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MacDonald ME, Wells NGM, Hassan BA, Dudley JA, Walters KJ, Korzhnev DM, Aramini JM, Smith CA. Effects of Xylanase A double mutation on substrate specificity and structural dynamics. J Struct Biol 2024; 216:108082. [PMID: 38438058 DOI: 10.1016/j.jsb.2024.108082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
While protein activity is traditionally studied with a major focus on the active site, the activity of enzymes has been hypothesized to be linked to the flexibility of adjacent regions, warranting more exploration into how the dynamics in these regions affects catalytic turnover. One such enzyme is Xylanase A (XylA), which cleaves hemicellulose xylan polymers by hydrolysis at internal β-1,4-xylosidic linkages. It contains a "thumb" region whose flexibility has been suggested to affect the activity. The double mutation D11F/R122D was previously found to affect activity and potentially bias the thumb region to a more open conformation. We find that the D11F/R122D double mutation shows substrate-dependent effects, increasing activity on the non-native substrate ONPX2 but decreasing activity on its native xylan substrate. To characterize how the double mutant causes these kinetics changes, nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations were used to probe structural and flexibility changes. NMR chemical shift perturbations revealed structural changes in the double mutant relative to the wild-type, specifically in the thumb and fingers regions. Increased slow-timescale dynamics in the fingers region was observed as intermediate-exchange line broadening. Lipari-Szabo order parameters show negligible changes in flexibility in the thumb region in the presence of the double mutation. To help understand if there is increased energetic accessibility to the open state upon mutation, alchemical free energy simulations were employed that indicated thumb opening is more favorable in the double mutant. These studies aid in further characterizing how flexibility in adjacent regions affects the function of XylA.
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Affiliation(s)
- Meagan E MacDonald
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States; Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, United States
| | - Nicholas G M Wells
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States
| | - Bakar A Hassan
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Joshua A Dudley
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, United States
| | - James M Aramini
- Structural Biology Initiative, Advanced Science Research Center, The City University of New York, New York, NY 10031, United States
| | - Colin A Smith
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States.
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Cao L, Lin M, Ning J, Meng X, Pu X, Zhang R, Wu Q, Huang Z, Zhou J. Critical Roles of Acidic Residues in Loop Regions of the Structural Surface for the Salt Tolerance of a GH39 β-d-Xylosidase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5805-5815. [PMID: 38451212 DOI: 10.1021/acs.jafc.3c07957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Xylan is the main component of hemicellulose. Complete hydrolysis of xylan requires synergistically acting xylanases, such as β-d-xylosidases. Salt-tolerant β-d-xylosidases have significant application benefits, but few reports have explored the critical amino acids affecting the salt tolerance of xylosidases. Herein, the site-directed mutation was used to demonstrate that negative electrostatic potentials generated by 19 acidic residues in the loop regions of the structural surface positively correlated with the improved salt tolerance of GH39 β-d-xylosidase JB13GH39P28. These mutants showed reduced negative potentials on structural surfaces as well as a 13-43% decrease in stability in 3.0-30.0% (w/v) NaCl. Six key residue sites, D201, D259, D297, D377, D395, and D474, were confirmed to influence both the stability and activity of GH39 β-d-xylosidase. The activity of the GH39 β-d-xylosidase was found promoting by SO42- and inhibiting by NO3-. Values of Km and Kcat/Km decreased aggravatedly in 30.0% (w/v) NaCl when mutation operated on residues E179 and D182 in the loop regions of the catalytic domain. Taken together, mutation on acidic residues in loop regions from catalytic and noncatalytic domains may cause the deformation of catalytic pocket and aggregation of protein particles then decrease the stability, binding affinity, and catalytic efficiency of the β-d-xylosidase.
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Affiliation(s)
- Lijuan Cao
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Mingyue Lin
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Juan Ning
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Xin Meng
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Xiong Pu
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Rui Zhang
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Qian Wu
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Zunxi Huang
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Junpei Zhou
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
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Pan K, Liu Z, Zhang Z, Jin S, Yu Z, Liu T, Zhang T, Zhao J, Li Z. Improving the Specific Activity and Thermostability of Psychrophilic Xylosidase AX543 by Comparative Mutagenesis. Foods 2022; 11:foods11162463. [PMID: 36010463 PMCID: PMC9407119 DOI: 10.3390/foods11162463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Improving the specific activity and thermostability of psychrophilic xylosidase is important for improving its enzymatic performance and promoting its industrial application. Herein, a psychrophilic xylosidase AX543 exhibited activity in the temperature range between 0 and 35 °C, with optimum activity at 20 °C, which is lower than that of other reported psychrophilic xylosidases. The thermostability, specific activity, and catalytic efficiency of the site-directed variants G110S, Q201R, and L2 were significantly enhanced, without affecting the optimal reaction temperature. Comparative protein structural analysis and molecular dynamics simulation indicated that these improvements might be the result of the increased hydrogen bonds interaction and improved structural rigidity. Furthermore, homologous module substitution with four segments demonstrated that the psychrophilic characteristics of AX543 are the results of the whole protein structure, and the C-terminal segment A4 appears to be more essential in determining psychrophilic characteristics, exhibiting potentiality to produce more psychrophilic xylosidases. This study provides valuable structural information on psychrophilic xylosidases and also offers attractive modification strategies to modify catalytic activity, thermostability, and optimal reaction temperature.
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Affiliation(s)
- Kungang Pan
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhongqi Liu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhengjie Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shanzheng Jin
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhao Yu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tianhui Liu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tongcun Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Junqi Zhao
- School of Chemical and Biological Engineering, Qilu Institute of Technology, Jinan 250200, China
- Correspondence: (J.Z.); (Z.L.)
| | - Zhongyuan Li
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Correspondence: (J.Z.); (Z.L.)
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The Emergence of New Catalytic Abilities in an Endoxylanase from Family GH10 by Removing an Intrinsically Disordered Region. Int J Mol Sci 2022; 23:ijms23042315. [PMID: 35216436 PMCID: PMC8874783 DOI: 10.3390/ijms23042315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 02/05/2023] Open
Abstract
Endoxylanases belonging to family 10 of the glycoside hydrolases (GH10) are versatile in the use of different substrates. Thus, an understanding of the molecular mechanisms underlying substrate specificities could be very useful in the engineering of GH10 endoxylanases for biotechnological purposes. Herein, we analyzed XynA, an endoxylanase that contains a (β/α)8-barrel domain and an intrinsically disordered region (IDR) of 29 amino acids at its amino end. Enzyme activity assays revealed that the elimination of the IDR resulted in a mutant enzyme (XynAΔ29) in which two new activities emerged: the ability to release xylose from xylan, and the ability to hydrolyze p-nitrophenyl-β-d-xylopyranoside (pNPXyl), a substrate that wild-type enzyme cannot hydrolyze. Circular dichroism and tryptophan fluorescence quenching by acrylamide showed changes in secondary structure and increased flexibility of XynAΔ29. Molecular dynamics simulations revealed that the emergence of the pNPXyl-hydrolyzing activity correlated with a dynamic behavior not previously observed in GH10 endoxylanases: a hinge-bending motion of two symmetric regions within the (β/α)8-barrel domain, whose hinge point is the active cleft. The hinge-bending motion is more intense in XynAΔ29 than in XynA and promotes the formation of a wider active site that allows the accommodation and hydrolysis of pNPXyl. Our results open new avenues for the study of the relationship between IDRs, dynamics and activity of endoxylanases, and other enzymes containing (β/α)8-barrel domain.
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Wang L, Cao K, Pedroso MM, Wu B, Gao Z, He B, Schenk G. Sequence- and structure-guided improvement of the catalytic performance of a GH11 family xylanase from Bacillus subtilis. J Biol Chem 2021; 297:101262. [PMID: 34600889 PMCID: PMC8546418 DOI: 10.1016/j.jbc.2021.101262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 12/02/2022] Open
Abstract
Xylanases produce xylooligosaccharides from xylan and have thus attracted increasing attention for their usefulness in industrial applications. Previously, we demonstrated that the GH11 xylanase XynLC9 from Bacillus subtilis formed xylobiose and xylotriose as the major products with negligible production of xylose when digesting corncob-extracted xylan. Here, we aimed to improve the catalytic performance of XynLC9 via protein engineering. Based on the sequence and structural comparisons of XynLC9 with the xylanases Xyn2 from Trichoderma reesei and Xyn11A from Thermobifida fusca, we identified the N-terminal residues 5-YWQN-8 in XynLC9 as engineering hotspots and subjected this sequence to site saturation and iterative mutagenesis. The mutants W6F/Q7H and N8Y possessed a 2.6- and 1.8-fold higher catalytic activity than XynLC9, respectively, and both mutants were also more thermostable. Kinetic measurements suggested that W6F/Q7H and N8Y had lower substrate affinity, but a higher turnover rate (kcat), which resulted in increased catalytic efficiency than WT XynLC9. Furthermore, the W6F/Q7H mutant displayed a 160% increase in the yield of xylooligosaccharides from corncob-extracted xylan. Molecular dynamics simulations revealed that the W6F/Q7H and N8Y mutations led to an enlarged volume and surface area of the active site cleft, which provided more space for substrate entry and product release and thus accelerated the catalytic activity of the enzyme. The molecular evolution approach adopted in this study provides the design of a library of sequences that captures functional diversity in a limited number of protein variants.
