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Manna B, Chanda P, Datta S, Ghosh A. Elucidating the Ionic Liquid-Induced Mixed Inhibition of GH1 β-Glucosidase H0HC94. J Phys Chem B 2023; 127:8406-8416. [PMID: 37751511 DOI: 10.1021/acs.jpcb.3c02125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Deciphering the ionic liquid (IL) tolerance of glycoside hydrolases (GHs) to improve their hydrolysis efficiency for fermentable sugar synthesis in the "one-pot" process has long been a hurdle for researchers. In this work, we employed experimental and theoretical approaches to investigate the 1-ethyl-3-methylimidazolium acetate ([C2C1im][MeCO2])-induced inhibition of GH1 β-glucosidase (H0HC94) from Agrobacterium tumefaciens 5A. At 10-15% [C2C1im][MeCO2] concentration, H0HC94 experiences competitive inhibition (R2 = 0.97, alpha = 2.8). As the IL content increased to 20-25%, the inhibition pattern shifted to mixed-type inhibition (R2 = 0.98, alpha = 3.4). These findings were further confirmed through characteristic inhibition plots using Lineweaver-Burk plots. Atomistic molecular dynamics simulations conducted with 0% [C2C1im][MeCO2], 10% [C2C1im][MeCO2], and 25% [C2C1im][MeCO2] revealed the accumulation of [C2C1im]+ at the negatively charged active site of H0HC94 in 10% [C2C1im][MeCO2], supporting the occurrence of competitive inhibition at lower IL concentrations. At higher IL concentrations, the cations and anions bound to the secondary binding sites (SBSs) of H0HC94, leading to a tertiary conformational change, as captured by the principal component analysis based on the free-energy landscape and protein structure networks. The altered conformation of H0HC94 affected the interaction with [C2C1im][MeCO2], which could possibly shift the inhibition from competitive to more mixed-type (competitive + noncompetitive) inhibition, as observed in the experiments. For the first time, we report a combined experimental and theoretical insight behind the mixed inhibition of a GH1 β-glucosidase. Our findings indicated the role of SBS in IL-induced inhibition, which could aid in developing more IL-tolerant β-glucosidases for biorefinery applications.
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Affiliation(s)
- Bharat Manna
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal741246, India
| | - Pinaki Chanda
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal741246, India
| | - Supratim Datta
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal741246, India
- Center for the Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
- Center for the Climate and Environmental Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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Paul M, Mohapatra S, Kumar Das Mohapatra P, Thatoi H. Microbial cellulases - An update towards its surface chemistry, genetic engineering and recovery for its biotechnological potential. BIORESOURCE TECHNOLOGY 2021; 340:125710. [PMID: 34365301 DOI: 10.1016/j.biortech.2021.125710] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The inherent resistance of lignocellulosic biomass makes it impervious for industrially important enzymes such as cellulases to hydrolyze cellulose. Further, the competitive absorption behavior of lignin and hemicellulose for cellulases, due to their electron-rich surfaces augments the inappropriate utilization of these enzymes. Hence, modification of the surface charge of the cellulases to reduce its non-specific binding to lignin and enhance its affinity for cellulose is an urgent necessity. Further, maintaining the stability of cellulases by the preservation of their secondary structures using immobilization techniques will also play an integral role in its industrial production. In silico approaches for increasing the catalytic activity of cellulase enzymes is also significant along with a range of substrate specificity. In addition, enhanced productivity of cellulases by tailoring the related genes through the process of genetic engineering and higher cellulase recovery after saccharification seems to be promising areas for efficient and large-scale enzyme production concepts.
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Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India
| | - Sonali Mohapatra
- Department of Biotechnology, College of Engineering & Technology, Bhubaneswar 751003, Odisha, India
| | - Pradeep Kumar Das Mohapatra
- Department of Microbiology, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India; PAKB Environment Conservation Centre, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India.
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Song Y, Wu X, Zhao Y, Jiang X, Wang L. Comparative molecular dynamics simulations identify a salt-sensitive loop responsible for the halotolerant activity of GH5 cellulases. J Biomol Struct Dyn 2021; 40:9522-9529. [PMID: 34043936 DOI: 10.1080/07391102.2021.1930167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Halotolerant glycoside hydrolases (GH) have broad application potentials in biorefinery industries. Elucidating the structure-activity relationship underlying the halotolerant catalysis is essential to design superior biocatalysts. Here, we performed molecular dynamics simulations to investigate the structural dynamics of two GH5 cellulases, namely the halotolerant Cel5R and non-halotolerant TfCel5A. Through characterizing the physical properties at different salt concentrations, the results revealed that the overall structures of Cel5R and TfCel5A were marginally affected by the increase in salt concentrations. However, a salt-sensitive loop was identified from both Cel5R and TfCel5A based on its significantly increased flexibility at high salt concentrations. Importantly, compared to TfCel5A the salt-sensitive loop of Cel5R engaged more sodium ions and water molecules around the active site of the enzyme. Besides, the unique residue motif of the salt-sensitive loop in Cel5R formed more intramolecular hydrogen bonds, stabilizing the active architecture of Cel5R at high salt concentrations. Collectively, the structural and dynamic differences may contribute to the various catalytic halotolerance of Cel5R and TfCel5A. These findings provide mechanistic insight into the halotolerant catalysis and will guide the ration design of GH5 cellulases with improved catalytic properties.Communicated by Ramaswamy H. Samy.
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Affiliation(s)
- Yuxuan Song
- Taishan College, Shandong University, Qingdao, China
| | - Xiuyun Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yue Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xukai Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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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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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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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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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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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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