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Bharmoria P, Tietze AA, Mondal D, Kang TS, Kumar A, Freire MG. Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment. Chem Rev 2024; 124:3037-3084. [PMID: 38437627 PMCID: PMC10979405 DOI: 10.1021/acs.chemrev.3c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024]
Abstract
Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.
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Affiliation(s)
- Pankaj Bharmoria
- CICECO
- Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
- Department
of Smart Molecular, Inorganic and Hybrid Materials, Institute of Materials Science of Barcelona (ICMAB-CSIC), 08193 Bellaterra, Barcelona, Spain
- Department
of Chemistry and Molecular Biology, Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, SE-412 96 Göteborg, Sweden
| | - Alesia A. Tietze
- Department
of Chemistry and Molecular Biology, Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, SE-412 96 Göteborg, Sweden
| | - Dibyendu Mondal
- CICECO
- Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
- Institute
of Plant Genetics (IPG), Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
- Centre
for Nano and Material Sciences, JAIN (Deemed-to-be
University), Jain Global
Campus, Bangalore 562112, India
| | - Tejwant Singh Kang
- Department
of Chemistry, UGC Center for Advance Studies-II,
Guru Nanak Dev University (GNDU), Amritsar 143005, Punjab, India
| | - Arvind Kumar
- Salt
and Marine Chemicals Division, CSIR-Central
Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India
| | - Mara G Freire
- CICECO
- Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
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2
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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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3
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Ghanta KP, Mondal S, Bandyopadhyay S. Exploring the Dynamic Heterogeneity at the Interface of a Protein in Aqueous Ionic Liquid Solutions. J Phys Chem B 2022; 126:7271-7285. [DOI: 10.1021/acs.jpcb.2c03940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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4
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Enhanced activity of hyperthermostable Pyrococcus horikoshii endoglucanase in superbase ionic liquids. Biotechnol Lett 2022; 44:961-974. [PMID: 35763164 PMCID: PMC9356960 DOI: 10.1007/s10529-022-03268-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/31/2022] [Indexed: 11/08/2022]
Abstract
Objectives Ionic liquids (ILs) that dissolve biomass are harmful to the enzymes that degrade lignocellulose. Enzyme hyperthermostability promotes a tolerance to ILs. Therefore, the limits of hyperthemophilic Pyrococcus horikoschii endoglucanase (PhEG) to tolerate 11 superbase ILs were explored. Results PhEG was found to be most tolerant to 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc) in soluble 1% carboxymethylcellulose (CMC) and insoluble 1% Avicel substrates. At 35% concentration, this IL caused an increase in enzyme activity (up to 1.5-fold) with CMC. Several ILs were more enzyme inhibiting with insoluble Avicel than with soluble CMC. Km increased greatly in the presence ILs, indicating significant competitive inhibition. Increased hydrophobicity of the IL cation or anion was associated with the strongest enzyme inhibition and activation. Surprisingly, PhEG activity was increased 2.0–2.5-fold by several ILs in 4% substrate. Cations exerted the main role in competitive inhibition of the enzyme as revealed by their greater binding energy to the active site. Conclusions These results reveal new ways to design a beneficial combination of ILs and enzymes for the hydrolysis of lignocellulose, and the strong potential of PhEG in industrial, high substrate concentrations in aqueous IL solutions. Supplementary Information The online version contains supplementary material available at 10.1007/s10529-022-03268-5.
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5
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Lee PY, Singh O, Bermudez H, Matysiak S. Recovery of enzyme structure and activity following rehydration from ionic liquid. Phys Chem Chem Phys 2022; 24:10365-10372. [PMID: 35438103 DOI: 10.1039/d2cp00608a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Long-term preservation of proteins at room temperature continues to be a major challenge. Towards using ionic liquids (ILs) to address this challenge, here we present a combination of experiments and simulations to investigate changes in lysozyme upon rehydration from IL mixtures using two imidazolium-based ILs (1-ethyl-3-methylimidazolium ethylsulfate, [EMIM][EtSO4] and 1-ethyl-3-methylimidazolium diethylphosphate, [EMIM][Et2PO4]). Various spectroscopic experiments and molecular dynamics simulations are performed to ascertain the structure and activity of lysozyme. Circular dichroism spectroscopy confirms that lysozyme maintains its secondary structure upon rehydration, even after 295 days. Increasing the IL concentration decreases the activity of lysozyme and is ultimately quenched at sufficiently high IL concentrations, but the rehydration of lysozyme from high IL concentrations completely restores its activity. Such rehydration occurs in the most common lysozyme activity assay, but without careful attention, this effect on the IL concentration can be overlooked. From simulations we observe occupation of [EMIM+] ions near the vicinity of the active site and the ligand-lysozyme complex is less stable in the presence of ILs, which results in the reduction of lysozyme activity. Upon rehydration, fast leaving of [EMIM+] is observed and the availability of active site is restored. In addition, suppression of structural fluctuations is also observed when in high IL concentrations, which also explains the decrease of activity. This structure suppression is recovered after undergoing rehydration. The return of native protein structure and activity indicates that after rehydration lysozyme returns to its original state. Our results also suggest a simple route to protein recovery following extended storage.
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Affiliation(s)
- Pei-Yin Lee
- Chemical Physics Program, Institute for Physical Science and Technology, University of Maryland, College Park, USA
| | - Onkar Singh
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA, USA.
| | - Harry Bermudez
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA, USA.
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.
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6
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El Harrar T, Frieg B, Davari MD, Jaeger KE, Schwaneberg U, Gohlke H. Aqueous ionic liquids redistribute local enzyme stability via long-range perturbation pathways. Comput Struct Biotechnol J 2021; 19:4248-4264. [PMID: 34429845 PMCID: PMC8355836 DOI: 10.1016/j.csbj.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/25/2023] Open
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.