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Affiliation(s)
- Lijuan Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Kun Cao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China.
| | - Zhen Gao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China.
| | - Bingfang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
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Vucinic J, Novikov G, Montanier CY, Dumon C, Schiex T, Barbe S. A Comparative Study to Decipher the Structural and Dynamics Determinants Underlying the Activity and Thermal Stability of GH-11 Xylanases. Int J Mol Sci 2021; 22:ijms22115961. [PMID: 34073139 PMCID: PMC8199483 DOI: 10.3390/ijms22115961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022] Open
Abstract
With the growing need for renewable sources of energy, the interest for enzymes capable of biomass degradation has been increasing. In this paper, we consider two different xylanases from the GH-11 family: the particularly active GH-11 xylanase from Neocallimastix patriciarum, NpXyn11A, and the hyper-thermostable mutant of the environmentally isolated GH-11 xylanase, EvXyn11TS. Our aim is to identify the molecular determinants underlying the enhanced capacities of these two enzymes to ultimately graft the abilities of one on the other. Molecular dynamics simulations of the respective free-enzymes and enzyme–xylohexaose complexes were carried out at temperatures of 300, 340, and 500 K. An in-depth analysis of these MD simulations showed how differences in dynamics influence the activity and stability of these two enzymes and allowed us to study and understand in greater depth the molecular and structural basis of these two systems. In light of the results presented in this paper, the thumb region and the larger substrate binding cleft of NpXyn11A seem to play a major role on the activity of this enzyme. Its lower thermal stability may instead be caused by the higher flexibility of certain regions located further from the active site. Regions such as the N-ter, the loops located in the fingers region, the palm loop, and the helix loop seem to be less stable than in the hyper-thermostable EvXyn11TS. By identifying molecular regions that are critical for the stability of these enzymes, this study allowed us to identify promising targets for engineering GH-11 xylanases. Eventually, we identify NpXyn11A as the ideal host for grafting the thermostabilizing traits of EvXyn11TS.
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Affiliation(s)
- Jelena Vucinic
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
- Université Fédérale de Toulouse, ANITI, INRAE, UR 875, 31326 Toulouse, France;
| | - Gleb Novikov
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Cédric Y. Montanier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Claire Dumon
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Thomas Schiex
- Université Fédérale de Toulouse, ANITI, INRAE, UR 875, 31326 Toulouse, France;
| | - Sophie Barbe
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
- Correspondence:
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Marneth K, van den Elst H, Cramer‐Blok A, Codee J, Overkleeft HS, Aerts JMFG, Ubbink M, Ben Bdira F. Tuning the Transglycosylation Reaction of a GH11 Xylanase by a Delicate Enhancement of its Thumb Flexibility. Chembiochem 2021; 22:1743-1749. [PMID: 33534182 PMCID: PMC8251542 DOI: 10.1002/cbic.202000856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/01/2021] [Indexed: 12/31/2022]
Abstract
Glycoside hydrolases (GHs) are attractive tools for multiple biotechnological applications. In conjunction with their hydrolytic function, GHs can perform transglycosylation under specific conditions. In nature, oligosaccharide synthesis is performed by glycosyltransferases (GTs); however, the industrial use of GTs is limited by their instability in solution. A key difference between GTs and GHs is the flexibility of their binding site architecture. We have used the xylanase from Bacillus circulans (BCX) to study the interplay between active-site flexibility and transglycosylation. Residues of the BCX "thumb" were substituted to increase the flexibility of the enzyme binding site. Replacement of the highly conserved residue P116 with glycine shifted the balance of the BCX enzymatic reaction toward transglycosylation. The effects of this point mutation on the structure and dynamics of BCX were investigated by NMR spectroscopy. The P116G mutation induces subtle changes in the configuration of the thumb and enhances the millisecond dynamics of the active site. Based on our findings, we propose the remodelling of the GH enzymes glycon site flexibility as a strategy to improve the transglycosylation efficiency of these biotechnologically important catalysts.
