Analysis and simulation of molecular dynamics of lysozyme in water cluster system |
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| Authors: | Ping Na Baihua Chen Yunfen Wang Jing Wang and Yanni Li |
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| Institution: | (School of Chemical Engineering and Technology,Tianjin University,Tianjin 300072,China) |
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| Abstract: | 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. |
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| Keywords: | molecular dynamics root mean square deviation lysozyme water cluster hydrogen bond |
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