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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
| | - Benedikt Frieg
- 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
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52428 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- DWI – Leibniz Institute for Interactive Materials e.V., 52074 Aachen, 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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7
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Understanding the conformational change and inhibition of hyperthermophilic GH10 xylanase in ionic liquid. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Hebal H, Boucherba N, Binay B, Turunen O. Activity and stability of hyperthermostable cellulases and xylanases in ionic liquids. BIOCATAL BIOTRANSFOR 2021. [DOI: 10.1080/10242422.2021.1882430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Hakim Hebal
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de La Nature et de La Vie (FSNV), Université de Bejaia, Bejaia, Algeria
- Faculty of Exact Sciences and Sciences of Nature and Life, Department of Biology, Mohamed Khider University of Biskra, Biskra, Algeria
| | - Nawel Boucherba
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de La Nature et de La Vie (FSNV), Université de Bejaia, Bejaia, Algeria
| | - Baris Binay
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
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9
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Piccoli V, Martínez L. Correlated counterion effects on the solvation of proteins by ionic liquids. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Improvement of PersiXyn2 activity and stability in presence of Trehalose and proline as a natural osmolyte. Int J Biol Macromol 2020; 163:348-357. [DOI: 10.1016/j.ijbiomac.2020.06.288] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/04/2023]
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11
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Hebal H, Parviainen A, Anbarasan S, Li H, Makkonen L, Bankar S, King AW, Kilpeläinen I, Benallaoua S, Turunen O. Inhibition of hyperthermostable xylanases by superbase ionic liquids. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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The effect of ionic liquid on the structure of active site pocket and catalytic activity of a β-glucosidase from Halothermothrix orenii. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112879] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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13
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Singh O, Lee PY, Matysiak S, Bermudez H. Dual mechanism of ionic liquid-induced protein unfolding. Phys Chem Chem Phys 2020; 22:19779-19786. [DOI: 10.1039/d0cp03138k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ionic liquids (ILs) are gaining attention as protein stabilizers and refolding additives.
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Affiliation(s)
- Onkar Singh
- Department of Polymer Science and Engineering
- University of Massachusetts
- Amherst
- USA
| | - Pei-Yin Lee
- Chemical Physics Program
- Institute for Physical Science and Technology
- University of Maryland
- College Park
- USA
| | - Silvina Matysiak
- Fischell Department of Bioengineering
- University of Maryland
- College Park
- USA
| | - Harry Bermudez
- Department of Polymer Science and Engineering
- University of Massachusetts
- Amherst
- USA
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14
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Manna B, Ghosh A. Structure and dynamics of ionic liquid tolerant hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus. RSC Adv 2020; 10:7933-7947. [PMID: 35492170 PMCID: PMC9049953 DOI: 10.1039/c9ra09612d] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/04/2020] [Indexed: 12/25/2022] Open
Abstract
Economic deconstruction of lignocellulose remains a challenge due to the complex architecture of cellulose, hemicellulose, and lignin. Advancements in pretreatment processes have introduced ionic liquids (ILs) as promising non-derivatizing solvents for reducing biomass recalcitrance and for promoting enzymatic hydrolysis. However, available commercial cellulases are destabilized or inactivated even in low concentration of residual ILs. Thus, a molecular understanding of IL-enzyme interactions is crucial for developing IL-tolerant enzymes with high catalytic activity. In this study, molecular insight behind the IL tolerance of hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus (RmCel12A) has been investigated in 20%, 40%, and 60% 1-ethyl-3-methylimidazolium acetate (EmimAc) through molecular dynamic simulations at 368 K. Though the enzyme retained its stability in all EmimAc concentrations, the activity was affected due to the loss of essential dynamic motions. A protein structure network was constructed using the snapshots of protein structures from the simulation trajectories and the hub properties of residues R20, Y59, W68, W197, E203, and F220 were found to be lost in 60% EmimAc. Emim cations were observed to intrude the active site tunnel and interact with more number of catalytic residues with higher cumulative fractional occupancy in 60% EmimAc than in 20% or 40% EmimAc. Some non-catalytic residues have also been identified at the active site, which can be probable mutation targets for improving the IL tolerance. Our findings reveal the molecular understanding behind the origin of activity loss of RmCel12A and proposed insights for the further improvement of IL sensitivity. Understanding the behavior of ionic liquid tolerant hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus in different concentrations of EmimAc.![]()
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Affiliation(s)
- Bharat Manna
- School of Energy Science and Engineering
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
| | - Amit Ghosh
- School of Energy Science and Engineering
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
- P.K. Sinha Centre for Bioenergy and Renewables
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15
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Dotsenko AS, Rozhkova AM, Zorov IN, Sinitsyn AP. Protein surface engineering of endoglucanase Penicillium verruculosum for improvement in thermostability and stability in the presence of 1-butyl-3-methylimidazolium chloride ionic liquid. BIORESOURCE TECHNOLOGY 2020; 296:122370. [PMID: 31734058 DOI: 10.1016/j.biortech.2019.122370] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/01/2019] [Accepted: 11/02/2019] [Indexed: 06/10/2023]
Abstract
Thermostability and stability in ionic liquids are essential properties of cellulases that are applied in industrial processes of bioconversion. Engineering of protein surface of endoglucanase II from Penicillium verruculosum was used to improve the enzyme thermostability and stability in 1-butyl-3-methylimidazolium chloride ([Bmim]Cl). The engineering was based on analysis of the protein surface topography and enhanced by multiple sequence alignment and ΔΔG calculations. In the case of the thermostability, half-life time was improved in 1.3-1.6 times at 70 °C and 1.2-1.4 times at 80 °C. In the case of the stability in [Bmim]Cl, the residual activity after 72 h of incubation in the presence of [Bmim]Cl (50 g/L, 50 °C, pH 4.5) was 1.7-1.9 times greater for the tailored enzyme. The yield of reducing sugars after enzymatic hydrolysis of aspen wood pretreated with [Bmim]Cl was 10-20% higher with the tailored endoglucanase.
