64 results on '"Liang, Yu-He"'
Search Results
52. Preparation, crystallization and preliminary X-ray analysis of the methionine synthase (MetE) from Streptococcus mutans.
- Author
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Fu, Tian-Min, Zhang, Xiao-Yan, Li, Lan-Fen, Liang, Yu-He, and Su, Xiao-Dong
- Subjects
METHIONINE ,STREPTOCOCCUS mutans ,CRYSTALLIZATION ,PROTEINS ,ENZYMES ,X-ray diffraction ,CATALYSTS - Abstract
The Streptococcus mutans metE gene encodes methionine synthase (MetE), which catalyzes the direct transfer of a methyl group from methyltetrahydrofolate to homocysteine in the last step of methionine synthesis. metE was cloned into pET28a and the gene product was expressed at high levels in the Escherichia coli strain BL21 (DE3). MetE was purified to homogeneity using Ni
2+ -chelating chromatography followed by size-exclusion chromatography. Crystals of the protein were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.2 Å resolution. The crystal belongs to space group P21 , with unit-cell parameters a = 52.85, b = 99.48, c = 77.88 Å, β = 94.55°. [ABSTRACT FROM AUTHOR]- Published
- 2006
- Full Text
- View/download PDF
53. Crystallization and preliminary crystallographic studies of bar-headed goose fluoromethaemoglobin with inositol hexaphosphate.
- Author
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Wang, Huan-Chen, Liang, Yu-He, Zhu, Jia-Peng, and Lu, Guang-Ying
- Subjects
INOSITOL phosphates ,CRYSTALLIZATION ,CRYSTALLOGRAPHY ,CRYSTALS ,MOLECULES ,FLUORIMETRY - Abstract
Bar-headed goose fluoromethaemoglobin (fluoromet-Hb) complexed with inositol hexaphosphate (IHP) has been crystallized using PEG 6000 as precipitant. The crystal belongs to space group P2!1@, with unit-cell parameters a = 59.8, b = 72.0, c = 79.8 Å, β = 102.1°, and diffracts to 2.5 Å resolution. To prove the presence of IHP, the structure was determined by the molecular-replacement method. IHP was observed at the entrance to the central cavity between the N and C termini of two β subunits. [ABSTRACT FROM AUTHOR]
- Published
- 2000
- Full Text
- View/download PDF
54. C4-Dicarboxylates Sensing Mechanism Revealed by the Crystal Structures of DctB Sensor Domain
- Author
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Zhou, Yan-Feng, Nan, Beiyan, Nan, Jie, Ma, Qingjun, Panjikar, Santosh, Liang, Yu-He, Wang, Yiping, and Su, Xiao-Dong
- Subjects
- *
MICROBIAL genetics , *GENETICS , *MICROBIOLOGY , *BACTERIAL genetics - Abstract
Abstract: C4-dicarboxylates are the major carbon and energy sources during the symbiotic growth of rhizobia. Responses to C4-dicarboxylates depend on typical two-component systems (TCS) consisting of a transmembrane sensor histidine kinase and a cytoplasmic response regulator. The DctB–DctD system is the first identified TCS for C4-dicarboxylates sensing. Direct ligand binding to the sensor domain of DctB is believed to be the first step of the sensing events. In this report, the water-soluble periplasmic sensor domain of Sinorhizobium meliloti DctB (DctBp) was studied, and three crystal structures were solved: the apo protein, a complex with C4 succinate, and a complex with C3 malonate. Different from the two structurally known CitA family of carboxylate sensor proteins CitA and DcuS, the structure of DctBp consists of two tandem Per–Arnt–Sim (PAS) domains and one N-terminal helical region. Only the membrane-distal PAS domain was found to bind the ligands, whereas the proximal PAS domain was empty. Comparison of DctB, CitA, and DcuS suggests a detailed stereochemistry of C4-dicarboxylates ligand perception. The structures of the different ligand binding states of DctBp also revealed a series of conformational changes initiated upon ligand binding and propagated to the N-terminal domain responsible for dimerization, providing insights into understanding the detailed mechanism of the signal transduction of TCS histidine kinases. [Copyright &y& Elsevier]
- Published
- 2008
- Full Text
- View/download PDF
55. Protein preparation, crystallization and preliminary X-ray crystallographic analysis of Smu.1475c from caries pathogen Streptococcus mutans
- Author
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Zhou, Yan-Feng, Mi, Wei, Li, Lanfen, Zhang, Xiaoyan, Liang, Yu-He, Su, Xiao-Dong, and Wei, Shicheng
