126
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Zheng F, Yang W, Ko MC, Liu J, Cho H, Gao D, Tong M, Tai HH, Woods JH, Zhan CG. Most efficient cocaine hydrolase designed by virtual screening of transition states. J Am Chem Soc 2008; 130:12148-55. [PMID: 18710224 DOI: 10.1021/ja803646t] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cocaine is recognized as the most reinforcing of all drugs of abuse. There is no anticocaine medication available. The disastrous medical and social consequences of cocaine addiction have made the development of an anticocaine medication a high priority. It has been recognized that an ideal anticocaine medication is one that accelerates cocaine metabolism producing biologically inactive metabolites via a route similar to the primary cocaine-metabolizing pathway, i.e., cocaine hydrolysis catalyzed by plasma enzyme butyrylcholinesterase (BChE). However, wild-type BChE has a low catalytic efficiency against the abused cocaine. Design of a high-activity enzyme mutant is extremely challenging, particularly when the chemical reaction process is rate-determining for the enzymatic reaction. Here we report the design and discovery of a high-activity mutant of human BChE by using a novel, systematic computational design approach based on transition-state simulations and activation energy calculations. The novel computational design approach has led to discovery of the most efficient cocaine hydrolase, i.e., a human BChE mutant with an approximately 2000-fold improved catalytic efficiency, promising for therapeutic treatment of cocaine overdose and addiction as an exogenous enzyme in human. The encouraging discovery resulted from the computational design not only provides a promising anticocaine medication but also demonstrates that the novel, generally applicable computational design approach is promising for rational enzyme redesign and drug discovery.
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127
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Pan Y, Gao D, Zhan CG. Modeling the catalysis of anti-cocaine catalytic antibody: competing reaction pathways and free energy barriers. J Am Chem Soc 2008; 130:5140-9. [PMID: 18341277 DOI: 10.1021/ja077972s] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The competing reaction pathways and the corresponding free energy barriers for cocaine hydrolysis catalyzed by an anti-cocaine catalytic antibody, mAb15A10, were studied by using a novel computational strategy based on the binding free energy calculations on the antibody binding with cocaine and transition states. The calculated binding free energies were used to evaluate the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis for each reaction pathway. The free energy barriers for the antibody-catalyzed cocaine hydrolysis were predicted to be the corresponding free energy barriers for the cocaine hydrolysis in water plus the calculated free energy barrier shifts. The calculated free energy barrier shift of -6.87 kcal/mol from the dominant reaction pathway of the cocaine benzoyl ester hydrolysis in water to the dominant reaction pathway of the antibody-catalyzed cocaine hydrolysis is in good agreement with the experimentally derived free energy barrier shift of -5.93 kcal/mol. The calculated mutation-caused shifts of the free energy barrier are also reasonably close to the available experimental activity data. The good agreement suggests that the protocol for calculating the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis may be used in future rational design of possible high-activity mutants of the antibody as anti-cocaine therapeutics. The general strategy of the free energy barrier shift calculation may also be valuable in studying a variety of chemical reactions catalyzed by other antibodies or proteins through noncovalent bonding interactions with the substrates.
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128
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Pestka KA, Maynard JD, Gao D, Carraro C. Measurement of the elastic constants of a columnar SiC thin film. PHYSICAL REVIEW LETTERS 2008; 100:055503. [PMID: 18352387 DOI: 10.1103/physrevlett.100.055503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Indexed: 05/26/2023]
Abstract
The technique of resonant ultrasound spectroscopy was used to measure the elastic properties of a polycrystalline cubic silicon carbide (3C-SiC) thin film. The film, grown on a silicon (100) substrate, was 1.69 microns thick with columnar crystalline grains and a (111) texture. The substrate with the film was placed between two transducers and the resonant frequencies were measured; measurements were repeated after selective, timed dry etching of the film, allowing a determination of the elastic constants of the film alone. The film elastic constants, c(11)=371 and c(12)=146 GPa, were within a few percent of the literature values (c(11)=386, c(12)=136 GPa) of crystalline 3C-SiC. However, the film elastic constant c(44), 111 GPa, was significantly smaller than the bulk literature value, 254 GPa. For the film, c44 approximately (c(11)-c(12))/2, indicating that, quite unlike a bulk 3C-SiC crystal, the thin film is elastically isotropic.
