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Andrys R, Monnier C, Antonijević Miljaković E, Mickova V, Musilek K, Zemanova L. Towards cost-effective drug discovery: Reusable immobilized enzymes for neurological disease research. Talanta 2024; 276:126263. [PMID: 38788378 DOI: 10.1016/j.talanta.2024.126263] [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: 07/25/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Enzyme handling and utilization bears many challenges such as their limited stability, intolerance of organic solvents, high cost, or inability to reuse. Most of these limitations can be overcome by enzyme immobilization on the surface of solid support. In this work, the recombinant form of human cholinesterases and monoamine oxidases as important drug targets for neurological diseases were immobilized on the surface of magnetic non-porous microparticles by a non-covalent bond utilizing the interaction between a His-tag terminus on the recombinant enzymes and cobalt (Co2+) ions immobilized on the magnetic microparticles. This type of binding led to targeted enzyme orientation, which completely preserved the catalytic activity and allowed high reproducibility of immobilization. In comparison with free enzymes, the immobilized enzymes showed exceptional stability in time and the possibility of repeated use. Relevant Km, Vmax, and IC50 values using known inhibitors were obtained using particular immobilized enzymes. Such immobilized enzymes on magnetic particles could serve as an excellent tool for a sustainable approach in the early stage of drug discovery.
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Affiliation(s)
- Rudolf Andrys
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic.
| | - Charline Monnier
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic.
| | - Evica Antonijević Miljaković
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic; Department of Toxicology "Akademik Danilo Soldatovic", University of Belgrade, Faculty of Pharmacy, Vojvode Stepe 450, 11 000, Belgrade, Serbia.
| | - Veronika Mickova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic.
| | - Kamil Musilek
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic.
| | - Lucie Zemanova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic.
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2
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Fatima U, Deenadayalu N, Venkatesu P. An eminent approach towards next generation solvents for sustainable packaging and stability of enzymes: a comprehensive study of ionic liquid and deep eutectic solvent mixtures. Phys Chem Chem Phys 2024; 26:14766-14776. [PMID: 38716816 DOI: 10.1039/d4cp00931b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid ionic fluids (HIFs) are newly emerging and fascinating sustainable solvent media, which are attracting a great deal of scientific interest in protecting the native structure of proteins. For a few decades, there has been a demand to consider ionic liquids (ILs) and deep eutectic solvents (DESs) as biocompatible solvent media for enzymes; however, in some cases, these solvent media also show limitations. Therefore, this work focuses on synthesising novel HIFs to intensify the properties of existing ILs and DESs by mixing them. Herein, HIFs have been synthesised by the amalgamation of a deep eutectic solvent (DES) and an ionic liquid (IL) with a common cation or anion. Later on, the stability and activity of hen's egg white lysozyme (Lyz) in the presence of biocompatible solvent media and HIFs were studied by various techniques such as UV-vis, steady-state fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) and dynamic light scattering (DLS) measurements. This work emphasises the effect of a DES (synthesised using 1 : 2 choline chloride and malonic acid) [Maline], ILs (1-butyl-3-methylimidazolium chloride [BMIM]Cl or choline acetate [Chn][Ac]) and their corresponding HIFs on the structure and functionality of Lyz. Moreover, we also studied the secondary structure, thermal stability, enzymatic activity and thermodynamic profile of Lyz at pH = 7 in the presence of varying concentrations (0.1 to 0.5 M) of [BMIM]Cl and [Chn][Ac] ILs, Maline as a DES, and Maline [BMIM]Cl (HIF1) and Maline [Chn][Ac] (HIF2). Spectroscopic results elucidate that ILs affect the activity and structural stability of Lyz. In contrast, the stability and activity are inhibited by DES and are enhanced by HIFs at all the studied concentrations. Overall, the experimental results studied explicitly elucidate that the structure and stability of Lyz are maintained in the presence of HIF1 while these properties are intensified in HIF2. This study shows various applications in biocompatible green solvents, particularly in the stability and functionality of proteins, due to their unique combination where the properties counteract the negative effect of either DESs or ILs in HIFs.
