In a genome the set of proteins are formed by duplication and combination of domain superfamilies. P-loop containing nucleotide triphosphate （NTP） hydrolases superfamily is massively duplicated and has the most diff...In a genome the set of proteins are formed by duplication and combination of domain superfamilies. P-loop containing nucleotide triphosphate （NTP） hydrolases superfamily is massively duplicated and has the most different partner superfamilies among archaea, bacteria and eukarya, Here, we study the distributions of duplication and combination of p-loop containing NTP hydrolases superfamily in 169 completed genomes. When the total number of domains in a genome is larger, duplication and combination partners of p-loop conraining NTP hydrolases are more. This phenomenon is more obvious in metazoa. The distributions of abundance and corn bination of partners relate to the functions of the protein. Those distributions in metazoa are very different from those in other kingdoms because of complexity of metazoa. Finally the relationship between duplication and combination of p-loop containing NTP hydrolases superfamily in different genomes is described. It fits a power law.展开更多
In order to illustrate the ion transport mechanism of chloride channel（Cl C） protein,a type of Cl C protein,Cl C-ec1,from Escherichia coli is embedded into an explicit membranewater system by using software VMD. The...In order to illustrate the ion transport mechanism of chloride channel（Cl C） protein,a type of Cl C protein,Cl C-ec1,from Escherichia coli is embedded into an explicit membranewater system by using software VMD. Then a parallel molecular dynamics（MD） simulation is employed to equilibrate the Cl C-ec1 structure for 27.5 ns at temperature 298.15 K. Based on this equilibrated structure,we compute the channel geometric size variation and electrostatic potential distribution along the channel. Meanwhile,Cl^- transport process is simulated using oriented random walk method under variable external potential. The simulation result shows that Cl^- transport velocity depends on the width of the narrowest channel region. Mutation of negative glutamate E148 can produce positive potential,which is beneficial for Cl^- transport,around external Cl^- binding region in the channel. The simulated current-voltage curves about Cl^- transporting in Cl C-ec1 protein agree with Jayaram＇s experimental results.展开更多
基金Supported by the National Natural Science Foun-dation of China (10374072)
文摘In a genome the set of proteins are formed by duplication and combination of domain superfamilies. P-loop containing nucleotide triphosphate （NTP） hydrolases superfamily is massively duplicated and has the most different partner superfamilies among archaea, bacteria and eukarya, Here, we study the distributions of duplication and combination of p-loop containing NTP hydrolases superfamily in 169 completed genomes. When the total number of domains in a genome is larger, duplication and combination partners of p-loop conraining NTP hydrolases are more. This phenomenon is more obvious in metazoa. The distributions of abundance and corn bination of partners relate to the functions of the protein. Those distributions in metazoa are very different from those in other kingdoms because of complexity of metazoa. Finally the relationship between duplication and combination of p-loop containing NTP hydrolases superfamily in different genomes is described. It fits a power law.
基金Supported by the National Natural Science Foundation of China(11304123)the Scientific Research Foundation of Jianghan University(2013016)
文摘In order to illustrate the ion transport mechanism of chloride channel（Cl C） protein,a type of Cl C protein,Cl C-ec1,from Escherichia coli is embedded into an explicit membranewater system by using software VMD. Then a parallel molecular dynamics（MD） simulation is employed to equilibrate the Cl C-ec1 structure for 27.5 ns at temperature 298.15 K. Based on this equilibrated structure,we compute the channel geometric size variation and electrostatic potential distribution along the channel. Meanwhile,Cl^- transport process is simulated using oriented random walk method under variable external potential. The simulation result shows that Cl^- transport velocity depends on the width of the narrowest channel region. Mutation of negative glutamate E148 can produce positive potential,which is beneficial for Cl^- transport,around external Cl^- binding region in the channel. The simulated current-voltage curves about Cl^- transporting in Cl C-ec1 protein agree with Jayaram＇s experimental results.