- Subjects
- *
PROTEINS , *STREPTOCOCCUS mutans , *DENTAL caries , *ESCHERICHIA coli , *CHROMATOGRAPHIC analysis , *PATHOGENIC microorganisms - Abstract
Abstract: The gene smu.1475c encodes a putative protein of 211 residues in Streptococcus mutans, a primary pathogen for human dental caries. In this work, smu.1475c was cloned into pET28a and expressed in good amount from the E. coli strain BL21 (DE3). Smu.1475c protein was purified to homogeneity in a two-step procedure of Ni2+ chelating and size exclusion chromatography. Crystals were obtained by hanging-drop vapor-diffusion method and diffracted to 2.7 Å resolution. The crystal belongs to orthorhombic space group P212121 with cell dimension of a =68.3 Å, b =105.9 Å, c =136.2 Å. The asymmetric unit is expected to contain four molecules with solvent content of 49.4%. [Copyright &y& Elsevier]
- Published
- 2006
- Full Text
- View/download PDF
56. Mir-30d increases intracellular survival of Helicobacter pylori through inhibition of autophagy pathway.
- Author
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Yang XJ, Si RH, Liang YH, Ma BQ, Jiang ZB, Wang B, and Gao P
- Subjects
- 3' Untranslated Regions, Autophagy-Related Protein 12 genetics, Autophagy-Related Protein 12 metabolism, Autophagy-Related Protein 5 genetics, Autophagy-Related Protein 5 metabolism, Autophagy-Related Proteins genetics, Autophagy-Related Proteins metabolism, Beclin-1 genetics, Beclin-1 metabolism, Cell Line, Tumor, Gastric Mucosa microbiology, Gastric Mucosa ultrastructure, Gene Expression Regulation, Neoplastic, Helicobacter Infections genetics, Helicobacter Infections microbiology, Host-Pathogen Interactions, Humans, Membrane Proteins genetics, Membrane Proteins metabolism, MicroRNAs genetics, Microbial Viability, Proto-Oncogene Proteins genetics, Proto-Oncogene Proteins metabolism, Signal Transduction, Stomach Neoplasms genetics, Stomach Neoplasms microbiology, Stomach Neoplasms ultrastructure, Time Factors, Transfection, Tumor Suppressor Proteins genetics, Tumor Suppressor Proteins metabolism, Up-Regulation, Vesicular Transport Proteins genetics, Vesicular Transport Proteins metabolism, Autophagy genetics, Gastric Mucosa metabolism, Helicobacter Infections metabolism, Helicobacter pylori metabolism, MicroRNAs metabolism, Stomach Neoplasms metabolism
- Abstract
Aim: To determine if mir-30d inhibits the autophagy response to Helicobacter pylori (H. pylori) invasion and increases H. pylori intracellular survival., Methods: The expression of mir-30d was detected by quantitative polymerase chain reaction (PCR), and autophagy level was examined by transmission electron microscopy, western blot, and GFP-LC3 puncta assay in human AGS cells and GES-1 cells. Luciferase reporter assay was applied to confirm the specificity of mir-30d regulation on the expression of several core molecules involved in autophagy pathway. The expression of multiple core proteins were analyzed at both the mRNA and protein level, and the intracellular survival of H. pylori after different treatments was detected by gentamicin protection assay., Results: Autophagy level was increased in AGS and GES-1 cells in response to H. pylori infection, which was accompanied by upregulation of mir-30d expression (P < 0.05, vs no H. pylori infection). In the two gastric epithelial cell lines, mimic mir-30d was found to repress the autophagy process, whereas mir-30d inhibitor increased autophagy response to H. pylori invasion. mir-30d mimic decreased the luciferase activity of wild type reporter plasmids carrying the 3' untranslated region (UTR) of all five tested genes (ATG2B, ATG5, ATG12, BECN1, and BNIP3L), whereas it had no effect on the mutant reporter plasmids. These five genes are core genes of autophagy pathway, and their expression was reduced significantly after mir-30d mimic transfection (P < 0.05, vs control cells without mir-30d mimic treatment). Mir-30d mimic transfection and direct inhibition of autophagy increased the intracellular survival of H. pylori in AGS cells., Conclusion: Mir-30d increases intracellular survival of H. pylori in gastric epithelial cells through inhibition of multiple core proteins in the autophagy pathway.