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Affiliation(s)
- Urooj Fatima
- Department of Chemistry, University of Delhi, Delhi-110 007, India.
| | - Nirmala Deenadayalu
- Department of Chemistry, Durban University of Technology, Durban - 4000, South Africa.
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Fatima U, Yadav N, Venkatesu P. Sustainable combination of ionic liquid and deep eutectic solvent for protecting and preserving of the protein structure: The synergistic interaction of enzymes and eco-friendly hybrid ionic fluids. Int J Biol Macromol 2024; 268:131997. [PMID: 38697420 DOI: 10.1016/j.ijbiomac.2024.131997] [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: 11/10/2023] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Hybrid ionic fluids (HIFs) are one of the emerging and fascinating sustainable solvent media, a novel environment-friendly solvent for biomolecules. The HIFs have been synthesized by combining a deep eutectic solvent (DES), an ionic liquid (IL) having a common ion. The stability and activity of hen's egg white lysozyme (Lyz) in the presence of a recently designed new class of biocompatible solvents, HIFs have been explored by UV-visible, steady-state fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) along with dynamic light scattering (DLS) measurements. This work emphasizes the effect of DES synthesized by using 1:2 choline chloride and glycerol [Glyn], ILs (1-butly-3-methylimidazolium chloride [BMIM]Cl and choline acetate [Chn][Ac]) and their corresponding HIFs on the structure and functionality of Lyz. Moving forward, we also studied the secondary structure, thermal stability and enzymatic activity and thermodynamic profile of Lyz at pH = 7 in the presence of varying concentrations (0.1 to 0.5) M of [BMIM]Cl, [Chn][Ac] ILs, [Glyn] DES and [Glyn][BMIM]Cl (hybrid ionic fluid1) as well as [Glyn][Chn][Ac] (hybrid ionic fluid2). Spectroscopic results elucidate that ILs affect the activity and structural stability of Lyz, whereas the stability and activity are increased by DES and are maintained by HIFs at all the studied concentrations. Overall, the experimental results studied elucidate expressly that the properties of Lyz are maintained in the presence of hybrid ionic fluid1 while these properties are intensified in hybrid ionic fluid2. This work has elucidated expressly biocompatible green solvents in protein stability and functionality due to the alluring properties of DES, which can counteract the negative effect of ILs in HIFs.
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Affiliation(s)
- Urooj Fatima
- Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Niketa Yadav
- Department of Chemistry, University of Delhi, Delhi 110 007, India
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Koopmann IK, Kramer A, Labes A. Development and validation of reliable astaxanthin quantification from natural sources. PLoS One 2022; 17:e0278504. [PMID: 36459522 PMCID: PMC9718415 DOI: 10.1371/journal.pone.0278504] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 11/09/2022] [Indexed: 12/04/2022] Open
Abstract
Astaxanthin derived from natural sources occurs in the form of various esters and stereomers, which complicates its quantitative and qualitative analysis. To simplify and standardize astaxanthin measurement with high precision, an enzymolysis-based astaxanthin quantification method was developed to hydrolyze astaxanthin esters and determine free astaxanthin in all its diastereomeric forms. Astaxanthin standards and differently processed Haematococcus pluvialis biomass were investigated. Linear correlation of standards of all-E-astaxanthin was observed in a measurement range between extract concentrations of 1.0 μg/mL and 11.2 μg/mL with a coefficient of variation below 5%. The diastereomers 9Z-, and 13Z-astaxanthin, and two di-Z-forms were detected. In contrast to the measurement of standards, the observed measurement range was extended to 30 μg/mL in extracts from H. pluvialis. The nature of the sample had to be taken into account for measurement, as cell, respectively, sample composition altered the optimal concentration for astaxanthin determination. The measurement precision of all-E-astaxanthin quantification in dried H. pluvialis biomass (1.2-1.8 mg dried biomass per sample) was calculated with a coefficient of variation of maximum 1.1%, whereas it was below 10% regarding the diastereomers. Complete enzymolysis was performed with 1.0 to 2.0 units of cholesterol esterase in the presence of various solvents with up to 2.0 mg biomass (dry weight). The method was compared with other astaxanthin determination approaches in which astaxanthin is converted to acetone in a further step before measurement. The developed method resulted in a higher total astaxanthin recovery but lower selectivity of the diastereomers. The reliability of photometric astaxanthin estimations was assessed by comparing them with the developed chromatographic method. At later stages in the cell cycle of H. pluvialis, all methods yielded similar results (down to 0.1% deviation), but photometry lost precision at earlier stages (up to 31.5% deviation). To optimize sample storage, the shelf life of astaxanthin-containing samples was investigated. Temperatures below -20°C, excluding oxygen, and storing intact H. pluvialis cells instead of dried or disrupted biomass reduced astaxanthin degradation.
