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Homology modeling and docking studies of IscS from extremophile Acidithiobacillus ferrooxidans

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Journal of Central South University of Technology 2007年第6期14卷 742-749页

作者：刘元东丁建南邱冠周王海东 School of Resources Processing and bioengineering Central South University

The gene iscS-3 from ,4cidithiobacillus 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 Glul05, Glu79, Ser203 and Hisl80 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.

关键词： bioleaching IscS Acidithiobacillus ferrooxidans homology modeling molecular dynamics docking pyridoxal 5'-phosphate(PLP) cysteine

Bioleaching and electrochemical properties of chalcopyrite by pure and mixed culture of Leptospirillum ferriphilum and Acidthiobacillus thiooxidans

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Journal of Central South University 2013年第1期20卷 178-183页

作者：顾帼华胡可婷李双棵 School of Minerals Processing and bioengineering Central South University

The bioleaching of chalcopyrite was investigated using a pure and mixed culture consisting of iron-oxidizing Leptospirillum ferriphilum （L. ferriphilum） and sulfur-oxidizing Acidthiobacillus thiooxidans （.4. thiooxidans）. The electrochemical tests were conducted to investigate the bioleaching behavior of chalcopyrite by various bacteria. Bioleaching efficiency of chalcopyrite in mixed culture is higher than that in the pure culture of *** alone. The iron-oxidizing *** plays a dominant role during bioleaching of chalcopyrite in the mixed culture of L. ferriphilum and A. thiooxidans. During bioleaching, certain values of redox potential are beneficial to the decomposition of chalcopyrite. Jarosite and sulfur are observed as products of bioleaching. The addition of A. thiooxidans during leaching by L. ferriphilum can change the electrochemical control steps of leaching. The corrosion current density is substantially promoted in the culture involving bacteria, especially in the mixed culture.

关键词： chalcopyrite bioleaching electrochemistry Leptospirillumferriphilum Acidthiobacillus thiooxidans

Exploring binding mode for styrylquinoline HIV-1 integrase inhibitors using comparative molecular field analysis and docking studies

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Acta Pharmacologica Sinica 2004年第7期25卷 104-112页

作者： Xiao-hui MA, Xiao-yi ZHANG, Jian-jun TAN, Wei-zu CHEN, Cun-xin WANG2 College of LifeScience and bioengineering, Beijing University of Technology, Beijing 100022, China College of Life Science and bioengineering Beijing University of Technology 北京 100022

AIM: To understand pharmacophore properties of styrylquinoline derivatives and to design inhibitors of HIV-1 integrase. METHODS: Comparative molecular field analysis (CoMFA) was performed to analyze three-dimen- sional quantitative structure-activity relationship (3D-QSAR) of styrylquinoline derivatives. Thirty-eight compounds were randomly divided into a training set of 28 compounds and a test set of 10 compounds. The stability of 3D- QSAR models was proved by the analysis of cross-validated and non-cross-validated methods. Moreover, the binding mode of these compounds and integrase was constructed by AutoDock program. RESULTS: The CoMFA model of the training compounds was reasonably predicted with cross-validated coefficient (q2) and conventional (r2) values (up to 0.696 and 0.754). Then the model was validated by the test set. The resulting CoMFA maps visualized structural requirements for the biological activity of these inhibitors. Docking results showed that a carboxyl group at C-7 and a hydroxyl group at C-8 in the quinoline subunit, bound closely to the divalent metal cofactor (Mg2+) around the integrase catalytic site. Moreover, there is a linear correlation between the binding energy of the inhibitors with integrase and their inhibitory effect. CONCLUSIONS: The present study indicated that the CoMFA model together with docking results could give us helpful hints for drug design as well as interpre- tation of the binding affinity between these inhibitors and integrase.

关键词： HIV integrase inhibitors quinolines comparative molecular field analysis AutoDock

Synthesis, characterization of monodispersed MgO microspheres and thermal decomposition kinetics of its precusor

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Journal of Central South University 2014年第9期21卷 3463-3469页

作者：袁培郭雅坤谷昆泓肖奇 School of Resources Processing and bioengineering Central South University

Monodispersed MgO microspheres were successfully synthesized by a simple solvothermal method using PEG-400 as solvent. The samples were characterized by X-ray diffraction(XRD) and scanning electron microscopy(SEM). The results reveal that the precusor was monoclinic Mg5(CO3)4(OH)2·4H2O and composed of nanosheets with the thickness of about 250 nm. By calcining the precusor at 500 °C for 5 min, cubic MgO with similar morphology was obtained. According to the SEM images, it is found that the volume ratio of PEG-400 to deionized water is considered as a crucial factor in the evolution of the morphology. Based on the SEM images obtained under different experimental conditions, a possible growth mechanism which involves self-assembly process was proposed. The thermal decomposition process of MgO precusor was studied by thermogravimetry-differential thermogravimetry(TG-DTG) at different heating rates in air. Thermal analysis kinetics results show that the most probale mechanism models of MgO precusor are An and D3, respectively. In addition, isothermal prediction was studied to quantitatively characterize the thermal decomposition process.