- Published
- 2016
- Full Text
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57. Protein preparation, crystallization and preliminary crystallographic studies of Bacillus subtilis glycinamide ribonucleotide transformylase.
- Author
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Liang YH, Liu XY, Wang J, and Li LF
- Subjects
- Crystallization, Crystallography, X-Ray, Solutions, Bacillus subtilis enzymology, Phosphoribosylglycinamide Formyltransferase chemistry
- Abstract
Glycinamide ribonucleotide transformylase (GART) catalyzes the transfer of a formyl group from formyl tetrahydrofolate (FTHF) to glycinamide ribonucleotide (GAR), which is an essential step in the de novo synthesis pathway of purines. In Bacillus subtilis, GART is encoded by the gene purN. In order to study the structure and function of B. subtilis GART, the purN gene was amplified, cloned into an expression vector and expressed in soluble form in Escherichia coli. The protein was purified to homogeneity and crystals suitable for X-ray data collection were obtained. These crystals diffracted to 2.5 A resolution and belonged to space group P3(1)21, with unit-cell parameters a = b = 95.5, c = 64.0 A.
- Published
- 2009
- Full Text
- View/download PDF
58. Preliminary X-ray crystallographic analysis of SMU.573, a putative sugar kinase from Streptococcus mutans.
- Author
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Zhou YF, Li LF, Yang C, Liang YH, and Su XD
- Subjects
- Amino Acid Sequence, Bacterial Proteins genetics, Bacterial Proteins isolation & purification, Conserved Sequence, Crystallography, X-Ray, Molecular Sequence Data, Molecular Weight, Peptide Fragments chemistry, Phosphotransferases (Alcohol Group Acceptor) genetics, Phosphotransferases (Alcohol Group Acceptor) isolation & purification, Sequence Alignment, Bacterial Proteins chemistry, Phosphotransferases (Alcohol Group Acceptor) chemistry, Streptococcus mutans enzymology
- Abstract
SMU.573 from Streptococcus mutans is a structurally and functionally uncharacterized protein that was selected for structural biology studies. Native and SeMet-labelled proteins were expressed with an N-His tag in Escherichia coli BL21 (DE3) and purified by Ni2+-chelating and size-exclusion chromatography. Crystals of the SeMet-labelled protein were obtained by the hanging-drop vapour-diffusion method and a 2.5 A resolution diffraction data set was collected using an in-house chromium radiation source. The crystals belong to space group I4, with unit-cell parameters a = b = 96.53, c = 56.26 A, alpha = beta = gamma = 90 degrees.
- Published
- 2008
- Full Text
- View/download PDF
59. Protein preparation, crystallization and preliminary X-ray crystallographic analysis of SMU.961 protein from the caries pathogen Streptococcus mutans.