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Affiliation(s)
- Inga K. Koopmann
- ZAiT, Center for Analytics in Technology Transfer of Bio and Food Technology Innovations, Flensburg University of Applied Sciences, Flensburg, Schleswig-Holstein, Germany
| | - Annemarie Kramer
- ZAiT, Center for Analytics in Technology Transfer of Bio and Food Technology Innovations, Flensburg University of Applied Sciences, Flensburg, Schleswig-Holstein, Germany
| | - Antje Labes
- ZAiT, Center for Analytics in Technology Transfer of Bio and Food Technology Innovations, Flensburg University of Applied Sciences, Flensburg, Schleswig-Holstein, Germany
- * E-mail:
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5
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Zhu P, Chen W, Liu L. A Fast and Easy-To-Go Method for the Preparation of Au Nanocluster and Its Application for Fe(III) Cation Sensing. Front Chem 2021; 9:794725. [PMID: 34950637 PMCID: PMC8688738 DOI: 10.3389/fchem.2021.794725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/15/2021] [Indexed: 11/18/2022] Open
Abstract
In this article, we reported the synthesis and characterization of gold nanoclusters (AuNCs) with a diameter of ∼2 nm. A simple method of microwave-assisted reaction was applied here, with L-cysteine as both reducing agent and stabilizer. The resulting AuNCs were analyzed by means of TEM, XPS, DLS, and IR. Their photophysical performance was then analyzed in detail, including UV-vis absorption, emission, quantum yield, and lifetime. Efficient red emission was observed from these AuNCs, originating from ligand-to-metal nanoparticle core charge transfer (LMNCT). This red emission was found quenchable by Fe(III) cations. The corresponding quenching curve and sensing performance were discussed. An effective working region of 0–80 μM with an LOD of 3.9 μM was finally observed. Their quenching mechanism was revealed as Fe(III) energy competing for the LMNCT process. The novelty and advancement of this work is the simple synthesis and impressive sensing performance, including wide working region, good linearity, and selectivity.
