Aqueous ionic liquids redistribute local enzyme stability via long-range perturbation pathways

Computational and Structural Biotechnology Journal, vol. 19, pp. 4248–4264

Abstract

Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co–)solvents for biocatalysis due to their unique properties. On the other hand, the incubation of enzymes in IL or aIL often reduces enzyme activity. Recent studies proposed various aIL-induced effects to explain the reduction, classified as direct effects, e.g., local dehydration or competitive inhibition, and indirect effects, e.g., structural perturbations or disturbed catalytic site integrity. However, the molecular origin of indirect effects has largely remained elusive. Here we show by multi-μs long molecular dynamics simulations, free energy computations, and rigidity analyses that aIL favorably interact with specific residues of Bacillus subtilis Lipase A (BsLipA) and modify the local structural stability of this model enzyme by inducing long-range perturbations of noncovalent interactions. The perturbations percolate over neighboring residues and eventually affect the catalytic site and the buried protein core. Validation against a complete experimental site saturation mutagenesis library of BsLipA (3620 variants) reveals that the residues of the perturbation pathways are distinguished sequence positions where substitutions highly likely yield significantly improved residual activity. Our results demonstrate that identifying these perturbation pathways and specific IL ion-residue interactions there effectively predicts focused variant libraries with improved aIL tolerance.

Authors 6

1. Till El Harrar Aachen Institute of Biotechnology

   RWTH Aachen University · Forschungszentrum Jülich · Jülich Supercomputing Centre · John von Neumann Institute for Computing

   Affiliation as printed

   Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany

   John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany

2. Benedikt Frieg

   Forschungszentrum Jülich · Jülich Supercomputing Centre · John von Neumann Institute for Computing

   Affiliation as printed

   John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany

3. Mehdi D. Davari Aachen Institute of Biotechnology

   RWTH Aachen University

   Affiliation as printed

   Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany

4. Karl‐Erich Jaeger

   Forschungszentrum Jülich · Heinrich Heine University Düsseldorf

   Affiliation as printed

   Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany

   Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52428 Jülich, Germany

5. Ulrich Schwaneberg Aachen DWI-Leibniz-Institute for Interactive Materials e.V Institute of Biotechnology

   RWTH Aachen University · DWI – Leibniz Institute for Interactive Materials

   Affiliation as printed

   DWI – Leibniz Institute for Interactive Materials e.V., 52074 Aachen, Germany

   Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany

6. Holger Gohlke corresponding

   Forschungszentrum Jülich · Heinrich Heine University Düsseldorf · Jülich Supercomputing Centre · John von Neumann Institute for Computing

   Affiliation as printed

   Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany

   John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany