A practical book chapter for using molecular simulation to guide protein engineering in organic solvents


Congratulations Haiyang (Ocean) Cui on his recent publication!

Biocatalysis in organic solvents (OSs) is very appealing for the industry in producing bulk and/or fine chemicals. The poor performance of enzymes in OSs negates OSs' excellent solvent properties. Molecular dynamics (MD) simulations provide a complementary method to study the relationship between enzymes dynamics and the stability in OSs. In Haiyang (Ocean)´s new book chapter, they described computational procedure for MD simulation of enzymes in OSs with an example of Bacillus subtilis lipase A (BSLA) in dimethyl sulfoxide (DMSO) cosolvent with software GROMACS. They discuss main essential practical issues considered (such as choice of force field, parameterization and simulation setup as well as trajectory analysis). The core part of this protocol (enzyme-OS system set-up, analysis of structural-based and solvation-based observables) is transferable to other enzymes and any OS systems. Combining with experimental studies, the obtained molecular knowledge is most likely to guide researchers to access rational protein engineering approaches to tailor OS resistant enzymes and expand the scope of biocatalysis in OS media.

This work was realized in the division Computational Biology and was supported by computing resources granted by JARA-HPC from RWTH Aachen University (JARA0169). Haiyang Cui is financially supported by the China Scholarship Council (CSC) scholarship.

To learn more, please access the full paper on publications and patents and

Cui, Haiyang, Markus Vedder, Ulrich Schwaneberg, and Mehdi D. Davari. "Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents." In Enzyme Engineering, pp. 179-202. Humana, New York, NY, 2022. https://doi.org/10.1007/978-1-0716-1826-4_10

  Computational workflow for MD simulation of protein-OS system. Copyright: © Humana Press (Springer) Computational workflow for MD simulation of protein-OS system.