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Affiliation(s)
- Kim Marneth
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hans van den Elst
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Anneloes Cramer‐Blok
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jeroen Codee
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Fredj Ben Bdira
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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Silva SRB, de Lima Neto JX, Fuzo CA, Fulco UL, Vieira DS. A quantum biochemistry investigation of the protein-protein interactions for the description of allosteric modulation on biomass-degrading chimera. Phys Chem Chem Phys 2020; 22:25936-25948. [PMID: 33164009 DOI: 10.1039/d0cp04415f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The worldwide dependence of population on fossil fuels continues to have several harmful implications for the environment. Bioethanol is an excellent option for renewable fuel to replace the current greenhouse gas emitters. In addition, its production by enzymatic route has gained space among the industrial processes because it replaces the traditional acid treatment. Due to its high versatility, the xylanase family is used in this process as an accessory enzyme for degrading the lignocellulosic substrate of biomass. A chimera built by a xylanolytic domain (Xyl) and a xylose-binding protein (XBP) showed an experimentally improved catalytic efficiency and interdomain allosteric modulation after xylose binding. In this context, we performed a quantum biochemistry characterization of the interactions between these domains and dynamic cross-correlation (DCC) analysis after performing molecular dynamics (DM) simulations of the systems in the presence and absence of xylose in the XBP active site. We used the density functional theory (DFT) within the molecular fractionation with the conjugated caps (MFCC) approach to describe the pair energies, and the corresponding energy difference between the chimera domains responsible for the allosteric effect and amino acid DCC to evaluate the interdomain coupling differences between the energy states. The detailed energetic investigation together with the related structural and dynamics counterparts revealed the molecular mechanisms of chimeric improvement of the xylanase activity observed experimentally. This mechanism was correlated with greater stability and high connectivity at the interdomain interface in the xylose bound relative to the free chimera. We identify the contributions of hydrogen bonds, hydrophobic interactions and water-mediated interactions in the interdomain region responsible for stability together with the structural and dynamical elements related to the allosteric effect. Taken together, these observations led to a comprehensive understanding of the chimera's modulatory action that occurs through the formation of a highly connected interface that makes the essential movements related to xylanolytic activity in xylanase correlated to those of the xylose-binding protein.
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Sun D, Liu X, Zhu M, Chen Y, Li C, Cheng X, Zhu Z, Lu F, Qin HM. Efficient Biosynthesis of High-Value Succinic Acid and 5-Hydroxyleucine Using a Multienzyme Cascade and Whole-Cell Catalysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12502-12510. [PMID: 31623431 DOI: 10.1021/acs.jafc.9b05529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Succinic acid (SA) is applied in the food, chemical, and pharmaceutical industries. 5-Hydroxyleucine (5-HLeu) is a promising precursor for the biosynthesis of antituberculosis drugs. Here, we designed a promising synthetic route for the simultaneous production of SA and 5-HLeu by combining l-leucine dioxygenase (NpLDO), l-glutamate oxidase (LGOX), and catalase (CAT). Two bioconversion systems: "a multienzyme cascade catalysis in vitro" (MECCS) and "whole-cell catalysis system" (WCCS) were constructed. A high-activity NpLDO mutant was screened by error-prone polymerase chain reaction (PCR) and showed 6.1-fold improvement of catalytic activity. After optimization of reaction conditions, MECSS yielded 3.15 g/L SA and 3.92 g/L 5-HLeu, while the production of SA and 5-HLeu by the most effective WCSS reached 15.12 and 18.83 g/L, respectively. This is the first attempt to use ferrous iron/α-ketoglutarate-dependent dioxygenases for the simultaneous production of SA and hydroxy-amino-acid. This research provides a tool for industrial production of food of high-value products from low-cost raw materials.