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Affiliation(s)
- Peibin Zhu
- School of Ocean Information Engineering, Jimei University, Xiamen, China
| | - Wen Chen
- School of Ocean Information Engineering, Jimei University, Xiamen, China
| | - Liang Liu
- School of Materials Science & Engineering, Jiangsu University, Zhenjiang, China
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6
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Shobhna, Kumari M, Kashyap HK. Mechanistic Insight on BioIL-Induced Structural Alterations in DMPC Lipid Bilayer. J Phys Chem B 2021; 125:11955-11966. [PMID: 34672578 DOI: 10.1021/acs.jpcb.1c06218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The emerging application risks of traditional ionic liquids (ILs) toward the ecosystem have changed the perception regarding their greenness. This resulted in the exploration of their more biocompatible alternatives known as biocompatible ILs (BioILs). Here, we have investigated the impact of two such biocompatible cholinium amino acid-based ILs on the structural behavior of model homogeneous DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) lipid bilayer using all-atom molecular dynamics simulation technique. Two classic cholinium-amino acid-based ILs, cholinium glycinate ([Ch][Gly]) and cholinium phenylalaninate ([Ch][Phe]), which differ only by the side chain lengths and hydrophobicity of the anions, have been utilized in the present work. Simultaneous analysis of the bilayer structural properties reveals that the existence of [Ch][Gly] BioIL above a particular concentration induces phase transition from fluid phase to gel phase in the DMPC lipid bilayer. Such a freezing of lipid bilayer upon the exposure to concentrated aqueous solution of [Ch][Gly] BioIL indicates the harmfulness of this BioIL toward the cell membranes majorly containing DMPC lipids, as the cell freezing can negatively affect its stability and functionality. Despite having a more hydrophobic amino acid side chain of [Phe]- anion in [Ch][Phe], in the case of bilayer-[Ch][Phe] systems we observe the minimal impact of [Ch][Phe] BioIL on the DMPC bilayer properties up to 10 mol % concentration. In the presence of these BioIL, we observe the thickening of the bilayer and accumulation of the cations and anions of the BioILs at the interface of DMPC lipid heads and tails. The transfer free-energy profile of a [Phe]- anion from aqueous phase to membrane center also indicates the anion partitioning at lipid head-tail interface and its inability to penetrate in the lipid membrane tail region. In contrast, the free-energy profile for a [Gly]- anion offers a very high energy barrier to the insertion of [Gly]- into the membrane interior, leading to accumulation of [Gly]- anions at the lipid head-water region.
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Affiliation(s)
- Shobhna
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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7
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Bhattacharyya R, Mukhopadhyay D, Nagarakshita VK, Bhattacharya S, Das A. Thermostable and organic solvent-tolerant acid pectinase from Aspergillus terreus FP6: purification, characterization and evaluation of its phytopigment extraction potential. 3 Biotech 2021; 11:487. [PMID: 34790511 DOI: 10.1007/s13205-021-03033-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/15/2021] [Indexed: 10/19/2022] Open
Abstract
The present study discusses the purification, characterization and application of pectinase from Aspergillus terreus FP6 in fruit pigment extraction. By the four-step purification involving precipitation, dialysis, ion-exchange chromatography, gel filtration chromatography, a 20.85-fold purification of the enzyme to homogeneity was achieved. The apparent molecular mass of the pectinase was 47 kDa, as found by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The optimum activity of the enzyme was recorded at pH 6.0 and 50 °C. The enzyme retained 80.3% and 79.1% residual activity, respectively at pH 6.0 and 50 °C for 90 min. The pectinase was best functional in the presence of toluene and retained its activity for 30 min. Cu2+ and Co2+ acted as enzyme activators, while Ca2+, β-mercaptoethanol, dimethyl sulfoxide and ethylenediaminetetraacetic acid proved to be the inhibitors. The K m and V max values of the pectinase with pectin as substrate were 0.002 mM and 27.39 U/mL, respectively thus indicating the high enzyme affinity towards the substrate. After 30-min treatment of the grape skin with the partially purified enzyme, microscopic observation revealed that a short time of the enzymatic treatment resulted in substantial loss of pigment and shrinkage of the grape skin cells thereby highlighting the high efficiency of the pectinase. The current study implies that the A. terreus FP6 pectinase may be applied as a bio-agent in the food and beverage industries and has the potential to replace harmful solvents by promoting a greener approach to extract plant pigments.
