Participation of Pseudomonas putida-derived methyl phenol（dmp） operon and Dmp R protein in the biodegradation of phenol or other harmful, organic, toxic pollutants was investigated at a molecular level. Documentatio...Participation of Pseudomonas putida-derived methyl phenol（dmp） operon and Dmp R protein in the biodegradation of phenol or other harmful, organic, toxic pollutants was investigated at a molecular level. Documentation documents that P. putida has Dmp R protein which positively regulates dmp operon in the presence of inducers; like phenols. From the operon,phenol hydroxylase encoded by dmp N gene, participates in degrading phenols after dmp operon is expressed. For the purpose, the 3-D models of the four domains from Dmp R protein and of the DNA sequences from the two Upstream Activation Sequences（UAS）present at the promoter region of the operon were demonstrated using discrete molecular modeling techniques. The best modeled structures satisfying their stereo-chemical properties were selected in each of the cases. To stabilize the individual structures, energy optimization was performed. In the presence of inducers, probable interactions among domains and then the two independent DNA structures with the fourth domain were perused by manifold molecular docking simulations. The complex structures were made to be stable by minimizing their overall energy. Responsible amino acid residues, nucleotide bases and binding patterns for the biodegradation, were examined. In the presence of the inducers, the biodegradation process is initiated by the interaction of phe50 from the first protein domain with the inducers. Only after the interaction of the last domain with the DNA sequences individually, the operon is expressed. This novel residue level study is paramount for initiating transcription in the operon; thereby leading to expression of phenol hydroxylase followed by phenol biodegradation.展开更多
针对宏-微机械手末端位姿、位置准确度的误差问题,受细胞学操纵子学说的启发,提出了基于操纵子模型的宏-微精密机械手运动的映射关系,研究精密机械手运动的影响因子和细胞学中的操纵子模型,分析机械手精密运动影响因子的影响方式和操纵...针对宏-微机械手末端位姿、位置准确度的误差问题,受细胞学操纵子学说的启发,提出了基于操纵子模型的宏-微精密机械手运动的映射关系,研究精密机械手运动的影响因子和细胞学中的操纵子模型,分析机械手精密运动影响因子的影响方式和操纵子模型的结构组成及其工作机理,结合操纵子模型的工作机理,分析宏-微机械手的控制系统,在此基础上,求解机械手精密运动控制系统的操纵子模型,考虑在几何因素的影响下,得出机械手末端位置在影响因子前后的误差值,通过基于粒子群算法的比例-积分-微分(Proportional-integral-differential,PID)控制器对误差结果进行优化,得出基于时间乘绝对误差积分准则(Time multiplied by the absolute error integral,ITAE)的粒子群算法(Particle swarm optimization,PSO)变化曲线和PID最优的控制参数。结论表明由映射关系推导出的控制系统能够满足一定的精度要求,并能进一步提高机械手的运动精度,为生物控制在机器人中进一步的创新研究提供了理论基础和依据。展开更多
Microbial redox reactions of inorganic sulfur compounds are one of the important reactions responsible for the recycling of this element to maintain the environmental sulfur balance. These reactions are carried out by...Microbial redox reactions of inorganic sulfur compounds are one of the important reactions responsible for the recycling of this element to maintain the environmental sulfur balance. These reactions are carried out by phylogenetically diverse set of microorganisms. The sulfur oxidizing gene cluster (sox) of thermo-neutrophilic bacterium Hydrogenobacter thermophilus consists of soxYZAXB. The bacterium shows optimal thiosulfate oxidation activity at 60°C. There are practically no reports regarding the structural biology of the sulfur oxidation proc- ess in this organism. In the present context, we employed homology modeling to construct the three dimensional structures of SoxY and SoxZ from Hydrogenobacter thermophilus. With the help of docking simulations we have identified the amino acid residues of these proteins in- volved in the interactions. The thermodynamics of the protein-protein interactions have also been analyzed. The probable biochemical mechanism of the binding of thiosulfate has been elucidated. Our study provides a rational framework to understand the molecular mechanism of the sulfur oxidation biochemistry.展开更多
