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Open Access Highly Accessed Research article

Modeling structure and flexibility of Candida antarctica lipase B in organic solvents

Peter Trodler and Jürgen Pleiss*

Author affiliations

Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany

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Citation and License

BMC Structural Biology 2008, 8:9  doi:10.1186/1472-6807-8-9

Published: 6 February 2008

Abstract

Background

The structure and flexibility of Candida antarctica lipase B in water and five different organic solvent models was investigated using multiple molecular dynamics simulations to describe the effect of solvents on structure and dynamics. Interactions of the solvents with the protein and the distribution of water molecules at the protein surface were examined.

Results

The simulated structure was independent of the solvent, and had a low deviation from the crystal structure. However, the hydrophilic surface of CALB in non-polar solvents decreased by 10% in comparison to water, while the hydrophobic surface is slightly increased by 1%. There is a large influence on the flexibility depending on the dielectric constant of the solvent, with a high flexibility in water and a low flexibility in organic solvents. With decreasing dielectric constant, the number of surface bound water molecules significantly increased and a spanning water network with an increasing size was formed.

Conclusion

The reduced flexibility of Candida antarctica lipase B in organic solvents is caused by a spanning water network resulting from less mobile and slowly exchanging water molecules at the protein-surface. The reduced flexibility of Candida antarctica lipase B in organic solvent is not only caused by the interactions between solvent-protein, but mainly by the formation of a spanning water network.