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8
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Guo T, Wang X, Shu Y, Wang J. Effects of alkyl side-chain length on binding with bovine serum albumin, cytotoxicity, and antibacterial properties of 1-alkyl-3-methylimidazolium dicyanamide ionic liquids. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Parui S, Jana B. Cold denaturation induced helix-to-helix transition and its implication to activity of helical antifreeze protein. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Kumari P, Kumari M, Kashyap HK. How Pure and Hydrated Reline Deep Eutectic Solvents Affect the Conformation and Stability of Lysozyme: Insights from Atomistic Molecular Dynamics Simulations. J Phys Chem B 2020; 124:11919-11927. [DOI: 10.1021/acs.jpcb.0c09873] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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11
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Han Q, Smith KM, Darmanin C, Ryan TM, Drummond CJ, Greaves TL. Lysozyme conformational changes with ionic liquids: Spectroscopic, small angle x-ray scattering and crystallographic study. J Colloid Interface Sci 2020; 585:433-443. [PMID: 33109332 DOI: 10.1016/j.jcis.2020.10.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/19/2020] [Accepted: 10/07/2020] [Indexed: 01/14/2023]
Abstract
Solvents that support protein functionality are important for biochemical applications, and new solvents are required. Here we employ FTIR and fluorescence spectroscopies, small angle X-ray scattering (SAXS) and X-ray crystallography to understand conformational changes of lysozyme with ionic liquids (ILs) added. Spectroscopic techniques identified that the secondary structure of lysozyme was maintained at the lower IL concentrations of 1 and 5 mol%, though the Tryptophan environment was significantly altered with nitrate-based ILs present. SAXS experiments indicated that the radius of gyration of lysozyme increased with 1 mol% IL present, and then decreased with increasing IL concentrations. The tertiary structure, particularly the loop regions, changed as a function of IL concentration, and this depended on the IL type. The crystallographic structure of lysozyme with the IL of ethylammonium nitrate present confirmed the loop region was extended, and identified three specific binding sites with nitrate ions, and that the positively charged areas were IL sensitive regions. This work provides a detailed understanding of lysozyme conformational changes in the presence of ILs. This approach can be extended to other functionally-important proteins.
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Affiliation(s)
- Qi Han
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Kate M Smith
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC, 3168, Australia
| | - Connie Darmanin
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, VIC 3086, Australia
| | - Timothy M Ryan
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC, 3168, Australia
| | - Calum J Drummond
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia.
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12
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Halder R, Jana B. On the Correlation between Pair Hydrophobicity and Mixing Enthalpies in Water–Alcohol Binary Mixtures. J Phys Chem B 2020; 124:8023-8031. [DOI: 10.1021/acs.jpcb.0c05952] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ritaban Halder
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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13
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Oh KI, You X, Flanagan JC, Baiz CR. Liquid-Liquid Phase Separation Produces Fast H-Bond Dynamics in DMSO-Water Mixtures. J Phys Chem Lett 2020; 11:1903-1908. [PMID: 32069416 DOI: 10.1021/acs.jpclett.0c00378] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Liquid-liquid phase separation is common in complex mixtures, but the behavior of nanoconfined liquids is poorly understood from a physical perspective. Dimethyl sulfoxide (DMSO) is an amphiphilic molecule with unique concentration-dependent bulk properties in mixtures with water. Here, we use ultrafast two-dimensional infrared (2D IR) spectroscopy to measure the H-bond dynamics of two probe molecules with different polarities: formamide (FA) and dimethylformamide (DMF). Picosecond H-bond dynamics are fastest in the intermediate concentration regime (20-50 mol % DMSO), because such confined water exhibits bulk-like dynamics. Each vibrational probe experiences a unique microscopic environment as a result of nanoscale phase separation. Molecular dynamics simulations show that the dynamics span multiple time scales, from femtoseconds to nanoseconds. Our studies suggest a previously unknown liquid environment, which we label "local bulk", in which despite the local heterogeneity, the ultrafast H-bond dynamics are similar to bulk water.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Xiao You
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Jennifer C Flanagan
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
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14
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Sindhu A, Kumar S, Mondal D, Bahadur I, Venkatesu P. Protein packaging in ionic liquid mixtures: an ecofriendly approach towards the improved stability of β-lactoglobulin in cholinium-based mixed ionic liquids. Phys Chem Chem Phys 2020; 22:14811-14821. [DOI: 10.1039/d0cp02151b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The present work demonstrates a pioneering approach for the packaging of β-LG with improved stability in the presence of aqueous solutions containing cholinium-based ionic liquid mixtures.
