcat = 15 s–1. The overall mechanism is finally confirmed by a subsequent DFT study of a truncated active-site model.
Co-reporter:Ruyin Cao, Yongdong Jin, and Dingguo Xu
The Journal of Physical Chemistry B 2012 Volume 116(Issue 21) pp:6087-6096
Publication Date(Web):May 14, 2012
DOI:10.1021/jp3010647
The basic function of carbohydrate binding module (CBM) is believed to enhance local concentration of glycosidases on the carbohydrate molecule, and thus facilitates the subsequent degradation of carbohydrate. Full understanding of the recognition mechanism of carbohydrates by CBM can be helpful to enhance the enzyme activity. In this work, the detailed recognition specificity of two soluble cello-oligosaccharide substrates, cellotetraose and cellohexaose, by a family 17 CBM from Clostridium cellulovorans was investigated by molecular dynamics simulation. Calculated binding free energies using molecular mechanics/generalized Born and surface area (MM/GBSA) approach are in excellent agreement with experimental values. Overall, based on the decomposition of total binding free energy, nonpolar terms are shown to have favorable contributions to the binding, while polar interactions make unfavorable contributions, no matter significant hydrogen bond network is formed between substrate and protein. On the basis of computational alanine scanning and per-residue free energy decomposition, Trp88 and Trp135 are shown to be two most important residues in the cellohexaose binding mainly via hydrophobic interactions. The calculated subtotal contributions for those polar residues, D54, R92, Q129, and N185, can compare very well with experimental data.
Co-reporter:Min Zheng, Hongling Zhang, and Dingguo Xu
The Journal of Physical Chemistry B 2012 Volume 116(Issue 36) pp:11166-11172
Publication Date(Web):August 23, 2012
DOI:10.1021/jp306754a
Hyaluronate lyase from Spectrococcus pneumonia can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. The major functions of hyaluronan are to regulate water balance and osmotic pressure and act as an ion-exchange resin. In this work, we focus on the prerequisite issue of the enzymatic reaction, i.e., the initial reactive conformer. Based on the quantum mechanical and molecular mechanical molecular dynamic simulations and free energy profiles, a near attack conformer was obtained for the degradation of hyaluronan catalyzed by the hyaluronate lyase. Along with the substrate binding, the phenylhydroxyl hydrogen atom of Tyr408 will transfer to nearby His399 via a near barrierless transition state, which results in a negatively charged Tyr408 and positively charged His399. The Tyr408, rather than the previously proposed His399, was suggested to act as the general base for the subsequent β-elimination reaction. The His399 was suggested to have the function of neutralizing the C5-carboxyl group.
Co-reporter:Jingli Liu, Chunchun Zhang, Dingguo Xu
Journal of Molecular Graphics and Modelling 2012 Volume 37() pp:67-76
Publication Date(Web):July 2012
DOI:10.1016/j.jmgm.2012.04.005
Xylanase Cex from Cellulomonas fimi is a bifunctional enzyme that catalyzes the degradation of both cellulose and xylan. As a result, it might find valuable applications in production of biofuels. In this work, we presented a detailed theoretical investigation of hydrolysis of the xylopentaose molecule catalyzed by Cex, using a hybrid quantum mechanical and molecular mechanical approach. Our results support the experimental observation that the hydrolysis proceeds via the net retention mechanism. More interestingly, our simulations indicate that the xylose unit at −1 binding site should take a boat (B2,5) conformation as a possible reactive conformer, while the oxo-carbenium ion-like transition states take the combination of B2,5/OS2 for glycosylation, and OS2/O,3B for deglycosylation. Our molecular dynamics simulations of mutants further suggest that two catalytic residues (E127 and E233) play the vital role in this ring distortion. Indeed, this conformational change is necessary to facilitate the first step of nucleophilic attack by E233 at the anomeric carbon center.Graphical abstractHighlights► Catalytic mechanism was analyzed for Xylanase using SCC-DFTB/MM method. ► Two dimensional potentials of mean force were computed for the hydrolysis reaction. ► The substrate distortion mechanism was suggested to be induced by protein environment.
Co-reporter:Xuemei Wang, Shanshan Wu, Dingguo Xu, Daiqian Xie, and Hua Guo
Journal of Chemical Information and Modeling 2011 Volume 51(Issue 5) pp:1074-1082
Publication Date(Web):April 26, 2011
DOI:10.1021/ci200083f
Angiotensin-converting enzyme (ACE) is an important zinc-dependent hydrolase responsible for converting the inactive angiotensin I to the vasoconstrictor angiotensin II and for inactivating the vasodilator bradykinin. However, the substrate binding mode of ACE has not been completely understood. In this work, we propose a model for an ACE Michaelis complex based on two known X-ray structures of inhibitor-enzyme complexes. Specifically, the human testis angiotensin-converting enzyme (tACE) complexed with two clinic drugs were first investigated using a combined quantum mechanical and molecular mechanical (QM/MM) approach. The structural parameters obtained from the 550 ps molecular dynamics simulations are in excellent agreement with the X-ray structures, validating the QM/MM approach. Based on these structures, a model for the Michaelis complex was proposed and simulated using the same computational protocol. Implications to ACE catalysis are discussed.
