51
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Jaeger V, Burney P, Pfaendtner J. Comparison of three ionic liquid-tolerant cellulases by molecular dynamics. Biophys J 2015; 108:880-892. [PMID: 25692593 PMCID: PMC4336362 DOI: 10.1016/j.bpj.2014.12.043] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 12/20/2014] [Accepted: 12/29/2014] [Indexed: 10/24/2022] Open
Abstract
We have employed molecular dynamics to investigate the differences in ionic liquid tolerance among three distinct family 5 cellulases from Trichoderma viride, Thermogata maritima, and Pyrococcus horikoshii. Simulations of the three cellulases were conducted at a range of temperatures in various binary mixtures of the ionic liquid 1-ethyl-3-methyl-imidazolium acetate with water. Our analysis demonstrates that the effects of ionic liquids on the enzymes vary in each individual case from local structural disturbances to loss of much of one of the enzyme's secondary structure. Enzymes with more negatively charged surfaces tend to resist destabilization by ionic liquids. Specific and unique structural changes in the enzymes are induced by the presence of ionic liquids. Disruption of the secondary structure, changes in dynamical motion, and local changes in the binding pocket are observed in less tolerant enzymes. Ionic-liquid-induced denaturation of one of the enzymes is indicated over the 500 ns timescale. In contrast, the most tolerant cellulase behaves similarly in water and in ionic-liquid-containing mixtures. Unlike the heuristic approaches that attempt to predict enzyme stability using macroscopic properties, molecular dynamics allows us to predict specific atomic-level structural and dynamical changes in an enzyme's behavior induced by ionic liquids and other mixed solvents. Using these insights, we propose specific experimentally testable hypotheses regarding the origin of activity loss for each of the systems investigated in this study.
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Affiliation(s)
- Vance Jaeger
- Department of Chemical Engineering, University of Washington, Seattle, Washington
| | - Patrick Burney
- Department of Chemical Engineering, University of Washington, Seattle, Washington
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington.
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52
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Burney PR, Nordwald EM, Hickman K, Kaar JL, Pfaendtner J. Molecular dynamics investigation of the ionic liquid/enzyme interface: Application to engineering enzyme surface charge. Proteins 2015; 83:670-80. [DOI: 10.1002/prot.24757] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/17/2014] [Accepted: 12/31/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Patrick R. Burney
- Department of Chemical Engineering; University of Washington; Seattle Washington 98105
| | - Erik M. Nordwald
- Department of Chemical and Biological Engineering; University of Colorado; Boulder Colorado 80309
| | - Katie Hickman
- Department of Chemical Engineering; University of Washington; Seattle Washington 98105
| | - Joel L. Kaar
- Department of Chemical and Biological Engineering; University of Colorado; Boulder Colorado 80309
| | - Jim Pfaendtner
- Department of Chemical Engineering; University of Washington; Seattle Washington 98105
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53
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Kumar A, Venkatesu P. A comparative study of myoglobin stability in the presence of Hofmeister anions of ionic liquids and ionic salts. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.09.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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54
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Carter JLL, Bekhouche M, Noiriel A, Blum LJ, Doumèche B. Directed evolution of a formate dehydrogenase for increased tolerance to ionic liquids reveals a new site for increasing the stability. Chembiochem 2014; 15:2710-8. [PMID: 25346488 DOI: 10.1002/cbic.201402501] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Indexed: 12/18/2022]
Abstract
The formate dehydrogenase (FDH) from Candida boidinii is a well-known enzyme in biocatalysis for NADH regeneration. Nevertheless, it has low activity in a water-miscible ionic liquid (1,3-dimethylimidazolium dimethyl phosphate, [MMIm][Me2 PO4 ]). In this work, this enzyme was subjected to directed evolution by using error-prone PCR, and a mutant (N187S/T321S) displaying higher activity was obtained following selection based on the formazan-based colorimetric assay. The mutation N187S is responsible for improved activity both in aqueous solution and in [MMIm][Me2 PO4 ], through an enhancement of the kcat value by a factor of 5.8. Fluorescence experiments performed in the presence of a quenching agent revealed that the mutant does not unfold in the presence of 50 % (v/v) [MMIm][Me2 PO4 ] whereas the wild-type enzyme does. Molecular modelling revealed that the mutation is located at the monomer-monomer interface and causes an increase in the pKa of residue E163 from 4.8 to 5.5. Calculation of the pKa of this residue in other microbial FDHs showed that thermostable FDHs have a highly basic glutamate at this position (pKa up to 6.2). We have identified a new site for improving FDH thermostability and tolerance to ionic liquids, and it is linked to the local charge of the enzymes in this class.
