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Russo S, Bodo E. Solvation of Model Biomolecules in Choline-Aminoate Ionic Liquids: A Computational Simulation Using Polarizable Force Fields. Molecules 2024; 29:1524. [PMID: 38611804 PMCID: PMC11013605 DOI: 10.3390/molecules29071524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
One can foresee a very near future where ionic liquids will be used in applications such as biomolecular chemistry or medicine. The molecular details of their interaction with biological matter, however, are difficult to investigate due to the vast number of combinations of both the biological systems and the variety of possible liquids. Here, we provide a computational study aimed at understanding the interaction of a special class of biocompatible ionic liquids (choline-aminoate) with two model biological systems: an oligopeptide and an oligonucleotide. We employed molecular dynamics with a polarizable force field. Our results are in line with previous experimental and computational evidence on analogous systems and show how these biocompatible ionic liquids, in their pure form, act as gentle solvents for protein structures while simultaneously destabilizing DNA structure.
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Affiliation(s)
| | - Enrico Bodo
- Chemistry Department, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy;
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2
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Sundaram V, Ramanan RN, Selvaraj M, Ahemad N, Vijayaraghavan R, MacFarlane DR, Ooi CW. Probing the molecular interactions between cholinium-based ionic liquids and insulin aspart: A combined computational and experimental study. Int J Biol Macromol 2023; 253:126665. [PMID: 37689282 DOI: 10.1016/j.ijbiomac.2023.126665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/11/2023]
Abstract
Despite extensive studies revealing the potential of cholinium-based ionic liquids (ILs) in protein stabilization, the nature of interaction between ILs' constituents and protein residues is not well understood. In this work, we used a combined computational and experimental approach to investigate the structural stability of a peptide hormone, insulin aspart (IA), in ILs containing a choline cation [Ch]+ and either dihydrogen phosphate ([Dhp]-) or acetate ([Ace]-) as anions. Although IA remained stable in both 1 M [Ch][Dhp] and 1 M [Ch][Ace], [Dhp]- exhibited a much stronger stabilization effect than [Ace]-. Both the hydrophilic ILs intensely hydrated IA and increased the number of water molecules in IA's solvation shell. Undeterred by the increased number of water molecules, the native state of IA's hydrophobic core was maintained in the presence of ILs. Importantly, our results reveal the importance of IL concentration in the medium which was critical to maintain a steady population of ions in the microenvironment of IA and to counteract the denaturing effect of water molecules. Through molecular docking, we confirm that the anions exert the dominant effect on the structure of IA, while [Ch]+ have the secondary influence. The computational results were validated using spectroscopic analyses (ultra-violet, fluorescence, and circular dichroism) along with dynamic light scattering measurements. The extended stability of IA at 30 °C for 28 days in 1 M [Ch][Dhp] and [Ch][Ace] demonstrated in this study reveals the possibility of stabilizing IA using cholinium-based ILs.
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Affiliation(s)
- Vidya Sundaram
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - Ramakrishnan Nagasundara Ramanan
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Arkema Thiochemicals Sdn Bhd, Oasis Ara Damansara, 47301 Petaling Jaya, Selangor, Malaysia
| | - Manikandan Selvaraj
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - R Vijayaraghavan
- School of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Douglas R MacFarlane
- School of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Chien Wei Ooi
- Chemical Engineering Department, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia.
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3
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Roman BH, Charęza M, Janus E, Drozd R. Evaluation of new L-amino acids triethanolammonium salts usability for controlling protease activity. Int J Biol Macromol 2023; 231:123218. [PMID: 36634803 DOI: 10.1016/j.ijbiomac.2023.123218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/23/2022] [Accepted: 01/07/2023] [Indexed: 01/11/2023]
Abstract
Twenty new triethanolammonium amino acid salts (TEA AA) have been prepared from triethanolammonium hydroxide and L-amino acids. The physicochemical properties of TEA AA depended on the applied amino acid. Five of the synthesised salts, i.e. mono- and bis-salts of L-glutamic acid, L-aspartic acid, and TEA salt of l-glutamine were solids with melting points between 127.32 °C to 171.51 °C. The other TEA AA exhibited glass transition temperatures from -68.45 °C for TEA Ser to -6.27 °C for TEA Trp and were assigned as amino acid ionic liquids (AAILs). The TEA His was characterised by the highest thermal stability, with an average temperature of 5 % weight loss at 186.4 °C, whereas the lowest stability was determined for TEA Asp (107.5 °C). The developed salts were tested as reaction medium additives for proteolytic enzymes (papain, subtilisin, bromelain). Most AAILs showed an inhibitory effect on tested proteases but with different mechanisms related to the enzyme substrate specificity and structural diversity. The TEA Ser was the most effective competitive inhibitor (Ki = 0.24 10-4 mol/L) for bromelain, while TEA Val uncompetitive inhibitor for papain (Ki = 0.25 10-4 mol/L). The developed TEA AA salts exhibit potential as enzyme-controlling agents for use in industrial processes.