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Affiliation(s)
- Anna S Dotsenko
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia.
| | - Aleksandra M Rozhkova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia
| | - Ivan N Zorov
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia; Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Arkady P Sinitsyn
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia; Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
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16
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Water-mediated weakening of inter-ionic interactions in aqueous mixtures of ionic liquid: An investigation combining quantum chemical calculations and molecular dynamics simulations. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.04.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Acharyya A, DiGiuseppi D, Stinger BL, Schweitzer-Stenner R, Vaden TD. Structural Destabilization of Azurin by Imidazolium Chloride Ionic Liquids in Aqueous Solution. J Phys Chem B 2019; 123:6933-6945. [DOI: 10.1021/acs.jpcb.9b04113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, Pennsylvania 19104, United States
| | - David DiGiuseppi
- Department of Chemistry, Drexel University, 32 S. 32nd Street, Philadelphia, Pennsylvania 19104, United States
| | - Brittany L. Stinger
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 32 S. 32nd Street, Philadelphia, Pennsylvania 19104, United States
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
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18
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Konar S, Sinha SK, Datta S, Ghorai PK. Probing the Effect of Glucose on the Activity and Stability of β-Glucosidase: An All-Atom Molecular Dynamics Simulation Investigation. ACS OMEGA 2019; 4:11189-11196. [PMID: 31460219 PMCID: PMC6648728 DOI: 10.1021/acsomega.9b00509] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/10/2019] [Indexed: 05/11/2023]
Abstract
β-Glucosidase (EC 3.2.1.21) plays an essential role in the removal of glycosyl residues from disaccharide cellobiose to produce glucose during the hydrolysis of lignocellulosic biomass. Although there exist a few β-glucosidase that are tolerant to large concentrations of glucose, these enzymes are typically prone to glucose inhibition. Understanding the basis of this inhibition is important for the production of cheaper biofuels from lignocellulose. In this study, all-atom molecular dynamics simulation at different temperatures and glucose concentrations was used to understand the molecular basis of glucose inhibition of GH1 β-glucosidase (B8CYA8) from Halothermothrix orenii. Our results show that glucose induces a broadening of the active site tunnel through residues lining the tunnel and facilitates the accumulation of glucose. In particular, we observed that glucose accumulates at the tunnel entrance and near the catalytic sites to block substrate accessibility and inhibit enzyme activity. The reduction of enzyme activity was also confirmed experimentally through specific activity measurements in the presence of 0-2.5 M glucose. We also show that the increase in glucose concentrations leads to a decrease in the number of water molecules inside the tunnel to affect substrate hydrolysis. Overall, the results help in understanding the role of residues along the active site tunnel for the engineering of glucose-tolerant β-glucosidase.
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Affiliation(s)
- Sukanya Konar
- Department
of Chemical Sciences, Protein Engineering Laboratory, Department
of Biological Sciences, Centre for Advanced Functional Materials, and Centre for Climate
Change and Environmental Sciences, Indian
Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Sushant K. Sinha
- Department
of Chemical Sciences, Protein Engineering Laboratory, Department
of Biological Sciences, Centre for Advanced Functional Materials, and Centre for Climate
Change and Environmental Sciences, Indian
Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Supratim Datta
- Department
of Chemical Sciences, Protein Engineering Laboratory, Department
of Biological Sciences, Centre for Advanced Functional Materials, and Centre for Climate
Change and Environmental Sciences, Indian
Institute of Science Education and Research Kolkata, Mohanpur 741246, India
- E-mail: (S.D.)
| | - Pradip Kr. Ghorai
- Department
of Chemical Sciences, Protein Engineering Laboratory, Department
of Biological Sciences, Centre for Advanced Functional Materials, and Centre for Climate
Change and Environmental Sciences, Indian
Institute of Science Education and Research Kolkata, Mohanpur 741246, India
- E-mail: (P.K.G.)
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19
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Sajeevan KA, Roy D. Principal Component Analysis of a Conotoxin Delineates the Link among Peptide Sequence, Dynamics, and Disulfide Bond Isoforms. J Phys Chem B 2019; 123:5483-5493. [DOI: 10.1021/acs.jpcb.9b04090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Karuna Anna Sajeevan
- Department of Chemistry, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar,
Kapra Mandal, Hyderabad, Telangana 500078, India
| | - Durba Roy
- Department of Chemistry, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar,
Kapra Mandal, Hyderabad, Telangana 500078, India
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20
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Carter EE, Heyert AJ, De Souza M, Baker JL, Lindberg GE. The ionic liquid [C4mpy][Tf2N] induces bound-like structure in the intrinsically disordered protein FlgM. Phys Chem Chem Phys 2019; 21:17950-17958. [DOI: 10.1039/c9cp01882d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide is shown to induce secondary structure similar to a bioactive state in the protein FlgM.
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Affiliation(s)
- Erin E. Carter
- Department of Chemistry and Biochemistry
- Northern Arizona University
- Flagstaff
- USA
| | | | | | | | - Gerrick E. Lindberg
- Department of Chemistry and Biochemistry
- Northern Arizona University
- Flagstaff
- USA
- Center for Materials Interfaces in Research and Applications
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21
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Nandi S, Parui S, Halder R, Jana B, Bhattacharyya K. Interaction of proteins with ionic liquid, alcohol and DMSO and in situ generation of gold nano-clusters in a cell. Biophys Rev 2018; 10:757-768. [PMID: 29147940 PMCID: PMC5988615 DOI: 10.1007/s12551-017-0331-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 10/23/2017] [Indexed: 12/27/2022] Open
Abstract
In this review, we give a brief overview on how the interaction of proteins with ionic liquids, alcohols and dimethyl sulfoxide (DMSO) influences the stability, conformational dynamics and function of proteins/enzymes. We present experimental results obtained from fluorescence correlation spectroscopy on the effect of ionic liquid or alcohol or DMSO on the size (more precisely, the diffusion constant) and conformational dynamics of lysozyme, cytochrome c and human serum albumin in aqueous solution. The interaction of ionic liquid with biomolecules (e.g. protein, DNA etc.) has emerged as a current frontier. We demonstrate that ionic liquids are excellent stabilizers of protein and DNA and, in some cases, cause refolding of a protein already denatured by chemical denaturing agents. We show that in ethanol-water binary mixture, proteins undergo non-monotonic changes in size and dynamics with increasing ethanol content. We also discuss the effect of water-DMSO mixture on the stability of proteins. We demonstrate how large-scale molecular dynamics simulations have revealed the molecular origin of this observed phenomenon and provide a microscopic picture of the immediate environment of the biomolecules. Finally, we describe how favorable interactions of ionic liquids may be utilized for in situ generation of fluorescent gold nano-clusters for imaging a live cell.
