Analysis and simulation of molecular dynamics of lysozyme in water cluster system

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.

Keywords

molecular dynamics / root mean square deviation / lysozyme / water cluster / hydrogen bond

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