Tris(pentafluoroethyl)trifluorophosphate ([FEP])-based ionic liquids have been widely applied in many fields. For better understanding the properties of [FEP]-based ionic liquids, the interactions between 1-hexyl-3-me...Tris(pentafluoroethyl)trifluorophosphate ([FEP])-based ionic liquids have been widely applied in many fields. For better understanding the properties of [FEP]-based ionic liquids, the interactions between 1-hexyl-3-methylimidazolium ([hmim])[FEP] and small molecules were investigated by molecular dynamics simulations in this work. The small molecules are water, methanol and dimethyl ether. The united-atom (UA) force fields were proposed for methanol and dimethyl ether based on AMBER force field. The densities, enthalpies of vaporization, excess molar properties, and diffusion coefficients of the mixtures were calculated, as well as the microscopic structures characterized by radial distribution functions. Both of the results of the excess energies and microscopic properties show that the strongest interaction is between [hmim][FEP] and dimethyl ether, whereas the interaction between [hmim][FEP] and water is the weakest. Moreover, [hmim][FEP] is more hydrophobic than [hmim] hexafluorophosphate ([PF6]), and the three solutes are mainly distributed around [FEP] anion.展开更多
The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.I...The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.展开更多
基金supported by the National Natural Science Foundation of China (21106146, 20976004, 20903098 and 21073194)
文摘Tris(pentafluoroethyl)trifluorophosphate ([FEP])-based ionic liquids have been widely applied in many fields. For better understanding the properties of [FEP]-based ionic liquids, the interactions between 1-hexyl-3-methylimidazolium ([hmim])[FEP] and small molecules were investigated by molecular dynamics simulations in this work. The small molecules are water, methanol and dimethyl ether. The united-atom (UA) force fields were proposed for methanol and dimethyl ether based on AMBER force field. The densities, enthalpies of vaporization, excess molar properties, and diffusion coefficients of the mixtures were calculated, as well as the microscopic structures characterized by radial distribution functions. Both of the results of the excess energies and microscopic properties show that the strongest interaction is between [hmim][FEP] and dimethyl ether, whereas the interaction between [hmim][FEP] and water is the weakest. Moreover, [hmim][FEP] is more hydrophobic than [hmim] hexafluorophosphate ([PF6]), and the three solutes are mainly distributed around [FEP] anion.
基金the National Natural Science Foundation of China(21003048,10974054,and 20933002)Shanghai PuJiang Program (09PJ1404000) for financial support XXY is also supported by "Scientific Research Foundation for Agricultural Machinery Bureau of Jiangsu Province (gxz10008)"CGJ is also supported by "the Fundamental Research Funds for the Central Universities"
文摘The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.
