A family of coupled map lattice （CML） models has been developed to simulate the evolutional mechanism of interactions of convection, diffusion, and dispersion in both weakly and strongly coupled cases. Not only cohe...A family of coupled map lattice （CML） models has been developed to simulate the evolutional mechanism of interactions of convection, diffusion, and dispersion in both weakly and strongly coupled cases. Not only coherent and turbulent properties as well as their relations, but also the transitional states between convection dominating, diffusion dominating and dispersion dominating are analyzed to demonstrate the essential characteristics of any state. Numerical results show that the models are capable of simulating both layered coupling and stochastic mechanism, and lead us to understand whether or not turbulence coherent structure is formed by modulation of wave packet. The duality of wave and particle characters of turbulence is illustrated in the numerical simulation; a sketch picture is given to explain the questions associated with the turbulent inverse cascade, which is the result of the mutual interactions among the physical factors of nonlinearity, dissipation and dispersion.展开更多
Interaction of a drug molecule with human serum albumin （HSA） is usually studied by fluorescence responses of the ligand or/and the single tryptophan residue （Trp-214） of the protein, but qualitative spectral info...Interaction of a drug molecule with human serum albumin （HSA） is usually studied by fluorescence responses of the ligand or/and the single tryptophan residue （Trp-214） of the protein, but qualitative spectral information may lead to multiple conclusions. In this work, we report a study on the interaction of hematoporphyrin monomethyl ether （HMME） with human serum albumin （HSA）, using the environment-sensitive spectra of HMME and reaction-induced fluorescence response of Trp-214. Particularly, the single kinetic parameter, the linear slope, was derived from the concentration-dependent absorbance or fluorescence of HMME in a certain solvent. A quantitative change in the slope at [HMME]/[HSA] = 1 ： 1 clearly demonstrated a specific binding of HMME to site I. The microenvironment in site I may be comparable to that in DMSO solvent, because of the similarity of the slope. Linear correlation of the fluorescence to the absorbance of HMME in site I indicates that the energy transfer is not responsible for Trp-214 fluorescence quenching but an electron transfer may be possible. In addition, much higher rate observed for the binding of HMME or 2-taurine-substituted HB （THB） with HSA than that of hypocrellin B was due to the electrostatic attraction under physiological condition.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 National Natural Science Foundation of China under Grant No.40535025
文摘A family of coupled map lattice （CML） models has been developed to simulate the evolutional mechanism of interactions of convection, diffusion, and dispersion in both weakly and strongly coupled cases. Not only coherent and turbulent properties as well as their relations, but also the transitional states between convection dominating, diffusion dominating and dispersion dominating are analyzed to demonstrate the essential characteristics of any state. Numerical results show that the models are capable of simulating both layered coupling and stochastic mechanism, and lead us to understand whether or not turbulence coherent structure is formed by modulation of wave packet. The duality of wave and particle characters of turbulence is illustrated in the numerical simulation; a sketch picture is given to explain the questions associated with the turbulent inverse cascade, which is the result of the mutual interactions among the physical factors of nonlinearity, dissipation and dispersion.
基金National Natural Science Foundation of China(Grant No.20872144)
文摘Interaction of a drug molecule with human serum albumin （HSA） is usually studied by fluorescence responses of the ligand or/and the single tryptophan residue （Trp-214） of the protein, but qualitative spectral information may lead to multiple conclusions. In this work, we report a study on the interaction of hematoporphyrin monomethyl ether （HMME） with human serum albumin （HSA）, using the environment-sensitive spectra of HMME and reaction-induced fluorescence response of Trp-214. Particularly, the single kinetic parameter, the linear slope, was derived from the concentration-dependent absorbance or fluorescence of HMME in a certain solvent. A quantitative change in the slope at [HMME]/[HSA] = 1 ： 1 clearly demonstrated a specific binding of HMME to site I. The microenvironment in site I may be comparable to that in DMSO solvent, because of the similarity of the slope. Linear correlation of the fluorescence to the absorbance of HMME in site I indicates that the energy transfer is not responsible for Trp-214 fluorescence quenching but an electron transfer may be possible. In addition, much higher rate observed for the binding of HMME or 2-taurine-substituted HB （THB） with HSA than that of hypocrellin B was due to the electrostatic attraction under physiological condition.
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.