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129
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Pan Y, Gao D, Yang W, Cho H, Zhan CG. Free energy perturbation (FEP) simulation on the transition states of cocaine hydrolysis catalyzed by human butyrylcholinesterase and its mutants. J Am Chem Soc 2007; 129:13537-43. [PMID: 17927177 DOI: 10.1021/ja073724k] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel computational protocol based on free energy perturbation (FEP) simulations on both the free enzyme and transition state structures has been developed and tested to predict the mutation-caused shift of the free energy change from the free enzyme to the rate-determining transition state for human butyrylcholinesterase (BChE)-catalyzed hydrolysis of (-)-cocaine. The calculated shift, denoted by DeltaDeltaG(1 --> 2), of such kind of free energy change determines the catalytic efficiency (kcat/KM) change caused by the simulated mutation transforming enzyme 1 to enzyme 2. By using the FEP-based computational protocol, the DeltaDeltaG(1 --> 2) values for the mutations A328W/Y332A --> A328W/Y332G and A328W/Y332G --> A328W/Y332G/A199S were calculated to be -0.22 and -1.94 kcal/mol, respectively. The calculated DeltaDeltaG(1 --> 2) values predict that the change from the A328W/Y332A mutant to the A328W/Y332G mutant should slightly improve the catalytic efficiency and that the change from the A328W/Y332G mutant to the A328W/Y332G/A199S mutant should significantly improve the catalytic efficiency of the enzyme for the (-)-cocaine hydrolysis. The predicted catalytic efficiency increases are supported by the experimental data showing that kcat/KM = 8.5 x 10(6), 1.4 x 10(7), and 7.2 x 10(7) min(-1) M(-1) for the A328W/Y332A, A328W/Y332G, and A328W/Y332G/A199S mutants, respectively. The qualitative agreement between the computational and experimental data suggests that the FEP simulations may provide a promising protocol for rational design of high-activity mutants of an enzyme. The general computational strategy of the FEP simulation on a transition state can be used to study the effects of a mutation on the activation free energy for any enzymatic reaction.
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130
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Liu Q, Wang C, Huang Y, Miao C, Gao D. Effects of Sel-Plex on rumen fermentation and
purine derivatives of urine in Simmental steers. JOURNAL OF ANIMAL AND FEED SCIENCES 2007. [DOI: 10.22358/jafs/75597/2007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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131
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Gao D, Zhan CG. Modeling effects of oxyanion hole on the ester hydrolysis catalyzed by human cholinesterases. J Phys Chem B 2007; 109:23070-6. [PMID: 16854005 DOI: 10.1021/jp053736x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular dynamics (MD) simulations and hydrogen bonding energy (HBE) calculations have been performed on the prereactive enzyme-substrate complexes (ES), transition states (TS1), and intermediates (INT1) for acetylcholinesterase (AChE)-catalyzed hydrolysis of acetylcholine (ACh), butyrylcholinesterase (BChE)-catalyzed hydrolysis of ACh, and BChE-catalyzed hydrolysis of (+)/(-)-cocaine to examine the protein environmental effects on the catalytic reactions. The hydrogen bonding of cocaine with the oxyanion hole of BChE is found to be remarkably different from that of ACh with AChE/BChE. Whereas G121/G116, G122/G117, and A204/A199 of AChE/BChE all can form hydrogen bonds with ACh to stabilize the transition state during the ACh hydrolysis, BChE only uses G117 and A199 to form hydrogen bonds with cocaine. The change of the estimated total HBE from ES to TS1 is ca. -5.4/-4.4 kcal/mol for AChE/BChE-catalyzed hydrolysis of ACh and ca. -1.7/-0.8 kcal/mol for BChE-catalyzed hydrolysis of (+)/(-)-cocaine. The remarkable difference of approximately 3 to 5 kcal/mol reveals that the oxyanion hole of AChE/BChE can lower the energy barrier of the ACh hydrolysis significantly more than that of BChE for the cocaine hydrolysis. These results help to understand why the catalytic activity of AChE against ACh is considerably higher than that of BChE against cocaine and provides valuable clues on how to improve the catalytic activity of BChE against cocaine.