- Author
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Gao XZ, Li LF, Su XD, Zhao X, and Liang YH
- Subjects
- Crystallography, X-Ray, Humans, Recombinant Proteins analysis, Streptococcus mutans pathogenicity, X-Ray Diffraction, Bacterial Proteins chemistry, Dental Caries microbiology, Recombinant Proteins chemistry, Streptococcus mutans chemistry
- Abstract
The smu.961 gene encodes a putative protein of 183 residues in Streptococcus mutans, a major pathogen in human dental caries. The gene was cloned into expression vector pET28a and expressed in a substantial quantity in Escherichia coli strain BL21 (DE3) with a His tag at its N-terminus. The recombinant protein SMU.961 was purified to homogeneity in a two-step procedure consisting of Ni2+-chelating and size-exclusion chromatography. Crystals suitable for X-ray diffraction were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.9 A resolution at beamline I911-3, MAX-II-lab, Sweden. The crystal belonged to space group C2, with unit-cell parameters a = 98.62, b = 73.73, c = 184.73 A, beta = 98.82 degrees.
- Published
- 2007
- Full Text
- View/download PDF
60. Protein preparation and preliminary X-ray crystallographic analysis of a putative glucosamine 6-phosphate deaminase from Streptococcus mutants.
- Author
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Hu GJ, Li LF, Li D, Liu C, Wei SC, Liang YH, and Su XD
- Subjects
- Aldose-Ketose Isomerases genetics, Aldose-Ketose Isomerases isolation & purification, Amino Acid Sequence, Bacterial Proteins chemistry, Bacterial Proteins isolation & purification, Conserved Sequence, Crystallization, Crystallography, X-Ray, Molecular Sequence Data, Polymerase Chain Reaction, Recombinant Proteins chemistry, Recombinant Proteins isolation & purification, Sequence Alignment, Aldose-Ketose Isomerases chemistry, Streptococcus mutans enzymology
- Abstract
The SMU.636 protein from Streptococcus mutans is a putative glucosamine 6-phosphate deaminase with 233 residues. The smu.636 gene was PCR-amplified from S. mutans genomic DNA and cloned into the expression vector pET-28a(+). The resultant His-tagged fusion protein was expressed in Escherichia coli and purified to homogeneity in two steps. Crystals of the fusion protein were obtained by the hanging-drop vapour-diffusion method. The crystals diffracted to 2.4 A resolution and belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 53.83, b = 82.13, c = 134.70 A.
- Published
- 2007
- Full Text
- View/download PDF
61. Crystallization and preliminary crystallographic analysis of D-alanine-D-alanine ligase from Streptococcus mutans.
- Author
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Lu YZ, Sheng Y, Li LF, Tang DW, Liu XY, Zhao X, Liang YH, and Su XD
- Subjects
- Amino Acid Sequence, Bacterial Proteins chemistry, Bacterial Proteins isolation & purification, Cloning, Molecular, Crystallization, Crystallography, X-Ray, Molecular Sequence Data, Peptide Fragments chemistry, Peptide Synthases isolation & purification, Recombinant Proteins chemistry, Recombinant Proteins isolation & purification, Peptide Synthases chemistry, Streptococcus mutans enzymology
- Abstract
D-Alanine-D-alanine ligase is encoded by the gene ddl (SMU_599) in Streptococcus mutans. This ligase plays a very important role in cell-wall biosynthesis and may be a potential target for drug design. To study the structure and function of this ligase, the gene ddl was amplified from S. mutans genomic DNA and cloned into the expression vector pET28a. The protein was expressed in soluble form in Escherichia coli strain BL21 (DE3). Homogeneous protein was obtained using a two-step procedure consisting of Ni2+-chelating and size-exclusion chromatography. Purified protein was crystallized and the cube-shaped crystal diffracted to 2.4 A. The crystal belongs to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 79.50, c = 108.97 A. There is one molecule per asymmetric unit.
- Published
- 2007
- Full Text
- View/download PDF
62. Purification, crystallization and preliminary X-ray analysis of the glucosamine-6-phosphate N-acetyltransferase from human liver.
