Details
| Original language | English |
|---|---|
| Pages (from-to) | 5322-5341 |
| Number of pages | 20 |
| Journal | Journal of Chemical Theory and Computation |
| Volume | 17 |
| Issue number | 8 |
| Early online date | 7 Jul 2021 |
| Publication status | Published - 10 Aug 2021 |
| Externally published | Yes |
Abstract
Deep eutectic solvents (DESs) have become popular as environmental-friendly solvents for biocatalysis. Molecular dynamics (MD) simulations offer an in-depth analysis of enzymes in DESs, but their performance depends on the force field chosen. Here, we present a comprehensive validation of three biomolecular force fields (CHARMM, Amber, and OPLS) for simulations of alcohol dehydrogenase (ADH) in DESs composed of choline chloride and glycerol/ethylene glycol with varying water contents. Different properties (e.g., protein structure and flexibility, solvation layer, and H-bonds) were used for validation. For two properties (viscosity and water activity) also experiments were performed. The viscosity was calculated with the periodic perturbation method, whereby its parameter dependency is disclosed. A modification of Amber was identified as the best-performing model for low water contents, whereas CHARMM outperforms the other models at larger water concentrations. An analysis of ADH's structure and interactions with the DESs revealed similar predictions for Amber and CHARMM.
ASJC Scopus subject areas
- Computer Science(all)
- Computer Science Applications
- Chemistry(all)
- Physical and Theoretical Chemistry
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In: Journal of Chemical Theory and Computation, Vol. 17, No. 8, 10.08.2021, p. 5322-5341.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Comparison and Validation of Force Fields for Deep Eutectic Solvents in Combination with Water and Alcohol Dehydrogenase
AU - Bittner, Jan Philipp
AU - Huang, Lei
AU - Zhang, Ningning
AU - Kara, Selin
AU - Jakobtorweihen, Sven
N1 - Funding Information: We want to gratefully thank Maria Alejandra Tibaquira Martinez for the support with the solvation free energy calculations. We thank Niels Hansen for sharing some force fields files in GROMACS format. This work was financially supported by Deutsche Forschungsgemeinschaft (DFG) grant nos. KA 4399/3-1 and JA 2500/5-1; jointly acquired project. Computational resources for the MD simulations of this work have been provided by the North-German Supercomputing Alliance (HLRN).
PY - 2021/8/10
Y1 - 2021/8/10
N2 - Deep eutectic solvents (DESs) have become popular as environmental-friendly solvents for biocatalysis. Molecular dynamics (MD) simulations offer an in-depth analysis of enzymes in DESs, but their performance depends on the force field chosen. Here, we present a comprehensive validation of three biomolecular force fields (CHARMM, Amber, and OPLS) for simulations of alcohol dehydrogenase (ADH) in DESs composed of choline chloride and glycerol/ethylene glycol with varying water contents. Different properties (e.g., protein structure and flexibility, solvation layer, and H-bonds) were used for validation. For two properties (viscosity and water activity) also experiments were performed. The viscosity was calculated with the periodic perturbation method, whereby its parameter dependency is disclosed. A modification of Amber was identified as the best-performing model for low water contents, whereas CHARMM outperforms the other models at larger water concentrations. An analysis of ADH's structure and interactions with the DESs revealed similar predictions for Amber and CHARMM.
AB - Deep eutectic solvents (DESs) have become popular as environmental-friendly solvents for biocatalysis. Molecular dynamics (MD) simulations offer an in-depth analysis of enzymes in DESs, but their performance depends on the force field chosen. Here, we present a comprehensive validation of three biomolecular force fields (CHARMM, Amber, and OPLS) for simulations of alcohol dehydrogenase (ADH) in DESs composed of choline chloride and glycerol/ethylene glycol with varying water contents. Different properties (e.g., protein structure and flexibility, solvation layer, and H-bonds) were used for validation. For two properties (viscosity and water activity) also experiments were performed. The viscosity was calculated with the periodic perturbation method, whereby its parameter dependency is disclosed. A modification of Amber was identified as the best-performing model for low water contents, whereas CHARMM outperforms the other models at larger water concentrations. An analysis of ADH's structure and interactions with the DESs revealed similar predictions for Amber and CHARMM.
UR - http://www.scopus.com/inward/record.url?scp=85111236689&partnerID=8YFLogxK
U2 - 10.1021/acs.jctc.1c00274
DO - 10.1021/acs.jctc.1c00274
M3 - Article
C2 - 34232662
AN - SCOPUS:85111236689
VL - 17
SP - 5322
EP - 5341
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
SN - 1549-9618
IS - 8
ER -