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Affiliation(s)
| | - Sumit Kumar
- Department of Chemistry
- University of Delhi
- Delhi
- India
| | - Dibyendu Mondal
- Centre for Nano & Material Science
- JAIN (deemed to be University)
- Jain Global Campus
- Bangalore-562112
- India
| | - Indra Bahadur
- Department of Chemistry, School of Physical and Chemical Sciences, Material Science Innovation & Modelling (MaSIM) Focus Area, Faculty of Natural and Agricultural Sciences
- North-West University (Mafikeng Campus)
- Private Bag X2046
- Mmabatho 2735
- South Africa
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15
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Kumar S, Sarkar S, Bagchi B. Anomalous viscoelastic response of water-dimethyl sulfoxide solution and a molecular explanation of non-monotonic composition dependence of viscosity. J Chem Phys 2019; 151:194505. [PMID: 31757141 DOI: 10.1063/1.5126381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Amphiphilic molecules such as dimethyl sulfoxide (DMSO) and its aqueous binary mixtures exhibit pronounced nonideality in composition dependence of several static and dynamic properties. We carry out detailed molecular dynamics simulations to calculate various properties including viscosity of the mixture and combine the results with a mode coupling theory analysis to show that this nonideality can be attributed to local structures that are stable on a short time scale but transient on a long time scale to maintain the large scale homogeneity of the solution. Although the existence of such quasistable structures has been deciphered from spectroscopy, a detailed characterization does not exist. We calculate stress-stress autocorrelation functions (SACFs) of water-DMSO binary mixtures. We employ two different models of water, SPC/E and TIP4P/2005, to check the consistency of our results. Viscosity shows a pronounced nonmonotonic composition dependence. The calculated values are in good agreement with the experimental results. Fourier transform of SACF provides frequency-dependent viscosity. The frequency-dependent viscosity (that is, viscoelasticity) is also found to be strongly dependent on composition. Viscoelasticity exhibits sharp peaks due to intramolecular vibrational modes of DMSO, which are also seen in the density of states. We evaluate the wavenumber dependent dynamic structure factor and wavenumber dependent relaxation time. The latter also exhibits a sharp nonmonotonic composition dependence. The calculated dynamic structure factor is used in mode coupling theory expression of viscosity to obtain a semiquantitative understanding of anomalous composition dependence of viscosity. Both the self-diffusion coefficients and rotational correlation times of water and DMSO molecules exhibit nonmonotonic composition dependence.
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Affiliation(s)
- Shubham Kumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sarmistha Sarkar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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16
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Parui S, Jana B. Relative Solvent Exposure of the Alpha-Helix and Beta-Sheet in Water Determines the Initial Stages of Urea and Guanidinium Chloride-Induced Denaturation of Alpha/Beta Proteins. J Phys Chem B 2019; 123:8889-8900. [DOI: 10.1021/acs.jpcb.9b06859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sridip Parui
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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Kratochvílová I, Kopečná O, Bačíková A, Pagáčová E, Falková I, Follett SE, Elliott KW, Varga K, Golan M, Falk M. Changes in Cryopreserved Cell Nuclei Serve as Indicators of Processes during Freezing and Thawing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7496-7508. [PMID: 30339402 DOI: 10.1021/acs.langmuir.8b02742] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The mechanisms underlying cell protection from cryoinjury are not yet fully understood. Recent biological studies have addressed cryopreserved cell survival but have not correlated the cryoprotection effectiveness with the impact of cryoprotectants on the most important cell structure, the nucleus, and the freeze/thaw process. We identified changes of cell nuclei states caused by different types of cryoprotectants and associate them with alterations of the freeze/thaw process in cells. Namely, we investigated both higher-order chromatin structure and nuclear envelope integrity as possible markers of freezing and thawing processes. Moreover, we analyzed in detail the relationship between nuclear envelope integrity, chromatin condensation, freeze/thaw processes in cells, and cryopreservation efficiency for dimethyl sulfoxide, glycerol, trehalose, and antifreeze protein. Our interdisciplinary study reveals how changes in cell nuclei induced by cryoprotectants affect the ability of cells to withstand freezing and thawing and how nuclei changes correlate with processes during freezing and thawing. Our results contribute to the deeper fundamental understanding of the freezing processes, notably in the cell nucleus, which will expand the applications and lead to the rational design of cryoprotective materials and protocols.
