Modeling Protein Stability and Structural Preference in Ionic Liquids
Burney, Patrick R.
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Ionic liquids have demonstrable suitability as niche alternatives to organic solvents in applied biochemistry. However, many of the known ionic liquids show little to no support for enzyme activity and many cases have been demonstrated where structurally and functionally similar enzymes exhibit discrepant retention of activity in ionic liquids. Although many experimental investigations have attempted to formulate rules that predict enzyme tolerance to ionic liquids, there are few rules that apply broadly. Molecular dynamics is a computational technique that is well suited to provide atomistic insight about the nature and effects of ionic liquid / enzyme interactions. This research has involved development and application of simulation methodology and analysis toward investigating these complex interactions as well as the structural stability of multiple enzymes in ionic liquids. Application of these techniques has indicated that the nature of enzyme deactivation by ionic liquids is just as complicated as the experimental results have suggested; different enzymes and different ionic liquids show indications of competitive inhibition by the solvent or destabilization. Through several independent studies we have observed and described: the dampening of enzyme fluctuations in high concentrations of ionic liquids; the organization of water and ionic liquid substituents about enzymes; and the loss of secondary structure that precedes denaturing and possibly enzyme aggregation. In recognition that future studies in this area will also need to go beyond classical MD simulations, we have applied special multiscale modeling techniques to a separate protein system to quantify how mutations induce changes in the preferred structural state of an important protein fragment.
- Chemical engineering