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132
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Wu SG, Wang GT, Xi BW, Gao D, Nie P. Population dynamics and maturation cycle of Camallanus cotti (Nematoda: Camallanidae) in the Chinese hooksnout carp Opsariichthys bidens (Osteichthyes: Cyprinidae) from a reservoir in China. Vet Parasitol 2007; 147:125-31. [PMID: 17459589 DOI: 10.1016/j.vetpar.2007.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 03/16/2007] [Accepted: 03/19/2007] [Indexed: 11/25/2022]
Abstract
The seasonal population dynamics and maturation cycle of the nematode Camallanus cotti in the posterior intestine of Chinese hooksnout carp Opsariichthys bidens have been studied in the Danjiangkou Reservoir of the Hubei Province in central China from September 2004 to November 2005. The overall prevalence, mean abundance and intensity of C. cotti among fish sampled (n=700 fish) were 47%, 2.29+/-12.38 (+/-S.D.) and 1-307 (average 4.89+/-17.74), respectively. The overall sexual ratio of female to male nematodes (excluding L3 and L4 juveniles) was 1.17:1. Statistical results showed weakly positive correlations between fish length and the number of nematodes per host. The dynamics of infection of the nematode exhibited significant seasonal pattern in changes in mean abundance. A similar pattern was found for changes in nematode prevalence, although this was not statistically significant. Higher levels of infection were observed among fish sampled in summer months and the lower in the winter. Neither the prevalence nor the abundance of the parasite was significantly different between male and female hosts. The pattern of frequency distribution of the parasite in the host was found to be over-dispersed throughout the sampling period. In addition, studies on the development and maturation of the parasite in O. bidens revealed that development (maturation), recruitment of the next generation, and reproduction may be continuous year-round, although reproduction may peak during the winter.
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133
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Yang GF, Wang HB, Yang WC, Gao D, Zhan CG. Publisher’s Note: “Formation of supramolecular permethrin/β-cyclodextrin nanorods” [J. Chem. Phys. 125, 111104 (2006)]. J Chem Phys 2007. [DOI: 10.1063/1.2434948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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134
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He Y, Gao D, Zhang M. Expression of the nucleoprotein gene of rabies virus for use as a diagnostic reagent. J Virol Methods 2006; 138:147-51. [PMID: 17034869 DOI: 10.1016/j.jviromet.2006.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2006] [Revised: 08/07/2006] [Accepted: 08/29/2006] [Indexed: 11/28/2022]
Abstract
The nucleoprotein (N) gene of rabies virus CTN strain, was cloned, sequenced and expressed in Escherichia coli as a fusion with maltose binding protein (MBP). The antigenicity of this recombinant MBP-N fusion protein was examined by Western blotting and enzyme linked immunosorbent assay (ELISA). Subsequently, an indirect ELISA was developed to detect rabies specific antibody levels. Using sera from naive and vaccinated animals the ELISA results were compared with virus neutralizing antibodies detected by a rapid fluorescent focus inhibition test (RFFIT). Neutralizing titres by RFFIT were found to correlate well with the OD values in the ELISA (r=0.9436) and the sensitivity and specificity of the ELISA were shown to be 93.4 and 100%, respectively. The data indicate that the recombinant MBP-N fusion protein can be expressed and isolated straightforwardly and may be useful as a safe and abundant source of antigen to monitor seropositivity in vaccinated canines.
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135
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Yang GF, Wang HB, Yang WC, Gao D, Zhan CG. Formation of supramolecular permethrin/β-cyclodextrin nanorods. J Chem Phys 2006; 125:111104. [PMID: 16999459 DOI: 10.1063/1.2354079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics simulations along with scanning tunneling microscopy (STM) imaging demonstrate the formation of a novel type of nanorods, with a stable [permethrin(beta-CD)(2)](n) structure in which the host:guest ratio is 2:1 and n=21-27 giving a length of approximately 30.0-38.5 nm and an average diameter of approximately 1.5 nm, self-assembled from an inclusion complex composed of permethrin and biocompatible beta-cyclodextrin.