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Affiliation(s)
- Somen Nandi
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India.
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India.
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462 066, India.
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22
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Shrivastav G, Remsing RC, Kashyap HK. Capillary evaporation of the ionic liquid [EMIM][BF4] in nanoscale solvophobic confinement. J Chem Phys 2018; 148:193810. [PMID: 30307173 DOI: 10.1063/1.5010259] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Gourav Shrivastav
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Richard C. Remsing
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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23
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Sajeevan KA, Roy D. Peptide Sequence and Solvent as Levers to Control Disulfide Connectivity in Multiple Cysteine Containing Venom Toxins. J Phys Chem B 2018; 122:5776-5789. [DOI: 10.1021/acs.jpcb.8b01437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Karuna Anna Sajeevan
- Department of Chemistry, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, Hyderabad, Telangana 500078, India
| | - Durba Roy
- Department of Chemistry, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, Hyderabad, Telangana 500078, India
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Zeindlhofer V, Schröder C. Computational solvation analysis of biomolecules in aqueous ionic liquid mixtures : From large flexible proteins to small rigid drugs. Biophys Rev 2018; 10:825-840. [PMID: 29687270 PMCID: PMC5988630 DOI: 10.1007/s12551-018-0416-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 03/26/2018] [Indexed: 01/07/2023] Open
Abstract
Based on their tunable properties, ionic liquids attracted significant interest to replace conventional, organic solvents in biomolecular applications. Following a Gartner cycle, the expectations on this new class of solvents dropped after the initial hype due to the high viscosity, hydrolysis, and toxicity problems as well as their high cost. Since not all possible combinations of cations and anions can be tested experimentally, fundamental knowledge on the interaction of the ionic liquid ions with water and with biomolecules is mandatory to optimize the solvation behavior, the biodegradability, and the costs of the ionic liquid. Here, we report on current computational approaches to characterize the impact of the ionic liquid ions on the structure and dynamics of the biomolecule and its solvation layer to explore the full potential of ionic liquids.
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Affiliation(s)
- Veronika Zeindlhofer
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstr. 17, Vienna, Austria
| | - Christian Schröder
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstr. 17, Vienna, Austria.
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25
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Uralcan B, Kim SB, Markwalter CE, Prud’homme RK, Debenedetti PG. A Computational Study of the Ionic Liquid-Induced Destabilization of the Miniprotein Trp-Cage. J Phys Chem B 2018; 122:5707-5715. [DOI: 10.1021/acs.jpcb.8b01722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Betul Uralcan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Chester E. Markwalter
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert K. Prud’homme
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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26
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Husson E, Auxenfans T, Herbaut M, Baralle M, Lambertyn V, Rakotoarivonina H, Rémond C, Sarazin C. Sequential and simultaneous strategies for biorefining of wheat straw using room temperature ionic liquids, xylanases and cellulases. BIORESOURCE TECHNOLOGY 2018; 251:280-287. [PMID: 29288956 DOI: 10.1016/j.biortech.2017.12.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/15/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Abstract
Sequential and simultaneous strategies for fractioning wheat straw were developed in combining 1-ethyl-3-methyl imidazolium acetate [C2mim][OAc], endo-xylanases from Thermobacillus xylanilyticus and commercial cellulases. After [C2mim][OAc]-pretreatment, hydrolysis catalyzed by endo-xylanases of wheat straw led to efficient xylose production with very competitive yield (97.6 ± 1.3%). Subsequent enzymatic saccharification allowed achieving a total degradation of cellulosic fraction (>99%). These high performances revealed an interesting complementarity of [C2mim][OAc]- and xylanase-pretreatments for increasing enzymatic digestibility of cellulosic fraction in agreement with the structural and morphological changes of wheat straw induced by each of these pretreatment steps. In addition a higher tolerance of endo-xylanases from T. xylaniliticus to [C2mim][AcO] until 30% v/v than cellulases from T. reesei was observed. Based on this property, a simultaneous strategy combining [C2mim][OAc]- and endo-xylanases as pretreatment in a one-batch produced xylose with similar yield than those obtained by the sequential strategy.
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Affiliation(s)
- Eric Husson
- Unité de Génie Enzymatique et Cellulaire, FRE 3580 CNRS, Université de Picardie Jules Verne, 33 rue Saint-Leu, 80039 Amiens Cedex, France
| | - Thomas Auxenfans
- Unité de Génie Enzymatique et Cellulaire, FRE 3580 CNRS, Université de Picardie Jules Verne, 33 rue Saint-Leu, 80039 Amiens Cedex, France
| | - Mickael Herbaut
- Unité de Génie Enzymatique et Cellulaire, FRE 3580 CNRS, Université de Picardie Jules Verne, 33 rue Saint-Leu, 80039 Amiens Cedex, France
| | - Manon Baralle
- UMR FARE 614 Fractionnement des AgroRessources et Environnement, Chaire AFERE, Université de Reims-Champagne-Ardenne, INRA, 51686 Reims Cedex, France
| | - Virginie Lambertyn
- Unité de Génie Enzymatique et Cellulaire, FRE 3580 CNRS, Université de Picardie Jules Verne, 33 rue Saint-Leu, 80039 Amiens Cedex, France
| | - Harivoni Rakotoarivonina
- UMR FARE 614 Fractionnement des AgroRessources et Environnement, Chaire AFERE, Université de Reims-Champagne-Ardenne, INRA, 51686 Reims Cedex, France
| | - Caroline Rémond
- UMR FARE 614 Fractionnement des AgroRessources et Environnement, Chaire AFERE, Université de Reims-Champagne-Ardenne, INRA, 51686 Reims Cedex, France
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire, FRE 3580 CNRS, Université de Picardie Jules Verne, 33 rue Saint-Leu, 80039 Amiens Cedex, France.