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Affiliation(s)
- Barbara Hanna Roman
- West Pomeranian University of Technology Szczecin, Faculty of Chemical Technology and Engineering, Department of Organic Chemical Technology and Polymeric Materials, Pułaski Ave.10, PL, 70-322 Szczecin, Poland
| | - Magdalena Charęza
- West Pomeranian University of Technology Szczecin, Faculty of Biotechnology and Animal Husbandry, Department of Microbiology and Biotechnology, Piastów Ave. 45, 70-311 Szczecin, Poland
| | - Ewa Janus
- West Pomeranian University of Technology Szczecin, Faculty of Chemical Technology and Engineering, Department of Organic Chemical Technology and Polymeric Materials, Pułaski Ave.10, PL, 70-322 Szczecin, Poland
| | - Radosław Drozd
- West Pomeranian University of Technology Szczecin, Faculty of Biotechnology and Animal Husbandry, Department of Microbiology and Biotechnology, Piastów Ave. 45, 70-311 Szczecin, Poland.
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4
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Kalhor S, Fattahi A. Design of ionic liquids containing glucose and choline as drug carriers, finding the link between QM and MD studies. Sci Rep 2022; 12:21941. [PMID: 36535965 PMCID: PMC9763358 DOI: 10.1038/s41598-022-25963-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Designing drug delivery systems for therapeutic compounds whose receptors are located in the cytosol of cells is challenging as a bilayer cell membrane is negatively charged. The newly designed drug delivery systems should assist the mentioned drugs in passing the membrane barriers and achieving their targets. This study concentrated on developing novel ionic liquids (ILs) that interact effectively with cell membranes. These ILs are based on glucose-containing choline and are expected to be non-toxic. The binding energies of the known pharmaceutically active ionic liquids were calculated at the B3LYP/6-311++G(d,p) level in the gas phase and compared with those of our newly designed carbohydrate-based ionic liquids. Subsequently, we employed MD simulations to obtain information about the interactions of these known and designed ILs with the cell membrane. In our approach, we adopted QM and MD studies and illustrated that there could be a link between the QM and MD results.
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Affiliation(s)
- Sepideh Kalhor
- grid.412553.40000 0001 0740 9747Department of Chemistry, Sharif University of Technology, Tehran, Iran
| | - Alireza Fattahi
- grid.412553.40000 0001 0740 9747Department of Chemistry, Sharif University of Technology, Tehran, Iran
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Mendanha K, Bruno Assis Oliveira L, Colherinhas G. Modeling, energetic and structural analysis of peptide membranes formed by arginine and phenylalanine (R2F4R2) using fully atomistic molecular dynamics. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kobayashi T, Smiatek J, Fyta M. Probing the distribution of ionic liquid mixtures at charged and neutral interfaces via simulations and lattice-gas theory. Phys Chem Chem Phys 2022; 24:16471-16483. [PMID: 35766260 DOI: 10.1039/d2cp01346k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Room temperature ionic liquid solutions confined between neutral and charged surfaces are investigated by means of atomistic Molecular Dynamics simulations. We study 1-ethyl-3-methylimidazolium dicyanamide ([EMIm]+[DCA]-) in water or dimethylsulfoxide (DMSO) mixtures in confinement between two interfaces. The analysis is based on the comparison of the molecular species involved and the charged state of the surfaces. Focus is given on the influence of different water/DMSO concentrations on the microstructuring and accumulation of each species. Thermodynamic aspects, such as the entropic contributions in the observed trends are obtained from the simulations using a lattice-gas theory. The results clearly underline the differences in these properties for the water and DMSO mixtures and unravel the underlying mechanisms and inherent details. We were able to pinpoint the importance of the size and the relative permittivity of the molecules in guiding their microstructuring in the vicinity of the surfaces, as well as their interactions with the latter, i.e. the solute-surface interactions. The influence of water and DMSO on the overscreening at charged interfaces is also discussed. The analysis on the molecular accumulation at the interfaces allows us to predict whether the accumulation is entropy or enthalpy driven, which has an impact in the removal of the molecular species from the surfaces. We discuss the impact of this work in providing an essential understanding towards a careful design of electrochemical elements.