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136
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Cho H, Huang L, Hamza A, Gao D, Zhan CG, Tai HH. Role of glutamine 148 of human 15-hydroxyprostaglandin dehydrogenase in catalytic oxidation of prostaglandin E2. Bioorg Med Chem 2006; 14:6486-91. [PMID: 16828555 DOI: 10.1016/j.bmc.2006.06.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2006] [Revised: 06/03/2006] [Accepted: 06/08/2006] [Indexed: 11/30/2022]
Abstract
NAD+-dependent 15-hydroxyprostaglandin dehydrogenase (15-PGDH), a member of the short-chain dehydrogenase/reductase (SDR) family, catalyzes the first step in the catabolic pathways of prostaglandins and lipoxins. This enzyme oxidizes the C-15 hydroxyl group of prostaglandins and lipoxins to produce 15-keto metabolites which exhibit greatly reduced biological activities. A three-dimensional (3D) structure of 15-PGDH based on the crystal structures of the levodione reductase and tropinone reductase-II was generated and used for docking study with NAD+ coenzyme and PGE2 substrate. Three well-conserved residues among SDR family which correspond to Ser-138, Tyr-151, and Lys-155 of 15-PGDH have been shown to participate in the catalytic reaction. Based on the molecular interactions observed from 3D structure of 15-PGDH, we further propose that Gln-148 in 15-PGDH is important in properly positioning the 15-hydroxyl group of PGE2 by hydrogen bonding with the side-chain oxygen atom of Gln-148. This residue is found to be less conserved and replaceable by glutamyl, histidinyl, and asparaginyl residues in SDR family. Accordingly, site-directed mutagenesis of Gln-148 of 15-PGDH to alanine, glutamic acid, histidine, and asparagine (Q148A, Q148E, Q148H, and Q148N) was carried out. The activity of mutant Q148A was not detectable, whereas those of mutants Q148E, Q148H, and Q148N were comparable to or higher than the wild type. This indicates that the side-chain oxygen or nitrogen atom at position 148 of 15-PGDH plays an important role in anchoring C-15 hydroxyl group of PGE2 through hydrogen bonding for catalytic reaction.
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137
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Huang X, Yan W, Gao D, Tong M, Tai HH, Zhan CG. Structural and functional characterization of human microsomal prostaglandin E synthase-1 by computational modeling and site-directed mutagenesis. Bioorg Med Chem 2006; 14:3553-62. [PMID: 16439136 DOI: 10.1016/j.bmc.2006.01.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 01/06/2006] [Accepted: 01/06/2006] [Indexed: 11/26/2022]
Abstract
Microsomal prostaglandin (PG) E synthase-1 (mPGES-1) has recently been recognized as a novel, promising drug target for inflammation-related diseases. Functional and pathological studies on this enzyme further stimulate to understand its structure and the structure-function relationships. Using an approach of the combined structure prediction, molecular docking, site-directed mutagenesis, and enzymatic activity assay, we have developed the first three-dimensional (3D) model of the substrate-binding domain (SBD) of mPGES-1 and its binding with substrates prostaglandin H2 (PGH2) and glutathione (GSH). In light of the 3D model, key amino acid residues have been identified for the substrate binding and the obtained experimental activity data have confirmed the computationally determined substrate-enzyme binding mode. Both the computational and experimental results show that Y130 plays a vital role in the binding with PGH2 and, probably, in the catalytic reaction process. R110 and T114 interact intensively with the carboxyl tail of PGH2, whereas Q36 and Q134 only enhance the PGH2-binding affinity. The modeled binding structure indicates that substrate PGH2 interacts with GSH through hydrogen binding between the peroxy group of PGH2 and the -SH group of GSH. The -SH group of GSH is expected to attack the peroxy group of PGH2, initializing the catalytic reaction transforming PGH2 to prostaglandin E2 (PGE2). The overall agreement between the calculated and experimental results demonstrates that the predicted 3D model could be valuable in future rational design of potent inhibitors of mPGES-1 as the next-generation inflammation-related therapeutic.