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Affiliation(s)
- Dengyue Sun
- Key Laboratory of Industrial Fermentation Microbiology , Ministry of Education , Tianjin 300457 , People's Republic of China
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
- Tianjin Key Laboratory of Industrial Microbiology , Tianjin 300457 , People's Republic of China
| | - Xin Liu
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Menglu Zhu
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Ying Chen
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Chao Li
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Xiaotao Cheng
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Zhangliang Zhu
- Key Laboratory of Industrial Fermentation Microbiology , Ministry of Education , Tianjin 300457 , People's Republic of China
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
- Tianjin Key Laboratory of Industrial Microbiology , Tianjin 300457 , People's Republic of China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology , Ministry of Education , Tianjin 300457 , People's Republic of China
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
- Tianjin Key Laboratory of Industrial Microbiology , Tianjin 300457 , People's Republic of China
- National Engineering Laboratory for Industrial Enzymes , Tianjin 300457 , People's Republic of China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology , Ministry of Education , Tianjin 300457 , People's Republic of China
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
- Tianjin Key Laboratory of Industrial Microbiology , Tianjin 300457 , People's Republic of China
- National Engineering Laboratory for Industrial Enzymes , Tianjin 300457 , People's Republic of China
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10
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Sun D, Gao D, Liu X, Zhu M, Li C, Chen Y, Zhu Z, Lu F, Qin HM. Redesign and engineering of a dioxygenase targeting biocatalytic synthesis of 5-hydroxyl leucine. Catal Sci Technol 2019. [DOI: 10.1039/c9cy00110g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The protein engineering and metabolic engineering strategies are performed to solve rate-limiting steps in the biosynthesis of 5-HLeu.
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Affiliation(s)
- Dengyue Sun
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Dengke Gao
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Xin Liu
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Menglu Zhu
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Chao Li
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Ying Chen
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Zhangliang Zhu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
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Sutthibutpong T, Rattanarojpong T, Khunrae P. Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays. J Biomol Struct Dyn 2017; 36:3978-3992. [DOI: 10.1080/07391102.2017.1404934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
- Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Triwit Rattanarojpong
- Department of Microbiology, Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi, 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Pongsak Khunrae
- Department of Microbiology, Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi, 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
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12
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Substitution of a non-active-site residue located on the T3 loop increased the catalytic efficiency of endo -polygalacturonases. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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13
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Tu T, Meng K, Luo H, Turunen O, Zhang L, Cheng Y, Su X, Ma R, Shi P, Wang Y, Yang P, Yao B. New Insights into the Role of T3 Loop in Determining Catalytic Efficiency of GH28 Endo-Polygalacturonases. PLoS One 2015; 10:e0135413. [PMID: 26327390 PMCID: PMC4556634 DOI: 10.1371/journal.pone.0135413] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 07/21/2015] [Indexed: 12/15/2022] Open
Abstract
Intramolecular mobility and conformational changes of flexible loops have important roles in the structural and functional integrity of proteins. The Achaetomium sp. Xz8 endo-polygalacturonase (PG8fn) of glycoside hydrolase (GH) family 28 is distinguished for its high catalytic activity (28,000 U/mg). Structure modeling indicated that PG8fn has a flexible T3 loop that folds partly above the substrate in the active site, and forms a hydrogen bond to the substrate by a highly conserved residue Asn94 in the active site cleft. Our research investigates the catalytic roles of Asn94 in T3 loop which is located above the catalytic residues on one side of the substrate. Molecular dynamics simulation performed on the mutant N94A revealed the loss of the hydrogen bond formed by the hydroxyl group at O34 of pentagalacturonic acid and the crucial ND2 of Asn94 and the consequent detachment and rotation of the substrate away from the active site, and that on N94Q caused the substrate to drift away from its place due to the longer side chain. In line with the simulations, site-directed mutagenesis at this site showed that this position is very sensitive to amino acid substitutions. Except for the altered Km values from 0.32 (wild type PG8fn) to 0.75–4.74 mg/ml, all mutants displayed remarkably lowered kcat (~3–20,000 fold) and kcat/Km (~8–187,500 fold) values and significantly increased △(△G) values (5.92–33.47 kJ/mol). Taken together, Asn94 in the GH28 T3 loop has a critical role in positioning the substrate in a correct way close to the catalytic residues.
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Affiliation(s)
- Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Kun Meng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Ossi Turunen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, FI-00076, Aalto, Finland
| | - Lujia Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yanli Cheng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Pengjun Shi
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Yaru Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Peilong Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- * E-mail:
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14
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Mhlongo NN, Ebrahim M, Skelton AA, Kruger HG, Williams IH, Soliman MES. Dynamics of the thumb-finger regions in a GH11 xylanase Bacillus circulans: comparison between the Michaelis and covalent intermediate. RSC Adv 2015. [DOI: 10.1039/c5ra16836h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The structure and dynamics of B. circulans β-1,4-xylanase (BCX) were comparatively studied utilizing molecular dynamics.
