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Ghanta KP, Mondal S, Mondal S, Bandyopadhyay S. Contrasting Effects of Ionic Liquids of Varying Degree of Hydrophilicity on the Conformational and Interfacial Properties of a Globular Protein. J Phys Chem B 2021; 125:9441-9453. [PMID: 34433280 DOI: 10.1021/acs.jpcb.1c04167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ionic liquids (ILs), depending on their cation-anion combinations, are known to influence the conformational properties and activities of proteins in a nonuniform manner. To obtain microscopic understanding of such influence, it is important to characterize protein-IL interactions and explore the modified solvation environment around the protein. In this work, molecular dynamics (MD) simulations of the globular protein α-lactalbumin have been carried out in aqueous IL solutions containing 1-butyl-3-methylimidazolium cations (BMIM+) in combination with a series of anions with varying degree of hydrophilicity, namely, hexafluorophosphate (PF6-), ethyl sulfate (ETS-), acetate (OAc-), chloride (Cl-), dicyanamide (DCA-), and nitrate (NO3-) . The calculations revealed that ILs with hydrophobic and hydrophilic anions have contrasting influence on conformational flexibility of the protein. It is further observed that the BMIM+ cations exhibit site-specific orientations at the interface depending on the hydrophilicity of the anion component. Most importantly, the results demonstrated enhanced propensity of hydrophilic ILs to replace relatively weaker protein-water hydrogen bonds by stronger protein-IL hydrogen bonds at the protein surface as compared to the hydrophobic ILs. Such breaking of protein-water hydrogen bonds at a greater extent leads to greater loss of water hydrating the protein in the presence of hydrophilic ILs, thereby reducing the protein's stability.
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Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Souvik Mondal
- 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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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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3
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Dasari S, Mallik BS. Association of Nucleobases in Hydrated Ionic Liquid from Biased Molecular Dynamics Simulations. J Phys Chem B 2018; 122:9635-9645. [PMID: 30260229 DOI: 10.1021/acs.jpcb.8b05778] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We employed metadynamics-based classical molecular dynamics simulations to methylated adenine-thymine (mA-mT) and guanine-cytosine (mG-mC) base pairs to see favorable conformations in various concentrations of hydrated 1-ethyl, 3-methyl imidazolium acetate. We investigated various stacked and hydrogen-bonded conformations of association of base pairs through appropriately chosen collective variables. Stacked conformations more favored in water for both base pairs, whereas Watson-Crick (WC) hydrogen-bonding conformations are favored in pure and hydrated ionic liquids (ILs) except for 0.75 mol fraction IL. We observe that EMIm cations surround the base pairs in WC conformations creating a kind of hydrophobic cavity and protect the hydrogen bonds between base pairs. However, the five-membered heteroaromatic rings of cations stack with the nucleobases in the cation-base-cation (π-π-π) model, which resembles the base-base-base stacking in a DNA duplex. Interestingly, from additional simulations of 0.5 mol fraction hydrated choline dihydrogen phosphate IL, we observe that the stacked conformations become more favored than the WC conformation due to the absence of π-bonds in cations. The calculated values of relative solubility of base pairs in pure and hydrated ionic liquids compared to those in pure water correlate well with the free energy values of WC and stacked conformations.
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Affiliation(s)
- Sathish Dasari
- Department of Chemistry , Indian Institute of Technology Hyderabad , Kandi , Sangareddy 502285 , Telangana , India
| | - Bhabani S Mallik
- Department of Chemistry , Indian Institute of Technology Hyderabad , Kandi , Sangareddy 502285 , Telangana , India
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Azov VA, Egorova KS, Seitkalieva MM, Kashin AS, Ananikov VP. "Solvent-in-salt" systems for design of new materials in chemistry, biology and energy research. Chem Soc Rev 2018; 47:1250-1284. [PMID: 29410995 DOI: 10.1039/c7cs00547d] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Inorganic and organic "solvent-in-salt" (SIS) systems have been known for decades but have attracted significant attention only recently. Molten salt hydrates/solvates have been successfully employed as non-flammable, benign electrolytes in rechargeable lithium-ion batteries leading to a revolution in battery development and design. SIS with organic components (for example, ionic liquids containing small amounts of water) demonstrate remarkable thermal stability and tunability, and present a class of admittedly safer electrolytes, in comparison with traditional organic solvents. Water molecules tend to form nano- and microstructures (droplets and channel networks) in ionic media impacting their heterogeneity. Such microscale domains can be employed as microreactors for chemical and enzymatic synthesis. In this review, we address known SIS systems and discuss their composition, structure, properties and dynamics. Special attention is paid to the current and potential applications of inorganic and organic SIS systems in energy research, chemistry and biochemistry. A separate section of this review is dedicated to experimental methods of SIS investigation, which is crucial for the development of this field.
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Affiliation(s)
- Vladimir A Azov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia.
| | - Ksenia S Egorova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia.
| | - Marina M Seitkalieva
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia.
| | - Alexey S Kashin
- 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. and Department of Chemistry, Saint Petersburg State University, Stary Petergof, 198504, Russia
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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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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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7
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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: 911] [Impact Index Per Article: 130.1] [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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Andersson CD, Martinez N, Zeller D, Rondahl SH, Koza MM, Frick B, Ekström F, Peters J, Linusson A. Changes in dynamics of α-chymotrypsin due to covalent inhibitors investigated by elastic incoherent neutron scattering. Phys Chem Chem Phys 2017; 19:25369-25379. [DOI: 10.1039/c7cp04041e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of chymotrypsin increases when bound to two different covalent inhibitors. These effects were analyzed by univariate and multivariate methods.
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Affiliation(s)
| | - N. Martinez
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
- Univ. Grenoble Alpes
- IBS and LiPhy
| | - D. Zeller
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
- Univ. Grenoble Alpes
- IBS and LiPhy
| | - S. H. Rondahl
- CBRN Defence and Security
- Swedish Defence Research Agency
- SE-90621 Umeå
- Sweden
| | - M. M. Koza
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
| | - B. Frick
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
| | - F. Ekström
- CBRN Defence and Security
- Swedish Defence Research Agency
- SE-90621 Umeå
- Sweden
| | - J. Peters
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
- Univ. Grenoble Alpes
- IBS and LiPhy
| | - A. Linusson
- Department of Chemistry
- Umeå University
- SE-90187 Umeå
- Sweden
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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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Fan Y, Dong X, Zhong Y, Li J, Miao J, Hua S, Li Y, Cheng B, Chen W. Effects of ionic liquids on the hydrolysis of casein by lumbrokinase. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.12.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Matsubara Y, Kadotani S, Nishihara T, Hikino Y, Fukaya Y, Nokami T, Itoh T. Phosphonium alkyl PEG sulfate ionic liquids as coating materials for activation ofBurkholderia cepacialipase. Biotechnol J 2015; 10:1944-51. [DOI: 10.1002/biot.201500413] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/23/2015] [Accepted: 10/19/2015] [Indexed: 01/17/2023]
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12
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Key factors affecting the activity and stability of enzymes in ionic liquids and novel applications in biocatalysis. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.03.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Latif MAM, Micaêlo N, Abdul Rahman MB. Solvation free energies in [bmim]-based ionic liquids: Anion effect toward solvation of amino acid side chain analogues. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.08.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Mohammad Latif MA, Micaêlo NM, Abdul Rahman MB. Influence of anion–water interactions on the behaviour of lipases in room temperature ionic liquids. RSC Adv 2014. [DOI: 10.1039/c4ra07460b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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15
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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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