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138
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Gao D, Zhan CG. Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase. Proteins 2006; 62:99-110. [PMID: 16288482 PMCID: PMC2882100 DOI: 10.1002/prot.20713] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Molecular dynamics (MD) simulations and quantum mechanical/molecular mechanical (QM/MM) calculations were performed on the prereactive enzyme-substrate complex, transition states, intermediates, and product involved in the process of human butyrylcholinesterase (BChE)-catalyzed hydrolysis of (-)-cocaine. The computational results consistently reveal a unique role of the oxyanion hole (consisting of G116, G117, and A199) in BChE-catalyzed hydrolysis of cocaine, compared to acetylcholinesterase (AChE)-catalyzed hydrolysis of acetylcholine. During BChE-catalyzed hydrolysis of cocaine, only G117 has a hydrogen bond with the carbonyl oxygen (O31) of the cocaine benzoyl ester in the prereactive BChE-cocaine complex, and the NH groups of G117 and A199 are hydrogen-bonded with O31 of cocaine in all of the transition states and intermediates. Surprisingly, the NH hydrogen of G116 forms an unexpected hydrogen bond with the carboxyl group of E197 side chain and, therefore, is not available to form a hydrogen bond with O31 of cocaine in the acylation. The NH hydrogen of G116 is only partially available to form a weak hydrogen bond with O31 of cocaine in some structures involved in the deacylation. The change of the estimated hydrogen-bonding energy between the oxyanion hole and O31 of cocaine during the reaction process demonstrates how the protein environment can affect the energy barrier for each step of the BChE-catalyzed hydrolysis of cocaine. These insights concerning the effects of the oxyanion hole on the energy barriers provide valuable clues on how to rationally design BChE mutants with a higher catalytic activity for the hydrolysis of (-)-cocaine.
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139
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Sun Y, Gao D, Liu Y, Huang J, Lessnick S, Tanaka S. IGF2 is critical for tumorigenesis by synovial sarcoma oncoprotein SYT-SSX1. Oncogene 2006; 25:1042-52. [PMID: 16247461 DOI: 10.1038/sj.onc.1209143] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Synovial sarcoma is an aggressive soft tissue tumor characterized by a specific chromosomal translocation between chromosome 18 and X. This translocation can generate a fusion transcript encoding SYT-SSX1, a transforming oncoprotein. We present evidence that SYT-SSX1 induces insulin-like growth factor II expression in fibroblast cells. SYT-SSX2, a fusion also frequently found in synovial sarcoma, is necessary for maintaining Igf2 expression in the synovial sarcoma cell line, and the increased IGF2 synthesis protects cells from anoikis and is required for tumor formation in vivo. We also found a loss of imprinting (LOI) for Igf2 in a limited number of primary synovial sarcomas despite demethylation of CpG dinucleotides critical for maintaining imprinting. These findings suggest that inhibition of the IGF2/IGF1-R signaling pathway may represent a significant therapeutic modality for treating synovial sarcoma.
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140
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Zhan CG, Gao D. Catalytic mechanism and energy barriers for butyrylcholinesterase-catalyzed hydrolysis of cocaine. Biophys J 2006; 89:3863-72. [PMID: 16319079 PMCID: PMC1366953 DOI: 10.1529/biophysj.105.070276] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The geometries of the transition states, intermediates, and prereactive enzyme-substrate complex and the corresponding energy barriers have been determined by performing hybrid quantum mechanical/molecular mechanical (QM/MM) calculations on butyrylcholinesterase (BChE)-catalyzed hydrolysis of (-)- and (+)-cocaine. The energy barriers were evaluated by performing QM/MM calculations with the QM method at the MP2/6-31+G* level and the MM method using the AMBER force field. These calculations allow us to account for the protein environmental effects on the transition states and energy barriers of these enzymatic reactions, showing remarkable effects of the protein environment on intermolecular hydrogen bonding (with an oxyanion hole), which is crucial for the transition state stabilization and, therefore, on the energy barriers. The calculated energy barriers are consistent with available experimental kinetic data. The highest barrier calculated for BChE-catalyzed hydrolysis of (-)- and (+)-cocaine is associated with the third reaction step, but the energy barrier calculated for the first step is close to the highest and is so sensitive to the protein environment that the first reaction step can be rate determining for (-)-cocaine hydrolysis catalyzed by a BChE mutant. The computational results provide valuable insights into future design of BChE mutants with a higher catalytic activity for (-)-cocaine.