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Affiliation(s)
- Ndumiso N. Mhlongo
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Mahasin Ebrahim
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Adam A. Skelton
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit
- School of Health Sciences University of KwaZulu-Natal
- Durban 4001
- South Africa
| | | | - Mahmoud E. S. Soliman
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences University of KwaZulu-Natal
- Durban 4001
- South Africa
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15
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Jaeger VW, Pfaendtner J. Structure, dynamics, and activity of xylanase solvated in binary mixtures of ionic liquid and water. ACS Chem Biol 2013; 8:1179-86. [PMID: 23517495 DOI: 10.1021/cb3006837] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have discovered that a family 11 xylanase from Trichoderma longibrachiatum maintains significant activity in low concentrations of the ionic liquids (IL) 1-ethyl-3-methyl-imidazolium acetate ([EMIM][OAc]) or 1-ethyl-3-methyl-imidazolium ethyl sulfate ([EMIM][EtSO4]) in water. In order to understand the mechanisms by which the ionic liquids affect the activity of xylanase, we conducted molecular dynamics simulations of the enzyme in various concentrations of the cosolvent. The simulations show that higher concentrations of ionic liquid correlate with less deviation from the starting crystallographic structure. Dynamic motion of the protein is severely dampened by even the lowest tested concentrations of ionic liquid as measured by root-mean-square fluctuation. Principal component analysis shows that the characteristics of the main modes of enzyme motion are greatly affected by the choice of solvent. Cations become kinetically trapped in the binding pocket, allowing them to act as a competitive inhibitor to the natural substrate. Dynamic light scattering and kinetic studies evaluated the stability of the enzyme in the new solvents. These studies indicate that likely factors in the loss of enzyme activity for this xylanase are the dampening of dynamic motion and kinetic trapping of cations in the binding pocket as opposed to the denaturing of the protein.
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Affiliation(s)
- Vance W. Jaeger
- 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
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16
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Cota J, Oliveira LC, Damásio ARL, Citadini AP, Hoffmam ZB, Alvarez TM, Codima CA, Leite VBP, Pastore G, de Oliveira-Neto M, Murakami MT, Ruller R, Squina FM. Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1492-500. [PMID: 23459129 DOI: 10.1016/j.bbapap.2013.02.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 01/23/2013] [Accepted: 02/20/2013] [Indexed: 01/27/2023]
Abstract
Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (kcat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes.
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Affiliation(s)
- Junio Cota
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Campinas, SP, Brazil
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17
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18
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Paës G, Cortés J, Siméon T, O'Donohue MJ, Tran V. Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase. Comput Struct Biotechnol J 2012; 1:e201207001. [PMID: 24688637 PMCID: PMC3962102 DOI: 10.5936/csbj.201207001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/23/2012] [Accepted: 05/27/2012] [Indexed: 12/17/2022] Open
Abstract
Dynamics is a key feature of enzyme catalysis. Unfortunately, current experimental and computational techniques do not yet provide a comprehensive understanding and description of functional macromolecular motions. In this work, we have extended a novel computational technique, which combines molecular modeling methods and robotics algorithms, to investigate functional motions of protein loops. This new approach has been applied to study the functional importance of the so-called thumb-loop in the glycoside hydrolase family 11 xylanase from Thermobacillus xylanilyticus (Tx-xyl). The results obtained provide new insight into the role of the loop in the glycosylation/deglycosylation catalytic cycle, and underline the key importance of the nature of the residue located at the tip of the thumb-loop. The effect of mutations predicted in silico has been validated by in vitro site-directed mutagenesis experiments. Overall, we propose a comprehensive model of Tx-xyl catalysis in terms of substrate and product dynamics by identifying the action of the thumb-loop motion during catalysis.
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Affiliation(s)
- Gabriel Paës
- CNRS, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; University of Nantes, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; INRA, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; University of Reims Champagne-Ardenne, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France
| | - Juan Cortés
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France ; University of Toulouse, LAAS, F-31400 Toulouse, France
| | - Thierry Siméon
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France ; University of Toulouse, LAAS, F-31400 Toulouse, France
| | - Michael J O'Donohue
- INRA, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; University of Reims Champagne-Ardenne, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; INRA, UMR792 LISBP, 137 avenue de Rangueil, F-31077 Toulouse, France ; INSA, UMR792 LISBP, 137 avenue de Rangueil, F-31077 Toulouse, France
| | - Vinh Tran
- CNRS, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; University of Nantes, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France
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