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Sprenger KG, Plaks JG, Kaar JL, Pfaendtner J. Elucidating sequence and solvent specific design targets to protect and stabilize enzymes for biocatalysis in ionic liquids. Phys Chem Chem Phys 2018. [PMID: 28650512 DOI: 10.1039/c7cp03013d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
For many different frameworks, the structure, function, and dynamics of an enzyme is largely determined by the nature of its interactions with the surrounding host environment, thus a molecular level understanding of enzyme/host interactions is essential to the design of new processes and applications. Ionic liquid (IL) solvents are a popular class of solvents in which to study enzyme behavior, yet it is still not possible to predict how a given enzyme will behave in a given IL solvent. Furthermore, a dearth of experimental data with which to evaluate simulation force fields has prevented the full integration of experimental and computational techniques to gain a complete picture of enzyme/IL interactions. Utilizing recently published crystallographic data of an enzyme in complex with an IL, this study aims to validate the use of current molecular force fields for studying enzyme/IL interactions, and to provide new mechanistic insight into enzyme stabilization in IL solvents. Classical molecular dynamics (MD) simulations have been performed on both the folded and unfolded state of Bacillus subtilis lipase A and a quadruple-mutant version of lipase A, in solutions of aqueous 1-butyl-3-methylimidazolium chloride. Results show classical MD simulations can predict the preferred surface binding locations of IL cations as well as reductions in IL anion binding to mutated surface residues with high accuracy. The results also point to a mechanistic difference between IL binding to the folded and unfolded state of an enzyme, which we call the "counter-ion effect". These findings could have important implications for future rational design efforts to stabilize enzymes in non-conventional media.
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Affiliation(s)
- K G Sprenger
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, USA.
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28
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Effect of water and ionic liquids on biomolecules. Biophys Rev 2018; 10:795-808. [PMID: 29423700 DOI: 10.1007/s12551-018-0399-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/23/2018] [Indexed: 12/23/2022] Open
Abstract
The remarkable progress in the field of ionic liquids (ILs) in the last two decades has involved investigations on different aspects of ILs in various conditions. The nontoxic and biocompatible nature of ILs makes them a suitable substance for the storage and application of biomolecules. In this regard, the aqueous IL solutions have attracted a large number of studies to comprehend the role of water in modulating various properties of biomolecules. Here, we review some of the recent studies on aqueous ILs that concern the role of water in altering the behavior of ILs in general and in case of biomolecules solvated in ILs. The different structural and dynamic effects caused by water have been highlighted. We discuss the different modes of IL interaction that are responsible for stabilization and destabilization of proteins and enzymes followed by examples of water effect on this. The role of water in the case of nucleic acid storage in ILs, an area which has mostly been underrated, also has been emphasized. Our discussions highlight the fact that the effects of water on IL behavior are not general and are highly dependent on the nature of the IL under consideration. Overall, we aim to draw attention to the significance of water dynamics in the aqueous IL solutions, a better understanding of which can help in developing superior storage materials for application purposes.
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29
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Fan Y, Wang X, Li J, Zhang L, Yang L, Gao P, Zhou Z. Kinetic study of the inhibition of ionic liquids on the trypsin activity. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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30
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Zhao J, Frauenkron-Machedjou VJ, Fulton A, Zhu L, Davari MD, Jaeger KE, Schwaneberg U, Bocola M. Unraveling the effects of amino acid substitutions enhancing lipase resistance to an ionic liquid: a molecular dynamics study. Phys Chem Chem Phys 2018; 20:9600-9609. [DOI: 10.1039/c7cp08470f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The key properties affecting lipase resistance towards an ionic liquid are uncovered through a molecular dynamics study.
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Affiliation(s)
- Jing Zhao
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- Tianjin Institute of Industrial Biotechnology
| | | | - Alexander Fulton
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52426 Jülich
- Germany
| | - Leilei Zhu
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- Tianjin Institute of Industrial Biotechnology
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52426 Jülich
- Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- DWI-Leibniz Institute for Interactive Materials
| | - Marco Bocola
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
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31
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Summers SR, Sprenger KG, Pfaendtner J, Marchant J, Summers MF, Kaar JL. Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids. J Phys Chem B 2017; 121:10793-10803. [DOI: 10.1021/acs.jpcb.7b08435] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Samantha R. Summers
- Department of Chemical
and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - K. G. Sprenger
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jan Marchant
- Howard Hughes Medical Institute and Department
of Chemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Michael F. Summers
- Howard Hughes Medical Institute and Department
of Chemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Joel L. Kaar
- Department of Chemical
and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
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32
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Borrell KL, Cancglin C, Stinger BL, DeFrates KG, Caputo GA, Wu C, Vaden TD. An Experimental and Molecular Dynamics Study of Red Fluorescent Protein mCherry in Novel Aqueous Amino Acid Ionic Liquids. J Phys Chem B 2017; 121:4823-4832. [PMID: 28425717 DOI: 10.1021/acs.jpcb.7b03582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The search for biocompatible ionic liquids (ILs) with novel biochemical and biomedical applications has recently gained greater attention. In this report, we characterize the effects of two novel amino acid-based aqueous ILs composed of tetramethylguanidinium (TMG) and amino acids on the structure and stability of a widely used red fluorescent protein (mCherry). Our experimental data shows that while the aspartic acid-based IL (TMGAsp) has effects similar to previously studied conventional ILs (BMIBF4, EMIAc, and TMGAc), the alanine-based IL (TMGAla) has a much stronger destabilization effect on the protein structure. Addition of 0.30 M TMGAla to mCherry decreases the unfolding temperature from 83 to 60 °C. Even at 25 °C, TMGAla results in a blue shift of the mCherry absorbance and fluorescence peaks and an increased Stokes shift. Molecular dynamics simulations show that the chromophore conformation and its interaction with mCherry with TMGAla are changed relative to those with TMGAsp or in the absence of ILs. Protein-ILs contact analysis indicates that the mCherry-Asp interactions are hydrophilic but the (fewer) mCherry-Ala interactions are more hydrophobic and may modulate the TMG interaction with the protein. Hence, the anion hydrophobicity may explain the special TMGAla destabilization of mCherry.