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141
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Yang GF, Wang HB, Yang WC, Gao D, Zhan CG. Bioactive Permethrin/β-Cyclodextrin Inclusion Complex. J Phys Chem B 2006; 110:7044-8. [PMID: 16571020 DOI: 10.1021/jp056809l] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Permethrin is popularly used in a variety of therapeutic areas. However, the poor water solubility of permethrin seriously limits its wider clinical applications. The present study demonstrates that solubility of permethrin in aqueous solution can considerably increase in the presence of beta-cyclodextrin (beta-CD). Extensive experimental data along with computational modeling reveal the formation of stable permethrin/beta-CD inclusion complexes, including permethrin(beta-CD) and permethrin(beta-CD)2, through hydrophobic binding. Both permethrin(beta-CD) and permethrin(beta-CD)2 complexes coexisted in aqueous solution, and the ratio of the concentration of permethrin(beta-CD) complex to that of permethrin(beta-CD)2 complex was dependent on the concentration of beta-CD. The complexation of permethrin with beta-CD significantly improved the bioavailability of permethrin and, therefore, increased the bioactivity. The significant increase of the bioactivity of permethrin in the presence of beta-CD provides an effective approach to improve the practical use of permethrin in public health and agriculture.
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142
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Gao D, Cho H, Yang W, Pan Y, Yang G, Tai HH, Zhan CG. Computational Design of a Human Butyrylcholinesterase Mutant for Accelerating Cocaine Hydrolysis Based on the Transition-State Simulation. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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143
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Gao D, Cho H, Yang W, Pan Y, Yang G, Tai HH, Zhan CG. Computational design of a human butyrylcholinesterase mutant for accelerating cocaine hydrolysis based on the transition-state simulation. Angew Chem Int Ed Engl 2006; 45:653-7. [PMID: 16355430 PMCID: PMC2878656 DOI: 10.1002/anie.200503025] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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144
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Pan Y, Gao D, Yang W, Cho H, Yang G, Tai HH, Zhan CG. Computational redesign of human butyrylcholinesterase for anticocaine medication. Proc Natl Acad Sci U S A 2005; 102:16656-61. [PMID: 16275916 PMCID: PMC1283827 DOI: 10.1073/pnas.0507332102] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics was used to simulate the transition state for the first chemical reaction step (TS1) of cocaine hydrolysis catalyzed by human butyrylcholinesterase (BChE) and its mutants. The simulated results demonstrate that the overall hydrogen bonding between the carbonyl oxygen of (-)-cocaine benzoyl ester and the oxyanion hole of BChE in the TS1 structure for (-)-cocaine hydrolysis catalyzed by A199S/S287G/A328W/Y332G BChE should be significantly stronger than that in the TS1 structure for (-)-cocaine hydrolysis catalyzed by the WT BChE and other simulated BChE mutants. Thus, the transition-state simulations predict that A199S/S287G/A328W/Y332G mutant of BChE should have a significantly lower energy barrier for the reaction process and, therefore, a significantly higher catalytic efficiency for (-)-cocaine hydrolysis. The theoretical prediction has been confirmed by wet experimental tests showing an approximately (456 +/- 41)-fold improved catalytic efficiency of A199S/S287G/A328W/Y332G BChE against (-)-cocaine. This is a unique study to design an enzyme mutant based on transitionstate simulation. The designed BChE mutant has the highest catalytic efficiency against cocaine of all of the reported BChE mutants, demonstrating that the unique design approach based on transition-state simulation is promising for rational enzyme redesign and drug discovery.