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Affiliation(s)
- Irena Kratochvílová
- Institute of Physics, v.v.i. , Czech Academy of Sciences , Na Slovance 2 , CZ-182 21 Prague 8 , Czech Republic
| | - Olga Kopečná
- Institute of Biophysics, v.v.i. , Czech Academy of Sciences , Královopolská 135 , CZ-612 65 Brno , Czech Republic
| | - Alena Bačíková
- Institute of Biophysics, v.v.i. , Czech Academy of Sciences , Královopolská 135 , CZ-612 65 Brno , Czech Republic
| | - Eva Pagáčová
- Institute of Biophysics, v.v.i. , Czech Academy of Sciences , Královopolská 135 , CZ-612 65 Brno , Czech Republic
| | - Iva Falková
- Institute of Biophysics, v.v.i. , Czech Academy of Sciences , Královopolská 135 , CZ-612 65 Brno , Czech Republic
| | - Shelby E Follett
- Department of Chemistry , University of Wyoming , 1000 E. University Avenue , Laramie , Wyoming 82071 , United States
| | - K Wade Elliott
- Department of Molecular, Cellular, and Biomedical Sciences , University of New Hampshire , 46 College Road , Durham , New Hampshire 03824 , United States
| | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Sciences , University of New Hampshire , 46 College Road , Durham , New Hampshire 03824 , United States
| | - Martin Golan
- Institute of Physics, v.v.i. , Czech Academy of Sciences , Na Slovance 2 , CZ-182 21 Prague 8 , Czech Republic
| | - Martin Falk
- Institute of Biophysics, v.v.i. , Czech Academy of Sciences , Královopolská 135 , CZ-612 65 Brno , Czech Republic
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Parui S, Jana B. Factors Promoting the Formation of Clathrate-Like Ordering of Water in Biomolecular Structure at Ambient Temperature and Pressure. J Phys Chem B 2019; 123:811-824. [PMID: 30605607 DOI: 10.1021/acs.jpcb.8b11172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Clathrate hydrate forms when a hydrophobic molecule is entrapped inside a water cage or cavity. Although biomolecular structures also have hydrophobic patches, clathrate-like water is found in only a limited number of biomolecules. Also, while clathrate hydrates form at low temperature and moderately higher pressure, clathrate-like water is observed in biomolecular structure at ambient temperature and pressure. These indicate presence of other factors along with hydrophobic environment behind the formation of clathrate-like water in biomolecules. In the current study, we presented a systematic approach to explore the factors behind the formation of clathrate-like water in biomolecules by means of molecular dynamics simulation of a model protein, maxi, which is a naturally occurring nanopore and has clathrate-like water inside the pore. Removal of either confinement or hydrophobic environment results in the disappearance of clathrate-like water ordering, indicating a coupled role of these two factors. Apart from these two factors, clathrate-like water ordering also requires anchoring groups that can stabilize the clathrate-like water through hydrogen bonding. Our results uncover crucial factors for the stabilization of clathrate-like ordering in biomolecular structure which can be used for the development of new biomolecular structure promoting clathrate formation.