Co-reporter:Pei W. Thomas, Min Zheng, Shanshan Wu, Hua Guo, Dali Liu, Dingguo Xu, and Walter Fast
Biochemistry 2011 Volume 50(Issue 46) pp:
Publication Date(Web):October 26, 2011
DOI:10.1021/bi201449r
New Delhi metallo-β-lactmase-1 (NDM-1) has recently emerged as a global threat because of its ability to confer resistance to almost all clinically used β-lactam antibiotics, its presence within an easily transmissible plasmid bearing a number of other antibiotic resistance determinants, its carriage in a variety of enterobacteria, and its presence in both nosocomial and community-acquired infections. To improve our understanding of the molecular basis of this threat, NDM-1 was purified and characterized. Recombinant NDM-1 bearing its native leader sequence was expressed in Escherichia coli BL21 cells. The major processed form found to be released into culture media contains a 35-residue truncation at the N-terminus. This form of NDM-1 is monomeric and can be purified with 1.8 or 1.0 equiv of zinc ion, depending on the experimental conditions. Treatment of dizinc NDM-1 with EDTA results in complete removal of both zinc ions, but the relatively weaker chelator PAR chelates only 1 equiv of zinc ion from folded protein but 1.9 equiv of zinc ion from denatured protein, indicating different affinities for each metal binding site. UV–vis spectroscopy of the dicobalt metalloform along with molecular dynamics simulations of the dizinc metallo form indicates that the dinuclear metal cluster at the active site of NDM-1 is similar in structure to other class B1 metallo-β-lactamases. Supplementation of excess zinc ions to monozinc NDM-1 has differential effects on enzyme activity with respect to three different classes of β-lactam substrates tested, penems, cephems, and carbapenems, and likely reflects dissimilar contributions of the second equivalent of metal ion to the catalysis of the hydrolysis of these substrates. Fits to these concentration dependencies are used to approximate the Kd value of the more weakly bound zinc ion (2 μM). NDM-1 achieved maximal activity with all substrates tested when supplemented with approximately 10 μM ZnSO4, displaying kcat/KM values ranging from 1.4 × 106 to 2.0 × 107 M–1 s–1, and a slight preference for cephem substrates. This work provides a foundation for an improved understanding of the molecular basis of NDM-1-mediated antibiotic resistance and should allow more quantitative studies to develop targeted therapeutics.
Co-reporter:Shanshan Wu, Chunchun Zhang, Ruyin Cao, Dingguo Xu, and Hua Guo
The Journal of Physical Chemistry B 2011 Volume 115(Issue 34) pp:10360-10367
Publication Date(Web):July 6, 2011
DOI:10.1021/jp2046504
The dipeptide glycyl-l-tyrosine (GY) can be either a substrate for carboxypeptidase A (CPA) or an inhibitor, depending on pH. In this work, we investigate the pH-dependent reactivity of this dipeptide in CPA-catalyzed hydrolysis using a combined quantum mechanical and molecular mechanical method. It is shown that the monoionic form of the dipeptide, prevalent at high pH, chelates the active site zinc ion, rendering the enzyme inactive. This inhibitory form is consistent with an earlier X-ray structure of the CPA–GY complex. On the other hand, the prevailing di-ionic form of the dipeptide at low pH was found to undergo hydrolysis via a nucleophilic mechanism, leading to an acyl–enzyme complex. The stability of this reaction intermediate is consistent with previous low-temperature solid-state NMR results. The calculated overall free-energy barrier of 20.1 kcal/mol is in excellent agreement with the experimental value of 19.9 kcal/mol.
Co-reporter:Shanshan Wu ; Dingguo Xu ;Hua Guo
Journal of the American Chemical Society 2010 Volume 132(Issue 51) pp:17986-17988
Publication Date(Web):December 7, 2010
DOI:10.1021/ja104241g
QM/MM studies of the hydrolysis of a β-lactam antibiotic molecule (biapenem) catalyzed by a monozinc β-lactamase (CphA) have revealed the complete reaction mechanism and shown that an experimentally determined enzyme−intermediate complex is a stable intermediate or product in a minor pathway.
