The influence of water on protein conformation was investigated by simulating the molecular dynamics of a model protein lysozyme in different water systems.The lysozyme-water system with TIP3P water model and lysozyme...The influence of water on protein conformation was investigated by simulating the molecular dynamics of a model protein lysozyme in different water systems.The lysozyme-water system with TIP3P water model and lysozyme-water cluster system with six-ring water model were evaluated.In addition,the radial distribution function of solvent around lysozyme was calculated.It is found that the distribution of water molecules around lysozyme is similar to that of water clusters.The analyses of dihedral angles and disulfide bonds of lysozyme show that the conformation of lysozyme is severely damaged in the lysozyme-water cluster system compared with that in the lysozyme-water system.This difference can be attributed to the formation of larger number of intermolecular hydrogen bonds between lysozyme and water cluster.It is in agreement with the analysis that water clusters can change the degree of denaturation in the process of heat denaturation of lysozyme.展开更多
We propose a monomer adsorption model, in which only the monomers are allowed to diffuse and adsorb onto other clusters. By means of the generalized rate equation we investigate the kinetic behavior of the system with...We propose a monomer adsorption model, in which only the monomers are allowed to diffuse and adsorb onto other clusters. By means of the generalized rate equation we investigate the kinetic behavior of the system with a special rate kernel. For the system without monomer input, the concentration aj（t） of the Aj clusters （j 〉 1） asymptotically retains a nonzero quantity, while for the system with monomer input, it decays with time and vanishes finally. We also investigate the kinetics of an interesting model with fixed-rate monomer adsorption. For the ease without monomer source, the evolution of the system will halt at a finite time; while the system evolves infinitely in time in the case with monomer source. Finally, we also suggest a connection between the fixed-rate monomer adsorption systems and growing networks.展开更多
基金Supported by National Natural Science Foundation of China (No. 20676094)
文摘The influence of water on protein conformation was investigated by simulating the molecular dynamics of a model protein lysozyme in different water systems.The lysozyme-water system with TIP3P water model and lysozyme-water cluster system with six-ring water model were evaluated.In addition,the radial distribution function of solvent around lysozyme was calculated.It is found that the distribution of water molecules around lysozyme is similar to that of water clusters.The analyses of dihedral angles and disulfide bonds of lysozyme show that the conformation of lysozyme is severely damaged in the lysozyme-water cluster system compared with that in the lysozyme-water system.This difference can be attributed to the formation of larger number of intermolecular hydrogen bonds between lysozyme and water cluster.It is in agreement with the analysis that water clusters can change the degree of denaturation in the process of heat denaturation of lysozyme.
基金Supported by the National Natural Science Foundation of China under Grant Nos. 10775104 and 10305009
文摘We propose a monomer adsorption model, in which only the monomers are allowed to diffuse and adsorb onto other clusters. By means of the generalized rate equation we investigate the kinetic behavior of the system with a special rate kernel. For the system without monomer input, the concentration aj（t） of the Aj clusters （j 〉 1） asymptotically retains a nonzero quantity, while for the system with monomer input, it decays with time and vanishes finally. We also investigate the kinetics of an interesting model with fixed-rate monomer adsorption. For the ease without monomer source, the evolution of the system will halt at a finite time; while the system evolves infinitely in time in the case with monomer source. Finally, we also suggest a connection between the fixed-rate monomer adsorption systems and growing networks.
