Design of robust malate dehydrogenases by assembly of motifs of halophilic and thermophilic enzyme based on interaction network

Ji, Zhehui; Huo, Heyu; Duan, Lingxuan; Wang, Shizhen

doi:10.1016/j.bej.2022.108758

Cited by 2 publications

(1 citation statement)

References 27 publications

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“…(For examples see: [17][18][19][20][21][22][23]. Studies of a halophilic protease from Salinivibrio sp., [24] a halophilic phenylalanine dehydrogenase from Natranaerobius thermophiles [25] and an engineered halophilic malate dehydrogenase [26] found ionic liquid systems wherein the enzyme showed increased activity compared to the free enzyme. Halophilic organisms thrive in high salt environments and have adapted their proteins to intracellular molar concentrations of salt.…”

Section: Introductionmentioning

confidence: 99%

Ion-combination specific effects driving enzymatic activity of halophilic Alcohol Dehydrogenase 2 from Haloferax volcanii in aqueous ionic liquid solvent mixtures

Schindl,

Hagen,

Jäger

et al. 2023

Preprint

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Biocatalysis in ionic liquids enables novel routes for bioprocessing. Enzymes derived from extremophiles promise greater stability and activity under ionic liquid (IL) influence. Here, we probe the enzyme Alcohol Dehydrogenase 2 from the halophilic archaeon Haloferax volcanii in thirteen different ion combinations for relative specific activity and analyse the results against MD simulations of the same IL systems. We probe the ionic liquid property space based on ion polarizability and molecular electrostatic potential. Using radial distribution functions, survival probabilities and spatial distribution functions of ions we show that cooperative ion-ion interactions determine ion-protein interaction, specifically, strong ion-ion interactions equate to higher enzymatic activity if neither of the ions interact strongly with the protein surface. We further demonstrate a tendency for ions interacting with the protein surface to be least detrimental to enzymatic activity if they show a low polarizability and a small range of molecular electrostatic potential. We also find that the IL ion influence is not mitigated by the surplus of negatively charged residues of the halophilic enzyme. This is shown by free energy landscape analysis in root mean square deviation and distance variation plots of active site gating residues (Trp43 and His273) demonstrating no protection of specific structural elements relevant to preserving enzymatic activity. On the other hand, we observe a general effect across all IL systems that a tight binding of water at acidic residues is preferentially interrupted at these residues through the increased presence of potassium ions. Overall, this study demonstrates a co-ion interaction dependent influence on allosteric surface residues controlling the active/inactive conformation of halophilic Alcohol Dehydrogenase 2 and the necessity to engineer ionic liquid systems for enzymes that rely on the integrity of functional surface residues regardless of their halophilicity or thermophilicity for use in bioprocessing.

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