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Myrtollari K, Calderini E, Kracher D, Schöngaßner T, Galušić S, Slavica A, Taden A, Mokos D, Schrüfer A, Wirnsberger G, Gruber K, Daniel B, Kourist R. Stability Increase of Phenolic Acid Decarboxylase by a Combination of Protein and Solvent Engineering Unlocks Applications at Elevated Temperatures. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2024; 12:3575-3584. [PMID: 38456190 PMCID: PMC10915792 DOI: 10.1021/acssuschemeng.3c06513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/16/2023] [Accepted: 01/25/2024] [Indexed: 03/09/2024]
Abstract
Enzymatic decarboxylation of biobased hydroxycinnamic acids gives access to phenolic styrenes for adhesive production. Phenolic acid decarboxylases are proficient enzymes that have been applied in aqueous systems, organic solvents, biphasic systems, and deep eutectic solvents, which makes stability a key feature. Stabilization of the enzyme would increase the total turnover number and thus reduce the energy consumption and waste accumulation associated with biocatalyst production. In this study, we used ancestral sequence reconstruction to generate thermostable decarboxylases. Investigation of a set of 16 ancestors resulted in the identification of a variant with an unfolding temperature of 78.1 °C and a half-life time of 45 h at 60 °C. Crystal structures were determined for three selected ancestors. Structural attributes were calculated to fit different regression models for predicting the thermal stability of variants that have not yet been experimentally explored. The models rely on hydrophobic clusters, salt bridges, hydrogen bonds, and surface properties and can identify more stable proteins out of a pool of candidates. Further stabilization was achieved by the application of mixtures of natural deep eutectic solvents and buffers. Our approach is a straightforward option for enhancing the industrial application of the decarboxylation process.
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Affiliation(s)
- Kamela Myrtollari
- Institute
of Molecular Biotechnology, Graz University
of Technology, Petersgasse
14, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, ACIB GmbH, Petersgasse 14/1, 8010 Graz, Austria
- Adhesive
Technologies, Henkel AG & Co. KGaA, Henkelstr. 67, 40191 Düsseldorf, Germany
| | - Elia Calderini
- Institute
of Molecular Biotechnology, Graz University
of Technology, Petersgasse
14, 8010 Graz, Austria
| | - Daniel Kracher
- Institute
of Molecular Biotechnology, Graz University
of Technology, Petersgasse
14, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse
12/II, 8010 Graz, Austria
| | - Tobias Schöngaßner
- Institute
of Molecular Biotechnology, Graz University
of Technology, Petersgasse
14, 8010 Graz, Austria
| | - Stela Galušić
- Institute
of Molecular Biotechnology, Graz University
of Technology, Petersgasse
14, 8010 Graz, Austria
| | - Anita Slavica
- Faculty
of Food Technology and Biotechnology, Department of Biochemical Engineering, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia
| | - Andreas Taden
- Adhesive
Technologies, Henkel AG & Co. KGaA, Henkelstr. 67, 40191 Düsseldorf, Germany
| | - Daniel Mokos
- Institute
of Molecular Biosciences, University of
Graz, NAWI Graz, Humboldtstraße
50/3, 8010 Graz, Austria
| | - Anna Schrüfer
- Institute
of Molecular Biosciences, University of
Graz, NAWI Graz, Humboldtstraße
50/3, 8010 Graz, Austria
| | - Gregor Wirnsberger
- Institute
of Molecular Biosciences, University of
Graz, NAWI Graz, Humboldtstraße
50/3, 8010 Graz, Austria
| | - Karl Gruber
- BioTechMed-Graz, Mozartgasse
12/II, 8010 Graz, Austria
- Institute
of Molecular Biosciences, University of
Graz, NAWI Graz, Humboldtstraße
50/3, 8010 Graz, Austria
| | - Bastian Daniel
- BioTechMed-Graz, Mozartgasse
12/II, 8010 Graz, Austria
- Institute
of Molecular Biosciences, University of
Graz, NAWI Graz, Humboldtstraße
50/3, 8010 Graz, Austria
| | - Robert Kourist
- Institute
of Molecular Biotechnology, Graz University
of Technology, Petersgasse
14, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, ACIB GmbH, Petersgasse 14/1, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse
12/II, 8010 Graz, Austria
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Cheng W, Nian B. Computer-Aided Lipase Engineering for Improving Their Stability and Activity in the Food Industry: State of the Art. Molecules 2023; 28:5848. [PMID: 37570817 PMCID: PMC10421223 DOI: 10.3390/molecules28155848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
As some of the most widely used biocatalysts, lipases have exhibited extreme advantages in many processes, such as esterification, amidation, and transesterification reactions, which causes them to be widely used in food industrial production. However, natural lipases have drawbacks in terms of organic solvent resistance, thermostability, selectivity, etc., which limits some of their applications in the field of foods. In this systematic review, the application of lipases in various food processes was summarized. Moreover, the general structure of lipases is discussed in-depth, and the engineering strategies that can be used in lipase engineering are also summarized. The protocols of some classical methods are compared and discussed, which can provide some information about how to choose methods of lipase engineering. Thermostability engineering and solvent tolerance engineering are highlighted in this review, and the basic principles for improving thermostability and solvent tolerance are summarized. In the future, comput er-aided technology should be more emphasized in the investigation of the mechanisms of reactions catalyzed by lipases and guide the engineering of lipases. The engineering of lipase tunnels to improve the diffusion of substrates is also a promising prospect for further enhanced lipase activity and selectivity.
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Affiliation(s)
| | - Binbin Nian
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China;
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
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 are available describing the energetic effects 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 provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- 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
| | - Holger Gohlke
- 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.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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