关键词： PEG-400 monodisphersed MgO thermal decomposition kinetics isothermal prediction

Synthesis of N,N-diethyl dodecyl amine and its flotation properties on bauxite

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Journal of Central South University of Technology 2008年第2期15卷 188-192页

作者：曹学锋张丽敏胡岳华刘长淼欧阳魁 School of Resources Processing and bioengineering Central South University

N, N-diethyl dodecyl amine（DEN12） was synthesized from dodecyl amine, formic acid and acetic aldehyde. The collecting property of DENI2 on diaspore, kaolinite and illite was investigated by flotation test and infrared spectrum. The results show that in the presence of 2.0× 10^-4 mol/L DEN12, the recoveries of kaolinite and illite are all higher than 78% and the recovery of diaspore is 50% in the pH range of 5.5-6.0. The mass ratio of A1203 to SiO2 in concentrate obtained from separation artificial mixture is higher than 10, suggesting that DEN12 can be used as a collector to separate the aluminosilicates from diaspore in bauxite ores at the pulp pH below 8. The measurements of the infrared spectrum approve that the action between aluminosilicates and tertiary amine collector is strong electrostatic adsorption and that of diaspore is weak electrostatic adsorption.

关键词： reverse flotation electrostatic adsorption infrared spectrum kaolinite illite diaspore N, N-diethyl-N-dodecyl amine(DENI2)

Bioleaching of sphalerite by Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans cultured in 9K medium modified with pyrrhotite

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Journal of Central South University of Technology 2008年第4期15卷 503-507页

作者：陈松邱冠周覃文庆蓝卓越 School of Resource Processing and bioengineering Central South University

Elective culture of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans in 9K medium modified with pyrrhotite was *** of flotation concentrate of sphalerite by the selected bacteria was carried *** results show that the microorganisms cultured by pyrrhotite are a mixture of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans,of which the capability to oxidize ferrous to ferric irons is enhanced by the high mass ratio of Fe to S in *** pyrrhotite samples were separated into various parts with corresponding S/Fe ratios by magnetic separation and were used to culture the elective bacteria as the *** association of the cultures could provide a more rapid and complete oxidation of sphalerite than that of bacteria cultivated by conventional methods.

关键词： bioleaching pyrrhotite elective culture sphalerite

FTIR analysis of adsorption of poly diallyl-dimethyl-ammonium chloride on kaolinite

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Journal of Central South University of Technology 2008年第3期15卷 373-377页

作者：孙伟刘文莉胡岳华 School of Resource Processing and bioengineering Central South University

The flocculation behavior of ultrafine kaolinite suspension was investigated through settlement tests and FTIR method was employed to probe the adsorption mechanism of flocculant on kaolinite. The results show that the maximum settling rate of kaolinite occurs at pH value of 3.33,which is close to the point of zero charge(PZC) of kaolinite (3.5). This result is in good agreement with the double electric layer theory. Kaolinite suspension reaches the largest settling rate at a low concentration of 39 g/t for poly diallyl-dimethyl-ammonium chloride(PDADMA) flocculant,whereas for polyacrylamides(PAM) the dosage is required to be 500 g/t. When macromolecule polymer is adsorbed on surface,kaolinite particles may be flocculant due to the bridging effect. There are cation flocculant characteristic bands on the spectrum of kaolinite but no obvious shifting. Thus,the adsorption of poly diallyl-dimethyl-ammonium chloride on kaolinite surface is physical adsorption.

关键词： adsorption FTIR spectrum kaolinite poly diallyl-dimethyl-ammonium chloride electrostatic flocculant

Removal of phosphorus from iron ores by chemical leaching

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Journal of Central South University of Technology 2006年第6期13卷 673-677页

作者：金勇士姜涛杨永斌李骞李光辉郭宇峰 School of Minerals Processing and bioengineering Central South University

Alkali-leaching and acid-leaching were proposed for the dephosphorization of Changde iron ore, which contains an average of 1.12% for phosphorus content. Sodium hydroxide, sulfuriced, hydrochloric and nitric acids were used for the preparation of leach solutions. The results show that phosphorus occurring as apatite phase could be removed by alkali-leaching, but those occurring in the iron phase could not. Sulfuric acid is the most effective among the three kinds of acid. 91.61% phosphorus removal was attained with 1% sulfuric acid after leaching for 20 rain at room temperature. Iron loss during acid-leaching can be negligible, which was less than 0.25%.The pH value of solution after leaching with1% sulfuric acid was about 0.86, which means acid would not be exhausted during the process and it could be recycled, and the recycle of sulfuric acid solution would make the dephosphorization process more economical.

关键词： iron ore dephosphorization acid-leaching alkali-leaching

Mathematical models and expert system for grate-kiln process of iron ore oxide pellet *** Ⅱ:Rotary kiln process control

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Journal of Central South University 2012年第6期19卷 1724-1727页

作者：范晓慧王祎陈许玲 School of Minerals Processing and bioengineering Central South University

Rotary kiln process for iron ore oxide pellet production is hard to detect and *** of one-dimensional model of temperature field in rotary kiln was *** the results lay a solid foundation for online *** of kiln process control expert system was presented,with maximum temperature of pellet and gas temperature at the feed end as control cores,and interval estimate as control *** was developed and put into application in a pellet *** results show that control guidance of this system is accurate and *** production application for nearly one year,the compressive strength and first grade rate of pellet are increased by 86 N and 2.54%,respectively,while FeO content is 0.05% *** system can reveal detailed information of real time kiln process,and provide a powerful tool for online control of pellet production.

关键词： mathematical model expert system one-dimensional temperature field rotary kiln iron ore oxide pellet