Yuan-dong LIU

Central South University, Ch’ang-sha-shih, Hunan, China

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Publications (8)1.49 Total impact

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    ABSTRACT: Four arsenic-resistance genes (arsB, arsC, arsH, arsR) have been discovered in Acidithiobacillus ferrooxidans. Their gene sequences have been identified and three different arsenic-resistance mechanisms have been elucidated. However, the function of the arsH gene in At. ferrooxidans remains unclear. In order to evaluate the function of the arsH gene, we cloned it and expressed it in Escherichia coli. The protein was purified and its relative molecular mass was determined by SDS-PAGE (Sodium dodecyl sulfate-polyacrylamide gel electrophoresis). The results indicated that the relative molecular mass of the purified ArsH was approximately 29 kDa. The purified protein ArsH from E.coli BL21 was a flavoprotein that oxidized in vitro NADPH with an optimal pH of 6.4.
    Transactions of Nonferrous Metals Society of China. 01/2010;
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    ABSTRACT: The putative thiol-disulphide interchange protein, DsbG, is involved in the formation and rearrangement of disulphide bonds in Acidithiobacillus ferrooxidans but its exact role is so far unclear. The gene encoding DsbG from A. ferrooxidans ATCC 23270 was cloned and expressed in Escherichia coli BL21 (DE3). The protein was purified by one-step affinity chromatography. The scRNaseA could be rescued to 89% of the native RNaseA activity by using the purified DsbG of A. ferrooxidans. This characteristic is unique and different from that of DsbG from E. coli, which does not catalyse the oxidative refolding of RNaseA in vitro. Site-directed mutagenesis of the DsbG protein revealed that Cys119A and Cys122A do not possess the disulphide isomerization activity, indicating Cys119 and Cys122 are catalytic residues and play a crucial role in disulphide isomerization.
    ScienceAsia 01/2010; 36100(36):100-104. · 0.40 Impact Factor
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    ABSTRACT: The superoxide dismutase(SOD) from Acidithiobacillus ferrooxidans may play an important role in its tolerance to the extremely toxic and oxidative environment of bioleaching. This gene was cloned and then successfully expressed in Escherichia coli. The expressed protein was finally purified by one-step affinity chromatography to homogeneity and observed to be dimer according to SDS-PAGE and MALDI-TOF-MS. The metal content determination and optical spectra results of the recombinant protein confirmed that the protein was an iron-containing superoxide dismutase. Molecular modeling for the protein revealed that the iron atom was ligated by His26, His75, Asp158 and His162.
    Transactions of Nonferrous Metals Society of China - TRANS NONFERROUS METAL SOC CH. 01/2008; 18(6):1361-1366.
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    ABSTRACT: A cysteine desulfurase protein, IscS, was encoded by the operon iscSUA in Acidithiobacillus ferrooxidans. The gene of IscS from Acidithiobacillus ferrooxidans ATCC 23270 was cloned and expressed in Escherichia coli. The protein was purified by one-step affinity chromatography to homogeneity. The final protein yield after affinity chromatography was 12.9%. The enzyme was characterized for thermal stability, pH and kinetic parameters. The molecular mass of recombinant IscS was 46 ku by SDS-PAGE. The optimum pH was 8.0−8.5. The enzyme had a temperature optimum at 30°C and was relatively stable at 40°C, with 67% loss of activity. 1,5-I-AEDANS significantly inhibited IscS activity. Kinetic parameters Km and Vmax were found to be 0.11 mmol/L and 2.57 μmol/(L·min).
    Transactions of Nonferrous Metals Society of China - TRANS NONFERROUS METAL SOC CH. 01/2008; 18(6):1450-1457.
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    ABSTRACT: The gene iscS-2 from extremophile Acidithiobacillus ferrooxidans may play a crucial role in nitrogenase maturation. To investigate the protein encoded by this gene, a reliable integral three-dimensional molecular structure was built. The obtained structure was further used to search binding sites, carry out the flexible docking with cofactor pyridoxal 5′-phosphate(PLP) and substrate cysteine, and identify its key residues. The docking results of PLP reveal that the residues of Lys203, His100, Thr73, Ser200, His202, Asp177 and Gln180 have large interaction energies and/or hydrogen bonds fixation with PLP. The docking results of cysteine show that the amino group in cysteine is very near His100, Lys203 and PLP, and the interaction energies for cysteine with them are very big. These identified residues are in line with the experimental facts of NifS from other sources. Moreover, the four residues of Asn152, Val179, Ala102 and Met148 in the PLP docking and the two residues of Lys208 and Ala102 in the cysteine docking also have large interaction energies, which are fitly conserved in NifS from all kinds of sources but have not been identified before. According to these results, this gene encodes NifS protein, and the substrate cysteine can be effectively recruited into the active site. Furthermore, all of the above detected key residues are directly responsible for the binding and/or catalysis of PLP and cysteine.