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Affiliation(s)
- Takeshi Kobayashi
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
| | - Maria Fyta
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
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7
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Sundaram V, Ramanan RN, Selvaraj M, Vijayaraghavan R, MacFarlane DR, Ooi CW. Enhanced structural stability of insulin aspart in cholinium aminoate ionic liquids. Int J Biol Macromol 2022; 208:544-552. [PMID: 35331796 DOI: 10.1016/j.ijbiomac.2022.03.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/14/2022]
Abstract
Cholinium aminoates [Ch][AA] have gained tremendous interest as a promising ionic liquid medium for the synthesis and storage of proteins. However, high alkalinity of [Ch][AA] limits its usage with pH-sensitive proteins. Here, we probed the structure, stability, and interactions of a highly unstable therapeutic protein, insulin aspart (IA), in a range of buffered [Ch][AA] (b-[Ch][AA]) using a combination of biophysical tools and in silico pipeline including ultraviolet-visible, fluorescence, and circular dichroism spectroscopies, dynamic light scattering measurements and molecular docking. b-[Ch][AA] used in the study differed in concentrations and their anionic counterparts. We reveal information on ion and residue specific solvent-protein interactions, demonstrating that the structural stability of IA was enhanced by a buffered cholinium prolinate. In comparison to the glycinate and alaninate anions, the hydrophilic prolinate anions established more hydrogen bonds with the residues of IA and provided a less polar environment that favours the preservation of IA in its active monomeric form, opening new opportunities for utilizing [Ch][AA] as storage medium.
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Affiliation(s)
- Vidya Sundaram
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Biological Enginerring Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar-382055, Gujarat, India
| | - Ramakrishnan Nagasundara Ramanan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - Manikandan Selvaraj
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - R Vijayaraghavan
- School of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Douglas R MacFarlane
- School of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Chien Wei Ooi
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia; Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
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8
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Guo Q, Liu Q, Zhao Y. Insights into the Structure and Dynamics of Imidazolium Ionic Liquid and Tetraethylene Glycol Dimethyl Ether Cosolvent Mixtures: A Molecular Dynamics Approach. Nanomaterials (Basel) 2021; 11:2512. [PMID: 34684952 DOI: 10.3390/nano11102512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022]
Abstract
In this work, the effect of molecular cosolvents tetraethylene glycol dimethyl ether (TEGDME) on the structure and versatile nature of mixtures of these compounds with imidazolium-based ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) is analyzed and discussed at a molecular level by means of all-atom molecular dynamics (MD) simulations. In the whole concentration range of the binary mixtures, the structures and properties evolution was studied by means of systematic molecular dynamics simulations of the fraction of hydrogen bonds, the radial and spatial distribution functions for the various molecular ions and molecular species in the system, together with the snapshots visualization of equilibrated simulation boxes with a color-coding scheme and the rotational dynamics of coumarin 153 (C153) in the binary mixtures. The goal of the work is to provide a molecular-level understanding of significant improvement of ionic conductivity and self-diffusion with the presence of TEGDME as a cosolvent, which causes an enhancement to the ion translational motion and fluidity in the [bmim][PF6] ionic liquids (ILs). Under a mixture concentration change, the microstructure changes of [bmim][PF6] with the TEGDME molar fraction (XTEG) above 0.50 show a slight difference from that of neat [bmim][PF6] IL and concentrated [bmim][PF6]/TEGDME mixture in terms of the radial and spatial distribution functions. The relative diffusivities of solvent molecules to cations as a function of concentration were found to depend on the solvent but not on the anion. A TEGDME increase is found to be advantageous to the dissipation of the polar regions as well as the nonpolar regions in the [bmim][PF6] ionic liquids. These conclusions are consistent with the experimental results, which verified that the unique, complex, and versatile nature of [bmim][PF6]/TEGDME mixture can be correctly modeled and discussed at a molecular level using MD simulation data.
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9
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Affiliation(s)
- Takeshi Kobayashi
- Institute for Computational Physics University of Stuttgart Allmandring 3 Stuttgart 70569 Germany
| | - Jens Smiatek
- Institute for Computational Physics University of Stuttgart Allmandring 3 Stuttgart 70569 Germany
| | - Maria Fyta
- Institute for Computational Physics University of Stuttgart Allmandring 3 Stuttgart 70569 Germany
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10
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Colherinhas G. Updating atomic charge parameters of aliphatic amino acids: a quest to improve the performance of molecular modeling via sequential molecular dynamics and DFT-GIAO-NMR calculations. Phys Chem Chem Phys 2021; 23:8413-8425. [PMID: 33876005 DOI: 10.1039/d1cp00183c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this work, we observe the behavior of the dipole moment, atomic charges, solute-solvent interactions and NMR spectroscopy of aliphatic amino acids in a water solution via the computational simulations of classical molecular dynamics and DFT quantum calculations. Our results indicate that the convergence of the atomic charge of the solute, from an iterative process, together with the dipole moment of the amino acid, alters the lifetime of hydrogen bonds present in the first solvation shell, resulting in the modification of its structure and dynamics. Using GIAO-DFT-NMR calculations, we assessed the impact of these structural solute-solvent modifications on the magnetic shielding constants of the solute carbon atoms. In this sense, we evaluate the importance of an update in parameters that describe atomic charges present in the CHARMM36 force field.