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Affiliation(s)
- Sridip Parui
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Biman Jana
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
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19
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Islam MM, Barik S, Sarkar M. Probing the Interactions of 1-Alkyl-3-methylimidazolium Tetrafluoroborate (Alkyl = Octyl, Hexyl, Butyl, and Ethyl) Ionic Liquids with Bovine Serum Albumin: An Alkyl Chain Length-Dependent Study. J Phys Chem B 2019; 123:1512-1526. [DOI: 10.1021/acs.jpcb.8b10795] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mullah Muhaiminul Islam
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, Bhimpur-Padanpur,
Jatni, Khurda 752050, Odisha, India
| | - Sahadev Barik
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, Bhimpur-Padanpur,
Jatni, Khurda 752050, Odisha, India
| | - Moloy Sarkar
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, Bhimpur-Padanpur,
Jatni, Khurda 752050, Odisha, India
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20
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Parui S, Jana B. Molecular Insights into the Unusual Structure of an Antifreeze Protein with a Hydrated Core. J Phys Chem B 2018; 122:9827-9839. [PMID: 30286600 DOI: 10.1021/acs.jpcb.8b05350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The primary driving force for protein folding is the formation of a well-packed, anhydrous core. However, recently, the crystal structure of an antifreeze protein, maxi, has been resolved where the core of the protein is filled with water, which apparently contradicts the existing notion of protein folding. Here, we have performed standard molecular dynamics (MD) simulation, replica exchange MD (REMD) simulation, and umbrella sampling using TIP4P water at various temperatures (300, 260, and 240 K) to explore the origin of this unusual structural feature. It is evident from standard MD and REMD simulations that the protein is found to be stable at 240 K in its unusual state. The core of protein has two layers of semi-clathrate water separating the methyl groups of alanine residues from different helical strands. However, with increasing temperature (260 and 300 K), the stability decreases as the core becomes dehydrated, and methyl groups of alanine are tightly packed driven by hydrophobic interactions. Calculation of the potential of mean force by an umbrella sampling technique between a pair of model hydrophobes resembling maxi protein at 240 K shows the stabilization of second solvent-separated minima (SSM), which provides a thermodynamic rationale of the unusual structural feature in terms of weakening of the hydrophobic interaction. Because the stabilization of SSMs is implicated for cold denaturation, it suggests that the maxi protein is so designed by nature where the cold denatured-like state becomes the biologically active form as it works near or below the freezing point of water.
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Affiliation(s)
- Sridip Parui
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Biman Jana
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
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21
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Nandi S, Parui S, Jana B, Bhattacharyya K. Local environment of organic dyes in an ionic liquid-water mixture: FCS and MD simulation. J Chem Phys 2018; 149:054501. [DOI: 10.1063/1.5027458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Somen Nandi
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
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22
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Halder R, Jana B. Unravelling the Composition-Dependent Anomalies of Pair Hydrophobicity in Water–Ethanol Binary Mixtures. J Phys Chem B 2018; 122:6801-6809. [DOI: 10.1021/acs.jpcb.8b02528] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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Nandi S, Ghosh S, Bhattacharyya K. Live Cell Microscopy: A Physical Chemistry Approach. J Phys Chem B 2018; 122:3023-3036. [PMID: 29389140 DOI: 10.1021/acs.jpcb.7b11689] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Probing dynamics of intracellular components using physical chemistry techniques is a remarkable bottom-up approach for understanding the structures and functions of a biological cell. In this "Feature Article", we give an overview on local polarity, solvation, viscosity, acid-base property, red-ox processes (thiol-disulfide exchange), and gene silencing at selected intracellular components inside a live cell. Significant differences have been observed between cancer cells and their noncancer counterparts. We demonstrate that thiol-disulfide exchange, calcium oscillation, and gene silencing are manifested in time dependence of fluorescence intensity. We show that fluorescent gold nanoclusters may be used in drug delivery (e.g., doxorubicin) and selective killing of cancer cells. Further, we discuss dynamics and structural changes of DNA quadruplexes and i-motifs, induced by different external conditions (e.g., pH) and additives (e.g., K+ and other target specific small molecules). We demonstrate that peptidomimetic analogues have high specificity over double-stranded DNA for binding with i-motifs and G-quadruplexes. These results may have significant biological implications.
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Affiliation(s)
- Somen Nandi
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road , Jadavpur, Kolkata , 700 032 West Bengal , India.,Academy of Scientific and Innovative Research (AcSIR) , CSIR-Indian Institute of Chemical Biology Campus , 4 Raja S. C. Mullick Road , Jadavpur, Kolkata 700 032 , India
| | - Kankan Bhattacharyya
- Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal , 462 066 Madhya Pradesh , India
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