    Transactions of Nonferrous Metals Society of China. 01/2008;
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    ABSTRACT: The gene iscS-3 from Acidithiobacillus ferrooxidans may play a central role in the delivery of sulfur to a variety of metabolic pathways in this organism. For insight into the sulfur metabolic mechanism of the bacteria, an integral three-dimensional (3D) molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and further used to search bind sites, carry out flexible docking with cofactor pyridoxal 5′-phosphate(PLP) and substrate cysteine and hereby detect its key residues. Through these procedures, the detail conformations of PLP-IscS(P-I) and cysteine-PLP-IscS(C-P-I) complexes were obtained. In P-I complex, the residues of Lys208, His106, Thr78, Ser205, His207, Asp182 and Gln185 have large interaction energies and/or hydrogen bonds fixation with PLP. In C-P-I complex, the amino group in cysteine is very near His106, Lys208 and PLP, the interaction energies for cysteine with them are very high. The above results are well consistent with those experimental facts of the homologues from other sources. Interestingly, the four residues of Glu105, Glu79, Ser203 and His180 in P-I docking and the residue of Lys213 in C-P-I docking also have great interaction energies, which are fitly conservation in IscSs from all kinds of sources but have not been identified before. From these results, this gene can be confirmed at 3D level to encode the iron-sulfur cluster assembly protein IscS and subsequently play a sulfur traffic role. Furthermore, the substrate cysteine can be presumed to be effectively recruited into the active site. Finally, the above detected key residues can be conjectured to be directly responsible for the bind and/or catalysis of PLP and cysteine.
    Journal of Central South University of Technology 11/2007; 14(6):742-749. · 0.36 Impact Factor
  • Yuan-dong Liu, Hai-dong Wang, Guan-zhou Qiu
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    ABSTRACT: The gene sod in Acidithiobacillus ferrooxidans may play a crucial role in its tolerance to the extremely acidic, toxic and oxidative environment of bioleaching. For insight into the anti-toxic mechanism of the bacteria, a three-dimensional (3D) molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and its key residues were further detected by evolutionary trace analysis. Through these procedures, some trace residues were identified and spatially clustered. Among them, the residues of Asn38, Gly103 and Glu161 are randomly scattered throughout the mapped structure; interestingly, the other residues are all distinctly clustered in a subgroup near Fe atom. From these results, this gene can be confirmed at 3D level to encode the Fe-depending superoxide dismutase and subsequently play an anti-toxic role. Furthermore, the detected key residues around Fe binding site can be conjectured to be directly responsible for Fe binding and catalytic function.
    Journal of Central South University of Technology 09/2007; 14(5):612-618. · 0.36 Impact Factor
  • Hai-dong Wang, Yuan-dong Liu
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    ABSTRACT: To address the problems that input variables should be reduced as much as possible and explain output variables fully in building neural network model of complicated system, a variable selection method based on cluster analysis was investigated. Similarity coefficient which describes the mutual relation of variables was defined. The methods of the highest contribution rate, part replacing whole and variable replacement are put forwarded and deduced by information theory. The software of the neural network based on cluster analysis, which can provide many kinds of methods for defining variable similarity coefficient, clustering system variable and evaluating variable cluster, was developed and applied to build neural network forecast model of cement clinker quality. The results show that all the network scale, training time and prediction accuracy are perfect. The practical application demonstrates that the method of selecting variables for neural network is feasible and effective.
    Journal of Central South University of Technology 01/2004; 11(2):220-224. · 0.36 Impact Factor