- Author
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Wang J, Zhou YF, Li LF, Liang YH, and Su XD
- Subjects
- Amino Acid Sequence, Base Sequence, Chromatography, Gel, Cloning, Molecular, Crystallization, DNA Primers, Escherichia coli enzymology, Escherichia coli genetics, Glucosamine 6-Phosphate N-Acetyltransferase isolation & purification, Humans, Molecular Sequence Data, Molecular Weight, Peptide Fragments chemistry, Recombinant Proteins chemistry, Recombinant Proteins isolation & purification, Glucosamine 6-Phosphate N-Acetyltransferase chemistry, Liver enzymology
- Abstract
Glucosamine-6-phosphate N-acetyltransferase from human liver, which catalyzes the transfer of an acetyl group from acetyl coenzyme A (AcCoA) to the primary amine of D-glucosamine 6-phosphate to form N-acetyl-D-glucosamine 6-phosphate, was expressed in a soluble form from Escherichia coli strain BL21 (DE3). The protein was purified to homogeneity using Ni(2+)-chelating chromatography followed by size-exclusion chromatography. Crystals of the protein were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.6 A resolution. The crystals belonged to space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 50.08, c = 142.88 A.
- Published
- 2006
- Full Text
- View/download PDF
63. Preparation, crystallization and preliminary X-ray analysis of YjcG protein from Bacillus subtilis.
- Author
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Li D, Chan C, Liang YH, Zheng X, Li L, and Su XD
- Subjects
- Amino Acid Sequence, Bacillus subtilis genetics, Bacillus subtilis metabolism, Bacterial Proteins genetics, Bacterial Proteins isolation & purification, Bacterial Proteins metabolism, Cloning, Molecular, Crystallization, Crystallography, X-Ray, Escherichia coli genetics, Escherichia coli metabolism, Molecular Sequence Data, Sequence Alignment, Sequence Homology, Bacillus subtilis enzymology, Bacterial Proteins chemistry
- Abstract
Bacillus subtilis YjcG is a functionally uncharacterized protein with 171 residues that has no structural homologue in the Protein Data Bank. However, it shows sequence homology to bacterial and archaeal 2'-5' RNA ligases. In order to identify its exact function via structural studies, the yjcG gene was amplified from B. subtilis genomic DNA and cloned into the expression vector pET21-DEST. The protein was expressed in a soluble form in Escherichia coli and was purified to homogeneity. Crystals suitable for X-ray analysis were obtained that diffracted to 2.3 A and belonged to space group C2, with unit-cell parameters a = 99.66, b = 73.93, c = 61.77 A, beta = 113.56 degrees.
- Published
- 2005
- Full Text
- View/download PDF
64. Expression, purification and crystallization of an extended-spectrum beta-lactamase from Klebsiella oxytoca.
- Author
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Wu SW, Liang YH, and Su XD
- Subjects
- Crystallography, X-Ray, Plasmids metabolism, Polyethylene Glycols chemistry, Protein Structure, Tertiary, Solvents chemistry, Temperature, beta-Lactamases isolation & purification, beta-Lactamases metabolism, beta-Lactamases pharmacology, Klebsiella oxytoca enzymology, beta-Lactamases chemistry
- Abstract
OXY-1a is an extended-spectrum beta-lactamase from the conditional pathogenic bacterium Klebsiella oxytoca. OXY-1a is responsible for the antibiotic resistance of this pathogen. A soluble form of OXY-1a with a His tag at its C-terminus was overexpressed in Escherichia coli. The recombinant protein was purified and crystallized at room temperature using PEG 4000 as the main precipitant. Two crystal forms were obtained from the same growth conditions. One was orthorhombic, with crystals that diffracted to better than 1.9 A, while the other was tetragonal, with crystals that only diffracted to about 3.0 A. Complete data sets were collected from both crystal forms. The orthorhombic crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 46.54, b = 73.43, c = 84.56 A, while the tetragonal crystal has unit-cell parameters a = b = 73.72, c = 96.81 A. The asymmetric unit of the orthorhombic crystal is estimated to contain one OXY-1a molecule, giving a crystal volume per protein weight (V(M)) of 2.25 A(3) Da(-1) and a solvent content of 45%.
- Published
- 2004
- Full Text
- View/download PDF
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