基金deeply indebted to DST-PURSE program 2012–2015 going on in Department of Biochemistry and Biophysics, University of Kalyani for providing different equipments and essential infrastructural supportDeep gratitude is extended to DBT sponsored Bioinformatics Infrastructure Facility in the Department of Biochemistry and Biophysics, University of Kalyani for the necessary support
文摘Participation of Pseudomonas putida-derived methyl phenol（dmp） operon and Dmp R protein in the biodegradation of phenol or other harmful, organic, toxic pollutants was investigated at a molecular level. Documentation documents that P. putida has Dmp R protein which positively regulates dmp operon in the presence of inducers; like phenols. From the operon,phenol hydroxylase encoded by dmp N gene, participates in degrading phenols after dmp operon is expressed. For the purpose, the 3-D models of the four domains from Dmp R protein and of the DNA sequences from the two Upstream Activation Sequences（UAS）present at the promoter region of the operon were demonstrated using discrete molecular modeling techniques. The best modeled structures satisfying their stereo-chemical properties were selected in each of the cases. To stabilize the individual structures, energy optimization was performed. In the presence of inducers, probable interactions among domains and then the two independent DNA structures with the fourth domain were perused by manifold molecular docking simulations. The complex structures were made to be stable by minimizing their overall energy. Responsible amino acid residues, nucleotide bases and binding patterns for the biodegradation, were examined. In the presence of the inducers, the biodegradation process is initiated by the interaction of phe50 from the first protein domain with the inducers. Only after the interaction of the last domain with the DNA sequences individually, the operon is expressed. This novel residue level study is paramount for initiating transcription in the operon; thereby leading to expression of phenol hydroxylase followed by phenol biodegradation.
文摘针对宏-微机械手末端位姿、位置准确度的误差问题,受细胞学操纵子学说的启发,提出了基于操纵子模型的宏-微精密机械手运动的映射关系,研究精密机械手运动的影响因子和细胞学中的操纵子模型,分析机械手精密运动影响因子的影响方式和操纵子模型的结构组成及其工作机理,结合操纵子模型的工作机理,分析宏-微机械手的控制系统,在此基础上,求解机械手精密运动控制系统的操纵子模型,考虑在几何因素的影响下,得出机械手末端位置在影响因子前后的误差值,通过基于粒子群算法的比例-积分-微分(Proportional-integral-differential,PID)控制器对误差结果进行优化,得出基于时间乘绝对误差积分准则(Time multiplied by the absolute error integral,ITAE)的粒子群算法(Particle swarm optimization,PSO)变化曲线和PID最优的控制参数。结论表明由映射关系推导出的控制系统能够满足一定的精度要求,并能进一步提高机械手的运动精度,为生物控制在机器人中进一步的创新研究提供了理论基础和依据。
文摘Microbial redox reactions of inorganic sulfur compounds are one of the important reactions responsible for the recycling of this element to maintain the environmental sulfur balance. These reactions are carried out by phylogenetically diverse set of microorganisms. The sulfur oxidizing gene cluster (sox) of thermo-neutrophilic bacterium Hydrogenobacter thermophilus consists of soxYZAXB. The bacterium shows optimal thiosulfate oxidation activity at 60°C. There are practically no reports regarding the structural biology of the sulfur oxidation proc- ess in this organism. In the present context, we employed homology modeling to construct the three dimensional structures of SoxY and SoxZ from Hydrogenobacter thermophilus. With the help of docking simulations we have identified the amino acid residues of these proteins in- volved in the interactions. The thermodynamics of the protein-protein interactions have also been analyzed. The probable biochemical mechanism of the binding of thiosulfate has been elucidated. Our study provides a rational framework to understand the molecular mechanism of the sulfur oxidation biochemistry.