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Affiliation(s)
- Kelsey L Borrell
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Christine Cancglin
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Brittany L Stinger
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Kelsey G DeFrates
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Chun Wu
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Timothy D Vaden
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
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Kumar A, Bisht M, Venkatesu P. Biocompatibility of ionic liquids towards protein stability: A comprehensive overview on the current understanding and their implications. Int J Biol Macromol 2017; 96:611-651. [DOI: 10.1016/j.ijbiomac.2016.12.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/02/2016] [Accepted: 12/04/2016] [Indexed: 10/20/2022]
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35
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Egorova KS, Gordeev EG, Ananikov VP. Biological Activity of Ionic Liquids and Their Application in Pharmaceutics and Medicine. Chem Rev 2017; 117:7132-7189. [PMID: 28125212 DOI: 10.1021/acs.chemrev.6b00562] [Citation(s) in RCA: 902] [Impact Index Per Article: 128.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ionic liquids are remarkable chemical compounds, which find applications in many areas of modern science. Because of their highly tunable nature and exceptional properties, ionic liquids have become essential players in the fields of synthesis and catalysis, extraction, electrochemistry, analytics, biotechnology, etc. Apart from physical and chemical features of ionic liquids, their high biological activity has been attracting significant attention from biochemists, ecologists, and medical scientists. This Review is dedicated to biological activities of ionic liquids, with a special emphasis on their potential employment in pharmaceutics and medicine. The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems. Dedicated attention is given to a novel active pharmaceutical ingredient-ionic liquid (API-IL) concept, which suggests using traditional drugs in the form of ionic liquid species. The main aim of this Review is to attract a broad audience of chemical, biological, and medical scientists to study advantages of ionic liquid pharmaceutics. Overall, the discussed data highlight the importance of the research direction defined as "Ioliomics", studies of ions in liquids in modern chemistry, biology, and medicine.
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Affiliation(s)
- Ksenia S Egorova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia
| | - Evgeniy G Gordeev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia
| | - Valentine P Ananikov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia.,Department of Chemistry, Saint Petersburg State University , Stary Petergof 198504, Russia
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36
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Jaeger VW, Pfaendtner J. Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations. J Phys Chem B 2016; 120:12079-12087. [DOI: 10.1021/acs.jpcb.6b09410] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Vance W. Jaeger
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Box 351750, Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Box 351750, Seattle, Washington 98195, United States
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37
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Kaar JL. Lipase Activation and Stabilization in Room-Temperature Ionic Liquids. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2016; 1504:25-35. [PMID: 27770412 DOI: 10.1007/978-1-4939-6499-4_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Widespread interest in the use of room-temperature ionic liquids (RTILs) as solvents in anhydrous biocatalytic reactions has largely been met with underwhelming results. Enzymes are frequently inactivated in RTILs as a result of the influence of solvent on the enzyme's microenvironment, be it through interacting with the enzyme or enzyme-bound water molecules. The purpose of this chapter is to present a rational approach to mediate RTIL-enzyme interactions, which is essential if we are to realize the advantages of RTILs over conventional solvents for biocatalysis in full. The underlying premise for this approach is the stabilization of enzyme structure via multipoint covalent immobilization within a polyurethane foam matrix. Additionally, the approach entails the use of salt hydrates to control the level of hydration of the immobilized enzyme, which is critical to the activation of enzymes in nonaqueous media. Although lipase is used as a model enzyme, this approach may be effective in activating and stabilizing virtually any enzyme in RTILs.
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Affiliation(s)
- Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA.
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38
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Anbarasan S, Wahlström R, Hummel M, Ojamo H, Sixta H, Turunen O. High stability and low competitive inhibition of thermophilic Thermopolyspora flexuosa GH10 xylanase in biomass-dissolving ionic liquids. Appl Microbiol Biotechnol 2016; 101:1487-1498. [DOI: 10.1007/s00253-016-7922-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/17/2016] [Accepted: 10/04/2016] [Indexed: 12/24/2022]
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40
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Warner L, Gjersing E, Follett SE, Elliott KW, Dzyuba SV, Varga K. The effects of high concentrations of ionic liquid on GB1 protein structure and dynamics probed by high-resolution magic-angle-spinning NMR spectroscopy. Biochem Biophys Rep 2016; 8:75-80. [PMID: 28717785 PMCID: PMC5510950 DOI: 10.1016/j.bbrep.2016.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Ionic liquids have great potential in biological applications and biocatalysis, as some ionic liquids can stabilize proteins and enhance enzyme activity, while others have the opposite effect. However, on the molecular level, probing ionic liquid interactions with proteins, especially in solutions containing high concentrations of ionic liquids, has been challenging. In the present work the 13C, 15N-enriched GB1 model protein was used to demonstrate applicability of high-resolution magic-angle-spinning (HR-MAS) NMR spectroscopy to investigate ionic liquid–protein interactions. Effect of an ionic liquid (1-butyl-3-methylimidazolium bromide, [C4-mim]Br) on GB1was studied over a wide range of the ionic liquid concentrations (0.6–3.5 M, which corresponds to 10–60% v/v). Interactions between GB1 and [C4-mim]Br were observed from changes in the chemical shifts of the protein backbone as well as the changes in 15N ps-ns dynamics and rotational correlation times. Site-specific interactions between the protein and [C4-mim]Br were assigned using 3D methods under HR-MAS conditions. Thus, HR-MAS NMR is a viable tool that could aid in elucidation of molecular mechanisms of ionic liquid–protein interactions. Probing IL interactions with proteins using conventional techniques is challenging. Here, HR-MAS NMR was used to investigate IL–protein interactions. Model protein GB1 was investigated in high concentrations of [C4-mim]Br. This technique facilitates atomic level characterization of protein-IL interactions.