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Affiliation(s)
- Guilherme Colherinhas
- Departamento de Física, CEPAE, Universidade Federal de Goiás, 74690-900, Goiânia, GO, Brazil.
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11
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Rakowska PW, Kloskowski A. Impact of the Alkyl Side Chains of Cations and Anions on the Activity and Renaturation of Lysozyme: A Systematic Study Performed Using Six Amino‐Acid‐Based Ionic Liquids. ChemistrySelect 2021. [DOI: 10.1002/slct.202004357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Paulina W. Rakowska
- Department of Physical Chemistry Faculty of Chemistry Gdańsk University of Technology ul. Narutowicza 11/12 Gdańsk 80-233 Poland
| | - Adam Kloskowski
- Department of Physical Chemistry Faculty of Chemistry Gdańsk University of Technology ul. Narutowicza 11/12 Gdańsk 80-233 Poland
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12
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Deepa PR, Nalini V, Surianarayanan M, Krishnakumar S. Towards safer non-volatile tissue fixatives: Evaluation of choline-based ionic liquids for fixing ocular tissues. Ecotoxicol Environ Saf 2021; 209:111777. [PMID: 33352431 DOI: 10.1016/j.ecoenv.2020.111777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/19/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
Volatile organic chemicals (VOCs) are routinely used for processing biological tissue samples in clinical laboratories. Recognizing their serious health and environmental impacts, a few non-volatile green solvents (choline based ionic liquids, ILs) were evaluated as tissue fixatives here. Microscopic evaluation of histo-morphology, fixation and staining quality, and macromolecular integrity (DNA and proteins) were assessed in human eye tissues (sclera, choroid, retinal layers and retinal pigmented epithelium, eyelid and orbit) after IL-fixation. Formalin-fixed tissues were used as standard reference. Microscopic examination revealed favorable histomorphology, tissue fixation and staining characteristics in most tissues immersed in ILs. Time taken to fix, and stability over a period of time (24 h, 48 h, 1 week, 1 month) was also recorded. Electrophoretic analysis revealed stability of cellular proteins and nucleic acids in IL-fixed scleral tissues. Heterogeneity in tissue fixation property relative to the type of ocular tissue, duration of fixation and storage, warrant further design and optimization of ILs to fix biological tissues. The simple cholinium salts based ILs tested here show favorable potential for tissue fixation application, and as an alternative approach to the use of VOCs, towards sustainable biomedical practice.
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Affiliation(s)
- P R Deepa
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani 333 031, Rajasthan, India.
| | - V Nalini
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani 333 031, Rajasthan, India; L&T Department of Ocular Pathology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, 18, College Road, 600 006 Chennai, India
| | - M Surianarayanan
- Cell for Industrial Safety and Risk Analysis (CISRA), Central Leather Research Institute (CSIR-CLRI), Adyar, Chennai, India
| | - S Krishnakumar
- L&T Department of Ocular Pathology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, 18, College Road, 600 006 Chennai, India.
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13
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Sundaram V, Ramanan RN, Selvaraj M, Vijayaraghavan R, MacFarlane DR, Ooi CW. Structural stability of insulin aspart in aqueous cholinium aminoate ionic liquids based on molecular dynamics simulation studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114501] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Galluzzi M, Schulte C, Milani P, Podestà A. Imidazolium-Based Ionic Liquids Affect Morphology and Rigidity of Living Cells: An Atomic Force Microscopy Study. Langmuir 2018; 34:12452-12462. [PMID: 30213187 DOI: 10.1021/acs.langmuir.8b01554] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The study of the toxicity, biocompatibility, and environmental sustainability of room-temperature ionic liquids (ILs) is still in its infancy. Understanding the impact of ILs on living organisms, especially from the aquatic ecosystem, is urgent, since large amounts of these substances are starting to be employed as solvents in industrial chemical processes, and on the other side, evidence of toxic effects of ILs on microorganisms and single cells have been observed. To date, the toxicity of ILs has been investigated by means of macroscopic assays aimed at characterizing the effective concentrations (like the EC50) that cause the death of a significant fraction of the population of microorganisms and cells. These studies allow us to identify the cell membrane as the first target of the IL interaction, whose effectiveness was correlated to the lipophilicity of the cation, i.e., to the length of the lateral alkyl chain. Our study aimed at investigating the molecular mechanisms underpinning the interaction of ILs with living cells. To this purpose, we carried out a combined topographic and mechanical analysis by atomic force microscopy of living breast metastatic cancer cells (MDA-MB-231) upon interaction with imidazolium-based ILs. We showed that ILs are able to induce modifications of the overall rigidity (effective Young's modulus) and morphology of the cells. Our results demonstrate that ILs act on the physical properties of the outer cell layer (the membrane linked to the actin cytoskeleton), already at concentrations below the EC50. These potentially toxic effects are stronger at higher IL concentrations, as well as with longer lateral chains in the cation.