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145
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Gao D, Subramaniam S, Fox RO, Hoffman DK. Objective decomposition of the stress tensor in granular flows. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 71:021302. [PMID: 15783319 DOI: 10.1103/physreve.71.021302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Indexed: 05/24/2023]
Abstract
A model for the stress tensor in granular flows [Volfson, Tsimring, and Aranson, Phys. Rev. Lett. 90, 254301 (2003)] is correctly generalized to an objective form that is independent of the coordinate system. The objective representation correctly models the isotropic and anisotropic parts of the stress tensor, whereas the original model for stress tensor components is dependent on the coordinate system. This general objective form of the model also relaxes the assumption in the original model that the principal axes of the granular stress tensor be coaxial with that of the "fluid" stress tensor. This generalization expands the applicability of the model to a wider class of granular flows. The objective representation is also useful in analyzing other models based on additive decomposition of the stress tensor in granular flows.
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146
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Gao D, Wagner AH, Fankhaenel S, Stojanovic T, Schweyer S, Panzner S, Hecker M. CD40 antisense oligonucleotide inhibition of trinitrobenzene sulphonic acid induced rat colitis. Gut 2005; 54:70-7. [PMID: 15591506 PMCID: PMC1774378 DOI: 10.1136/gut.2003.029587] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Revised: 05/17/2004] [Accepted: 06/03/2004] [Indexed: 01/23/2023]
Abstract
BACKGROUND CD154/CD40 interactions play a pivotal role both in humoral and cellular immune responses. Their involvement in the pathogenesis of chronic inflammatory bowel disease (IBD) has been revealed by increased expression of CD40 and CD154 in the inflamed mucosa of patients and the therapeutic effects of anti-CD154 antibodies in experimental colitis. Because of adverse side effects however, the use of such antibodies in patients with IBD may be limited. AIMS An alternative approach to blocking CD154/CD40 interactions by employing a CD40 antisense oligonucleotide (ODN) was explored. RESULTS After sequencing of the rat CD40 gene, five antisense ODNs were designed, of which one (rAS3) effectively downregulated CD40 expression in rat vascular smooth muscle cells as well as the subsequent changes in gene expression in response to CD40 stimulation. The therapeutic potency of rAS3 was evaluated in the 2,4,6-trinitrobenzene sulphonic acid (TNBS) induced colitis model of the rat. Single intracolonic injection of a liposomal formulation of rAS3 either prior to or post colitis induction markedly suppressed the inflammatory reaction in these animals monitored both macroscopically and microscopically over one week, while application of a scrambled control ODN had no such effects. Moreover, reverse transcription-polymerase chain reaction analyses revealed reduced expression of vascular cell adhesion molecule 1, interleukin 12 p40, and monocyte chemoatractive protein 1 in the inflamed mucosa, which in turn may have contributed to the decrease in leucocyte infiltration judged by immunohistochemistry. CONCLUSIONS These results suggest that CD40 antisense ODNs effectively interfere with CD154/CD40 interactions in vivo and, therefore, may provide a novel approach to the treatment of patients with chronic IBD.
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MESH Headings
- Animals
- CD40 Antigens/genetics
- CD40 Antigens/metabolism
- CD40 Ligand/metabolism
- Cells, Cultured
- Colitis/chemically induced
- Colitis/immunology
- Colitis/prevention & control
- Crohn Disease/chemically induced
- Crohn Disease/immunology
- Crohn Disease/prevention & control
- Drug Design
- Gene Expression Regulation/immunology
- Immunity, Mucosal
- Intestinal Mucosa/immunology
- Liposomes
- Male
- Muscle, Smooth, Vascular/immunology
- Muscle, Smooth, Vascular/metabolism
- Oligonucleotides, Antisense/administration & dosage
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/therapeutic use
- Rats
- Rats, Wistar
- Transfection
- Trinitrobenzenesulfonic Acid
- Vascular Cell Adhesion Molecule-1/metabolism
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147
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Morley N, Smolentsev S, Munipalli R, Ni MJ, Gao D, Abdou M. Progress on the modeling of liquid metal, free surface, MHD flows for fusion liquid walls. FUSION ENGINEERING AND DESIGN 2004. [DOI: 10.1016/j.fusengdes.2004.07.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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148
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Zhao X, Kinouchi Y, Yasuno E, Gao D, Iritani T, Morimoto T, Takeuchi M. A new method for noninvasive measurement of multilayer tissue conductivity and structure using divided electrodes. IEEE Trans Biomed Eng 2004; 51:362-70. [PMID: 14765709 DOI: 10.1109/tbme.2003.820403] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This paper outlines a new method for measuring multilayer tissue conductivity and structure by using divided electrodes, in which current electrodes are divided into several parts. Our purpose is to estimate the multilayer tissue structure and the conductivity distribution in a cross section of the local tissue by using bioresistance data measured noninvasively. The effect of the new method is assessed by computer simulations using a typical two-dimensional (2-D) model. In this paper, the conductivity distribution in the model is analyzed based on a finite difference method (FDM) and a steepest descent method (SDM). Simulation results show that the conductivity values of skin, fat, and muscle layers can be estimated with an error of less than 0.1%. When random noise at various levels is added to the measured resistance values, estimates of the conductivity values for skin, fat, and muscle layers are still reasonably precise: their root mean square errors are about 1.06%, 1.39%, and 1.61% for 10% noise. In a 2-D model, increasing the number of divided electrodes permits simultaneous estimates of tissue structure and conductivity distribution. Optimal configuration for divided electrodes is examined in terms of dividing pattern.
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149
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Zheng GD, Chen TB, Gao D, Luo W. Dynamic of lead speciation in sewage sludge composting. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2004; 50:75-82. [PMID: 15580997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A large-scale sewage sludge composting experiment was conducted to develop an understanding of changes that occur to Pb chemical speciation, distribution and bio-availability during the course of composting. The four-stage Tessier sequential extraction method was employed to investigate the dynamics of heavy metal Pb speciation (exchangeable, bound to carbonates, bound to Fe-Mn oxides, bound to organic matter and sulphides, residual) during the course of sewage sludge composting. The concentrations of the total Pb and the five Pb fractions concentrations were increased during the whole stage of compost. However, the percentages of Pb distribution with respect to total Pb were changed in the following manner: exchangeable, bound to Fe-Mn oxides and bound to carbonates Pb with respect to total Pb were increased, while the percentages of bound to organic matter and sulphides, and residual Pb with respect to total Pb were decreased during composting. The data showed that the quantity of Pb in the less toxic portion, such as consisting of organic matter and sulphides bound and residual Pb, was increased, and that the contamination and bio-availability of heavy metal Pb in sewage sludge was reduced during the composting process.
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150
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Proctor MH, Moore LL, Gao D, Cupples LA, Bradlee ML, Hood MY, Ellison RC. Television viewing and change in body fat from preschool to early adolescence: The Framingham Children's Study. Int J Obes (Lond) 2003; 27:827-33. [PMID: 12821969 DOI: 10.1038/sj.ijo.0802294] [Citation(s) in RCA: 261] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To prospectively examine the relation between television watching and body fat change in children from preschool to early adolescence. METHODS In a longitudinal study, 106 children were enrolled during preschool years (mean age 4.0 y) and followed into early adolescence (mean age 11.1 y). Parents completed an annual questionnaire on the child's television and video habits. Body mass index (BMI), triceps skinfolds, and sum of five skinfolds were recorded yearly at annual clinic visits. Longitudinal statistical analyses were carried out using mixed modeling procedures to control for potential confounding by a number of factors. RESULTS Television watching was an independent predictor of the change in the child's BMI, triceps, and sum of five skinfolds throughout childhood. Its effect was only slightly attenuated by controlling for the baseline body fat, level of physical activity (as measured repeatedly by Caltrac accelerometer), percent of calories from fat, total calorie intake, or the parents' BMI or education. By age 11, children who watched 3.0 h or more of television per day had a mean sum of skinfolds of 106.2 mm, compared with a mean sum of skinfolds of 76.5 mm for those who watched less than 1.75 h per day (P=0.007). Furthermore, the adverse effect of television viewing was worse for those children who were also sedentary or had a higher-fat diet. CONCLUSIONS Children who watched the most television during childhood had the greatest increase in body fat over time. Healthy lifestyle education designed to prevent obesity and its consequences should target television-watching habits of children.
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