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Affiliation(s)
- Lisa Warner
- National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Erica Gjersing
- National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Shelby E Follett
- Department of Chemistry, University of Wyoming, Laramie, WY, 82071, USA
| | - K Wade Elliott
- Department of Chemistry, University of Wyoming, Laramie, WY, 82071, USA
| | - Sergei V Dzyuba
- Department of Chemistry and Biochemistry, Texas Christian University, Fort Worth, TX, 76129 USA
| | - Krisztina Varga
- Department of Chemistry, University of Wyoming, Laramie, WY, 82071, USA
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41
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Johnson LB, Snow CD. Molecular dynamics simulations of cellulase homologs in aqueous 1-ethyl-3-methylimidazolium chloride. J Biomol Struct Dyn 2016; 35:1990-2002. [DOI: 10.1080/07391102.2016.1204364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Lucas B. Johnson
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO 80523-1370, USA
| | - Christopher D. Snow
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO 80523-1370, USA
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42
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Yu T, Anbarasan S, Wang Y, Telli K, Aslan AS, Su Z, Zhou Y, Zhang L, Iivonen P, Havukainen S, Mentunen T, Hummel M, Sixta H, Binay B, Turunen O, Xiong H. Hyperthermostable Thermotoga maritima xylanase XYN10B shows high activity at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids. Extremophiles 2016; 20:515-24. [PMID: 27240671 PMCID: PMC4921120 DOI: 10.1007/s00792-016-0841-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/15/2016] [Indexed: 01/16/2023]
Abstract
The gene of Thermotoga maritima GH10 xylanase (TmXYN10B) was synthesised to study the extreme limits of this hyperthermostable enzyme at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids (ILs). TmXYN10B expressed from Pichia pastoris showed maximal activity at 100 °C and retained 92 % of maximal activity at 105 °C in a 30-min assay. Although the temperature optimum of activity was lowered by 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc), TmXYN10B retained partial activity in 15-35 % hydrophilic ILs, even at 75-90 °C. TmXYN10B retained over 80 % of its activity at 90 °C in 15 % [EMIM]OAc and 15-25 % 1-ethyl-3-methylimidazolium dimethylphosphate ([EMIM]DMP) during 22-h reactions. [EMIM]OAc may rigidify the enzyme and lower V max. However, only minor changes in kinetic parameter K m showed that competitive inhibition by [EMIM]OAc of TmXYN10B is minimal. In conclusion, when extended enzymatic reactions under extreme conditions are required, TmXYN10B shows extraordinary potential.
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Affiliation(s)
- Tianyi Yu
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Sasikala Anbarasan
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Yawei Wang
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Kübra Telli
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Aşkın Sevinç Aslan
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Zhengding Su
- Hubei University of Technology, Wuhan, 430068, China
| | - Yin Zhou
- Wuhan Sunhy Biology Co., Ltd, Wuhan, 430074, China
| | - Li Zhang
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Piia Iivonen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Sami Havukainen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Tero Mentunen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Michael Hummel
- Department of Forest Products Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Herbert Sixta
- Department of Forest Products Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Baris Binay
- Department of Bioengineering, Gebze Technical University, 41400, Gebze Kocaeli, Turkey
| | - Ossi Turunen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland.
| | - Hairong Xiong
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China.
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43
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Sprenger K, Choudhury A, Kaar JL, Pfaendtner J. Lytic Polysaccharide Monooxygenases ScLPMO10B and ScLPMO10C Are Stable in Ionic Liquids As Determined by Molecular Simulations. J Phys Chem B 2016; 120:3863-72. [DOI: 10.1021/acs.jpcb.6b01688] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K.G. Sprenger
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Alaksh Choudhury
- Department
of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Joel L. Kaar
- Department
of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Jim Pfaendtner
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
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44
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Miller MC, Hanna SL, DeFrates KG, Fiebig OC, Vaden TD. Kinetics and mass spectrometric measurements of myoglobin unfolding in aqueous ionic liquid solutions. Int J Biol Macromol 2016; 85:200-7. [DOI: 10.1016/j.ijbiomac.2015.12.067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 12/14/2015] [Accepted: 12/19/2015] [Indexed: 01/27/2023]
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45
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Goswami S, Gupta N, Datta S. Using the β-glucosidase catalyzed reaction product glucose to improve the ionic liquid tolerance of β-glucosidases. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:72. [PMID: 27006691 PMCID: PMC4802596 DOI: 10.1186/s13068-016-0484-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/10/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Pretreating biomass with ionic liquids (IL) increases enzyme accessibility and cellulose is typically recovered through precipitation with an anti-solvent. An industrially feasible pretreatment and hydrolysis process requires robust cellulases that are stable and active in the presence of either small amounts of ILs co-precipitated with recovered cellulose or for saccharifications in the presence of IL. β-glucosidase (BG) hydrolyzes cellobiose into two molecules of glucose (Glc) and is the last step of biomass hydrolysis. These enzymes are prone not only to product inhibition by glucose but also to inactivation by ILs. With increasing interest in IL-based pretreatment methods, there is increasing focus toward a search for Glc-tolerant and IL-tolerant BG. RESULTS We identified a BG belonging to the GH1 family, H0HC94, encoded in Agrobacterium tumefaciens 5A, and cloned and overexpressed the protein in Escherichia coli. H0HC94 exhibited high enzymatic activity with β-glycosidic substrates (248 µmol/min/mg on pNPGlc and 262 µmol/min/mg on cellobiose) and tolerant to Glc (apparent K i = 686 mM). Further evidence of Glc-based stabilization came from the increase in melting temperature of H0HC94, with increasing Glc concentrations. The half-life of H0HC94 also increased between 2- and 20-fold in the presence of increasing concentrations of Glc. In the presence of 0.9 M of different [C2mim]-based ionic liquids, the specific activity of H0HC94 decreased by around 20-30 %. However, the addition of 100 mM glucose to the IL-enzyme mix resulted in a more stable enzyme as evidenced by the slight recovery of H0HC94 melting temperature and up to tenfold increase in half-life. This higher stability came at a cost of 2-10 % decrease in specific activity. The steady-state kinetic analyses for a subset of the ionic liquids tested indicate that the enzyme undergoes uncompetitive inhibition by glucose and ionic liquid, indicating the possibility of binding of the ionic liquid and glucose to the enzyme-substrate complex. CONCLUSIONS H0HC94 is a Glc-stabilized BG that is also tolerant up to 0.9 M concentrations of different IL's and indicates the possibilities of using an IL-Glc-based cellulose solvent that displays enzyme-compatibility.