Co-reporter:Shanshan Wu, Chunchun Zhang, Dingguo Xu and Hua Guo
The Journal of Physical Chemistry B 2010 Volume 114(Issue 28) pp:9259-9267
Publication Date(Web):June 28, 2010
DOI:10.1021/jp101448j
The catalytic mechanism of carboxypeptidase A (CPA) for the hydrolysis of ester substrates is investigated using hybrid quantum mechanical/molecular mechanical (QM/MM) methods and high-level density functional theory. The prevailing mechanism was found to utilize an active-site water molecule assisted by Glu270, and this so-called promoted-water pathway is similar to that in the CPA catalyzed proteolytic reaction (D. Xu and H. Guo, J. Am. Chem. Soc. 2009, 131, 9780). On the other hand, our simulations indicated the existence of an alternative pathway due to direct nucleophilic attack of Glu270 on the scissile carbonyl carbon. This so-called nucleophilic pathway, which is not viable in proteolytic reactions, leads to a stable acyl−enzyme complex. However, the nucleophilic pathway is nonproductive as it is blocked by a high barrier in the deacylation step. On the basis of results reported here and in our earlier publication, a unified model is proposed to account for nearly all experimental observations concerning the catalysis of CPA.
Co-reporter:Jingli Liu, Xuemei Wang and Dingguo Xu
The Journal of Physical Chemistry B 2010 Volume 114(Issue 3) pp:1462-1470
Publication Date(Web):December 31, 2009
DOI:10.1021/jp909177e
Cellulase Cel5A from Acidothermus cellulolyticus is an endoglucanase which features the retention mechanism for the cleavage of the β-1,4-glycosidic bond. In this work, we investigated the detailed catalytic steps in the formation of two cellobiose units from the hydrolysis of a cellotetraose molecule using a combined QM/MM approach. The understanding of the catalysis process at the atomistic level may help further protein engineering research. Molecular dynamics, potentials of mean force (PMFs), and reaction path calculations confirmed that the hydrolysis of cellotetraose has a retention mechanism via oxocarbenium-like transition states for both the glycosylation and deglycosylation steps.
Co-reporter:Dingguo Xu ;Hua Guo
Journal of the American Chemical Society 2009 Volume 131(Issue 28) pp:9780-9788
Publication Date(Web):June 24, 2009
DOI:10.1021/ja9027988
Carboxypeptidase A is a zinc-containing enzyme that cleaves the C-terminal residue in a polypeptide substrate. Despite much experimental work, there is still a significant controversy concerning its catalytic mechanism. In this study, the carboxypeptidase A-catalyzed hydrolysis of the hippuryl-l-Phe molecule (kcat = 17.7 ± 0.7 s−1) is investigated using both density functional theory and a hybrid quantum mechanical/molecular mechanical approach. The enzymatic reaction was found to proceed via a promoted-water pathway with Glu270 serving as the general base and general acid. Free-energy calculations indicate that the first nucleophilic addition step is rate-limiting, with a barrier of 17.9 kcal/mol. Besides activating the zinc-bound water nucleophile, the zinc cofactor also serves as an electrophilic catalyst that stabilizes the substrate carbonyl oxygen during the formation of the tetrahedral intermediate. In the Michaelis complex, Arg127, rather than Zn(II), is responsible for the polarization of the substrate carbonyl and it also serves as the oxyanion hole. As a result, its mutation leads to a higher free-energy barrier, in agreement with experimental observations.
Co-reporter:Kangcai Wang, Daibing Luo, Dingguo Xu, Furong Guo, Lin Liu and Zhien Lin
Dalton Transactions 2014 - vol. 43(Issue 36) pp:NaN13479-13479
Publication Date(Web):2014/07/29
DOI:10.1039/C4DT01503G
Presented here are two novel open-framework cobalt sulfate-oxalates constructed from molecular and chain-like building blocks. The two compounds have different structures: an hcb-type layer with 20-ring windows and a mog-type framework with 12-ring channels. Amine molecules play dual roles in the two structures: as a chelating ligand and a charge-balancing agent.
Co-reporter:Tingzhi Liu, Daibing Luo, Dingguo Xu, Hongmei Zeng and Zhien Lin
Dalton Transactions 2013 - vol. 42(Issue 2) pp:NaN371-371
Publication Date(Web):2012/11/07
DOI:10.1039/C2DT31394D
Two new photoluminescent magnesium-based coordination polymers, Mg(int)2·H2O (1) and Mg(nt)2 (2), were synthesized under solvothermal conditions. Structural analyses reveal that they have different 3,6-connected frameworks with rutile- and anatase-type topologies, respectively. Compound 1 remains stable after the removal of its guest molecules and it exhibits weak ferroelectric behavior.
Acetic acid, (diphenylphosphinyl)-, 4-nitrophenyl ester
Benzene, 1,4-bis(3-bromopropoxy)-
Benzene, 1,4-bis(4-bromobutoxy)-
L-Leucine,N-benzoylglycyl-L-histidyl-
b-Cyclodextrin, 6A-deoxy-6A-iodo-
Sulfuric acid,beryllium salt (1:1)
1-METHYL-4-(3-METHYLPHENYL)PIPERAZINE