The Faculty of Mathematics and Natural Sciences

Permanent URI for this communityhttps://researchdata.hhu.de/handle/entry/45

The Faculty of Mathematics and Natural Sciences (MNF) employs more than 800 Scientists in seven departments: Biology, Chemistry, Computer Sciences, Mathematics, Pharmacy, Physics and Psychology. Among the wide-ranging research areas covered by the faculty, several cooperative programmes put specific emphasis on Life Sciences and Physics.

Browse

Browsing The Faculty of Mathematics and Natural Sciences by Author "El Harrar, Till"

Filter results by typing the first few letters
Now showing 1 - 2 of 2
  • No Thumbnail Available
    Item
    Data for "Influence of ionic liquids on enzymatic asymmetric carboligations"
    (N/A, 2025) El Harrar, Till; Gohlke, Holger
    The asymmetric mixed carboligation of aldehydes catalyzed by thiamine diphosphate (ThDP)-dependent enzymes provides a sensitive system for monitoring changes in activity, chemo-, and enantioselectivity. While previous studies have shown that organic cosolvents influence these parameters, we now demonstrate that similar effects occur upon addition of water-miscible ionic liquids (ILs). In this study, six ThDP-dependent enzymes were analyzed in the presence of 14 ILs under comparable conditions to assess their influence on enzymatic carboligation reactions yielding 2-hydroxy ketones. ILs exerted a moderate to strong influence on activity and, more notably, altered enantioselectivity. (R)-selective reactions were generally stable upon IL addition, while (S)-selective reactions frequently showed reduced selectivity or even inversion to the (R)-enantiomer. The most significant change was observed for the ApPDC_E469G variant of pyruvate decarboxylase from Acetobacter pasteurianus, where the enantiomeric excess shifted from 86% (S) to 60% (R) in the presence of 9% (w/v) Ammoeng 102. Control experiments indicated that this shift was primarily due to the Ammoeng cation rather than the anion. To explore the molecular basis of this phenomenon, all-atom molecular dynamics (MD) simulations were performed on wild-type ApPDC and the E469G variant in Ammoeng 101 and Ammoeng 102. The simulations revealed that hydrophobic and hydrophilic regions of the Ammoeng cations interact with the (S)-selective binding pocket, thereby favoring formation of the (R)-product. These results highlight the potential of solvent engineering for modulating enzyme selectivity and demonstrate that MD simulations can capture functionally relevant enzyme–solvent interactions at the atomic level.
  • No Thumbnail Available
    Item
    Millisecond-long sampling for a comprehensive energetic evaluation of aqueous ionic liquid effects on amino acid interactions
    (N/A, 2022-09-01) El Harrar, Till; Gohlke, Holger
    The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data is available describing the energetic effect of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of > 1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol 1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provides explanations at the atomistic and energetic level for complex IL effects on protein stability and should help improve the prediction accuracy of computational tools that estimate protein stability based on (free) energy functions.