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Affiliation(s)
- Shubhasish Goswami
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 India
| | - Neha Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 India
| | - Supratim Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 India
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46
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Understanding the molecular behaviour of Renilla luciferase in imidazolium-based ionic liquids, a new model for the α/β fold collapse. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.10.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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47
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Sprenger K, Pfaendtner J. Using Molecular Simulation to Study Biocatalysis in Ionic Liquids. Methods Enzymol 2016; 577:419-41. [DOI: 10.1016/bs.mie.2016.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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48
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Xu J, Xiong P, He B. Advances in improving the performance of cellulase in ionic liquids for lignocellulose biorefinery. BIORESOURCE TECHNOLOGY 2016; 200:961-70. [PMID: 26602145 DOI: 10.1016/j.biortech.2015.10.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/02/2015] [Accepted: 10/03/2015] [Indexed: 05/07/2023]
Abstract
Ionic liquids (ILs) have been considered as a class of promising solvents that can dissolve lignocellulosic biomass and then provide enzymatic hydrolyzable holocellulose. However, most of available cellulases are completely or partially inactivated in the presence of even low concentrations of ILs. To more fully exploit the benefits of ILs to lignocellulose biorefinery, it is critical to improve the compatibility between cellulase and ILs. Various attempts have been made to screen natural IL-tolerant cellulases from different microhabitats. Several physical and chemical methods for stabilizing cellulases in ILs were also developed. Moreover, recent advances in protein engineering have greatly facilitated the rational engineering of cellulases by site-directed mutagenesis for the IL stability. This review is aimed to provide the first detailed overview of the current advances in improving the performance of cellulase in non-natural IL environments. New ideas from the most representative progresses and technical challenges will be summarized and discussed.
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Affiliation(s)
- Jiaxing Xu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China.
| | - Peng Xiong
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China; Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
| | - Bingfang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing 210000, China
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49
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Baker JL, Furbish J, Lindberg GE. Influence of the ionic liquid [C4mpy][Tf2N] on the structure of the miniprotein Trp-cage. J Mol Graph Model 2015; 62:202-212. [PMID: 26479192 DOI: 10.1016/j.jmgm.2015.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/14/2015] [Accepted: 10/06/2015] [Indexed: 10/22/2022]
Abstract
We examine the effect of the ionic liquid [C4mpy][Tf2N] on the structure of the miniprotein Trp-cage and contrast these results with the behavior of Trp-cage in water. We find the ionic liquid has a dramatic effect on Trp-cage, though many similarities with aqueous Trp-cage are observed. We assess Trp-cage folding by monitoring root mean square deviation from the crystallographic structure, radius of gyration, proline cis/trans isomerization state, protein secondary structure, amino acid contact formation and distance, and native and non-native contact formation. Starting from an unfolded configuration, Trp-cage folds in water at 298 K in less than 500 ns of simulation, but has very little mobility in the ionic liquid at the same temperature, which can be ascribed to the higher ionic liquid viscosity. At 365 K, the mobility of the ionic liquid is increased and initial stages of Trp-cage folding are observed, however Trp-cage does not reach the native folded state in 2 μs of simulation in the ionic liquid. Therefore, in addition to conventional molecular dynamics, we also employ scaled molecular dynamics to expedite sampling, and we demonstrate that Trp-cage in the ionic liquid does closely approach the aqueous folded state. Interestingly, while the reduced mobility of the ionic liquid is found to restrict Trp-cage motion, the ionic liquid does facilitate proline cis/trans isomerization events that are not seen in our aqueous simulations.
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Affiliation(s)
- Joseph L Baker
- Department of Chemistry, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, United States.
| | - Jeffrey Furbish
- Department of Chemistry, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, United States
| | - Gerrick E Lindberg
- Department of Chemistry and Biochemistry, Northern Arizona University, 700 S. Osbourne Drive, Flagstaff, AZ 86011, United States.
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50
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Nordwald EM, Plaks JG, Snell JR, Sousa MC, Kaar JL. Crystallographic Investigation of Imidazolium Ionic Liquid Effects on Enzyme Structure. Chembiochem 2015; 16:2456-9. [PMID: 26388426 DOI: 10.1002/cbic.201500398] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 01/11/2023]
Abstract
We present the first crystallographic insight into the interactions of an ionic liquid (IL) with an enzyme, which has widespread implications for stabilizing enzymes in IL media for biocatalysis. Structures of Bacillus subtilis lipase A (lipA) and an IL-stable variant (QM-lipA) were obtained in the presence of increasing concentrations of 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). These studies revealed that the [BMIM] cation interacts with surface residues through hydrophobic and cation-π interactions. Of specific interest was the disruption of internal stacking interactions of aromatic side chains by [BMIM], which provides structural evidence for the mechanism of enzyme denaturation by ILs. The interaction of [BMIM] and Cl ions with lipA was reduced by the stabilizing mutations Y49E and G158E in QM-lipA. Ultimately, these findings present the molecular basis for stabilizing enzymes from IL-induced inactivation, as well as the selection of ILs that are less denaturing.
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Affiliation(s)
- Erik M Nordwald
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA
| | - Joseph G Plaks
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA
| | - Jared R Snell
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA
| | - Marcelo C Sousa
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA.
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