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Affiliation(s)
- Julie L L Carter
- Génie Enzymatique, Membranes Biomimétiques et Assemblages Supramoléculaires (GEMBAS), Institut de Chimie et Biochimie Moléculaire et Supramoléculaire (ICBMS), UMR CNRS 5246, Université Claude Bernard Lyon 1, 43 boulevard du 11 Novembre 1918, Villeurbanne 69622 (France)
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55
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Nordwald EM, Armstrong GS, Kaar JL. NMR-Guided Rational Engineering of an Ionic-Liquid-Tolerant Lipase. ACS Catal 2014. [DOI: 10.1021/cs500978x] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Erik M. Nordwald
- Department of Chemical and Biological Engineering, ‡Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Geoffrey S. Armstrong
- Department of Chemical and Biological Engineering, ‡Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Joel L. Kaar
- Department of Chemical and Biological Engineering, ‡Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
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56
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Zhong Z, Li M, Qing Y, Dai N, Guan W, Liang W, Wang D. Signal-on electrochemical immunoassay for APE1 using ionic liquid doped Au nanoparticle/graphene as a nanocarrier and alkaline phosphatase as enhancer. Analyst 2014; 139:6563-8. [DOI: 10.1039/c4an01712a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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57
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Thermal behaviour and tolerance to ionic liquid [emim]OAc in GH10 xylanase from Thermoascus aurantiacus SL16W. Extremophiles 2014; 18:1023-34. [DOI: 10.1007/s00792-014-0679-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 07/13/2014] [Indexed: 02/01/2023]
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58
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Kumar A, Rani A, Venkatesu P, Kumar A. Quantitative evaluation of the ability of ionic liquids to offset the cold-induced unfolding of proteins. Phys Chem Chem Phys 2014; 16:15806-10. [DOI: 10.1039/c4cp01001a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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59
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Murata H, Cummings CS, Koepsel RR, Russell AJ. Rational Tailoring of Substrate and Inhibitor Affinity via ATRP Polymer-Based Protein Engineering. Biomacromolecules 2014; 15:2817-23. [DOI: 10.1021/bm5008629] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hironobu Murata
- Disruptive
Health Technology Institute, ICES, 1201 Hamburg Hall, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Chad S. Cummings
- Department
of Biomedical Engineering, Doherty Hall 2100, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Richard R. Koepsel
- Disruptive
Health Technology Institute, ICES, 1201 Hamburg Hall, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Alan J. Russell
- Disruptive
Health Technology Institute, ICES, 1201 Hamburg Hall, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
- Department
of Biomedical Engineering, Doherty Hall 2100, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
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60
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Minten IJ, Abello N, Schooneveld-Bergmans MEF, van den Berg MA. Post-production modification of industrial enzymes. Appl Microbiol Biotechnol 2014; 98:6215-31. [PMID: 24903809 DOI: 10.1007/s00253-014-5799-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/23/2014] [Accepted: 04/27/2014] [Indexed: 12/24/2022]
Abstract
Industry has an increasing interest in the use of enzymes as environmentally friendly, highly efficient, and specific bio-catalysts. Enzymes have primarily evolved to function in aqueous environments at ambient temperature and pressure. These conditions however do not always correspond with industrial processes or applications, and only a small portion of all known enzymes are therefore suitable for industrial use. Protein engineering can sometimes be applied to convey more desirable properties to enzymes, such as increased stability, but is limited to the 20 naturally occurring amino acids or homologs thereof. Using post-production modification, which has the potential to combine desirable properties from the enzyme and the conjugated compounds, enzymes can be modified with both natural and synthetic molecules. This offers access to a myriad of possibilities for tuning the properties of enzymes. At this moment, however, the effects of post-production modification cannot yet be reliably predicted. The increasing number of applications will improve this so that the potential of this technology can be fully exploited. This review will focus on post-production modification of enzymes and its use and opportunities in industry.
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Affiliation(s)
- Inge J Minten
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands,
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61
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Nordwald EM, Brunecky R, Himmel ME, Beckham GT, Kaar JL. Charge engineering of cellulases improves ionic liquid tolerance and reduces lignin inhibition. Biotechnol Bioeng 2014; 111:1541-9. [DOI: 10.1002/bit.25216] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Erik M. Nordwald
- Department of Chemical and Biological Engineering; University of Colorado; Campus Box 596 Boulder Colorado 80309
| | - Roman Brunecky
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Michael E. Himmel
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Gregg T. Beckham
- National Bioenergy Center; National Renewable Energy Laboratory; Golden Colorado
| | - Joel L. Kaar
- Department of Chemical and Biological Engineering; University of Colorado; Campus Box 596 Boulder Colorado 80309
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62
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63
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Hu Y, Yang J, Jia R, Ding Y, Li S, Huang H. Chemical modification with functionalized ionic liquids: a novel method to improve the enzymatic properties of Candida rugosa lipase. Bioprocess Biosyst Eng 2014; 37:1617-26. [DOI: 10.1007/s00449-014-1134-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/16/2014] [Indexed: 01/04/2023]
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64
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Notable Stabilization of α-Chymotrypsin by the Protic Ionic Additive, [ch][dhp]: Calorimetric Evidence for a Fine Enthalpy/Entropy Balance. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:834189. [PMID: 27437474 PMCID: PMC4897175 DOI: 10.1155/2014/834189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/23/2014] [Indexed: 01/21/2023]
Abstract
An impact of 0.5 to 3 M choline dihydrogen phosphate, [ch][dhp], the biotechnologically relevant ionic substance, on the thermal stability of a model globular protein, α-chymotrypsin (α-CT), has been studied exploiting the highly sensitive differential scanning calorimetry (DSC) technique. The notable overall stabilizing effect of 11 ± 2 K regarding the thermal transition (melting) temperature, T m , has been detected. For this kind of series, for the first time, the calorimetric melting enthalpy (ΔH cal) and transition entropy (ΔS m ) parameters have been determined simultaneously throughout. The first analysis indicated a two-phase impact implying (a) the initial, dramatic drop in both ΔH cal and ΔS m , obviously connected to specific, direct interaction between the [ch][dhp] components and α-CT's charged groups (within 0 to 1 mol/L [ch][dhp]), leading to the essential rearrangement of the interfacial hydrogen-bonded (HB) network; and (b) the follow-up (within 1 to 3.0 mol/L [ch][dhp]), modest changes in ΔH cal and lack of changes in ΔS m , seemingly connected with a subsequent steady strengthening of already reformed HB network, respectively. These changes, presumably, are primarily facilitated by Coulombic interactions between the [dhp] anions and solvent-exposed positively charged amino groups of α-CT.
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65
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Li H, Kankaanpää A, Xiong H, Hummel M, Sixta H, Ojamo H, Turunen O. Thermostabilization of extremophilic Dictyoglomus thermophilum GH11 xylanase by an N-terminal disulfide bridge and the effect of ionic liquid [emim]OAc on the enzymatic performance. Enzyme Microb Technol 2013; 53:414-9. [PMID: 24315645 DOI: 10.1016/j.enzmictec.2013.09.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/04/2013] [Accepted: 09/11/2013] [Indexed: 11/27/2022]
Abstract
In the present study, an extremophilic GH11 xylanase was stabilized by an engineered N-terminal disulphide bridge. The effect of the stabilization was then tested against high temperatures and in the presence of a biomass-dissolving ionic liquid, 1-ethyl-3-methylimidazolium acetate ([emim]OAc). The N-terminal disulfide bridge increased the half-life of a GH11 xylanase (XYNB) from the hyperthermophilic bacterium Dictyoglomus thermophilum by 10-fold at 100°C. The apparent temperature optimum increased only by ∼5°C, which is less than the corresponding increase in mesophilic (∼15°C) and moderately thermophilic (∼10°C) xylanases. The performance of the enzyme was increased significantly at 100-110°C. The increasing concentration of [emim]OAc almost linearly increased the inactivation level of the enzyme activity and 25% [emim]OAc inactivated the enzyme almost fully. On the contrary, the apparent temperature optimum did not decrease to a similar extent, and the degree of denaturation of the enzyme was also much lower according to the residual activity assays. Also, 5% [emim]OAc largely counteracted the benefit obtained by the stabilizing disulfide bridge in the temperature-dependent activity assays, but not in the stability assays. Km was increased in the presence of [emim]OAc, indicating that [emim]OAc interfered the substrate-enzyme interactions. These results indicate that the effect of [emim]OAc is targeted more to the functioning of the enzyme than the basic stability of the hyperthermophilic GH11 xylanase.
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Affiliation(s)
- He Li
- Aalto University, School of Chemical Technology, Department of Biotechnology and Chemical Technology, P.O. Box 16100, 00076 Aalto, Finland
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66
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Nordwald EM, Kaar JL. Mediating Electrostatic Binding of 1-Butyl-3-methylimidazolium Chloride to Enzyme Surfaces Improves Conformational Stability. J Phys Chem B 2013; 117:8977-86. [DOI: 10.1021/jp404760w] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Erik M. Nordwald
- 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
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