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Affiliation(s)
- Massimiliano Galluzzi
- Shenzhen Key Laboratory of Nanobiomechanics , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , Guangdong , China
- C.I.Ma.I.Na and Dipartimento di Fisica "Aldo Pontremoli" , Università degli Studi di Milano , via Celoria 16 , 20133 Milano , Italy
| | - Carsten Schulte
- C.I.Ma.I.Na and Dipartimento di Fisica "Aldo Pontremoli" , Università degli Studi di Milano , via Celoria 16 , 20133 Milano , Italy
| | - Paolo Milani
- C.I.Ma.I.Na and Dipartimento di Fisica "Aldo Pontremoli" , Università degli Studi di Milano , via Celoria 16 , 20133 Milano , Italy
| | - Alessandro Podestà
- C.I.Ma.I.Na and Dipartimento di Fisica "Aldo Pontremoli" , Università degli Studi di Milano , via Celoria 16 , 20133 Milano , Italy
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15
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Zeindlhofer V, Schröder C. Computational solvation analysis of biomolecules in aqueous ionic liquid mixtures : From large flexible proteins to small rigid drugs. Biophys Rev 2018; 10:825-840. [PMID: 29687270 PMCID: PMC5988630 DOI: 10.1007/s12551-018-0416-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 03/26/2018] [Indexed: 01/07/2023] Open
Abstract
Based on their tunable properties, ionic liquids attracted significant interest to replace conventional, organic solvents in biomolecular applications. Following a Gartner cycle, the expectations on this new class of solvents dropped after the initial hype due to the high viscosity, hydrolysis, and toxicity problems as well as their high cost. Since not all possible combinations of cations and anions can be tested experimentally, fundamental knowledge on the interaction of the ionic liquid ions with water and with biomolecules is mandatory to optimize the solvation behavior, the biodegradability, and the costs of the ionic liquid. Here, we report on current computational approaches to characterize the impact of the ionic liquid ions on the structure and dynamics of the biomolecule and its solvation layer to explore the full potential of ionic liquids.
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Affiliation(s)
- Veronika Zeindlhofer
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstr. 17, Vienna, Austria
| | - Christian Schröder
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstr. 17, Vienna, Austria.
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16
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Abstract
Ionic liquids (ILs) have recently emerged as versatile solvents and additives in the field of biotechnology, particularly as stabilizers of proteins and enzymes. Of interest to the biotechnology industry is the formulation of stable biopharmaceuticals, therapeutic proteins, and vaccines which have revolutionized the treatment of many diseases including debilitating conditions such as cancers and auto-immune diseases. The stabilization of therapeutic proteins is typically achieved using additives that prevent unfolding and aggregation of these proteins during manufacture, transport, and long-term storage. To determine if ILs could be used in the formulation of stable therapeutic proteins, a thorough understanding of the effects of ILs on protein stability is needed, as well as understanding the toxicity of ILs on humans, and other considerations for formulation development such as viscosity and osmolality. In this review, we summarize recent developments on the stabilization of proteins and enzymes using ILs, with emphasis on identifying biocompatible ILs that may be suitable for the formulation of stable biopharmaceuticals in the future.
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Affiliation(s)
- Mouhamad Reslan
- Faculty of Pharmacy, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Veysel Kayser
- Faculty of Pharmacy, The University of Sydney, Sydney, NSW, 2006, Australia.
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17
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Chaban VV, Fileti EE. Atomically precise understanding of nanofluids: nanodiamonds and carbon nanotubes in ionic liquids. Phys Chem Chem Phys 2018; 18:26865-26872. [PMID: 27711712 DOI: 10.1039/c6cp04786f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A nanofluid (NF) is composed of a base liquid and suspended nanoparticles (NPs). High-performance NFs exhibit significantly better heat conductivities, as compared to their base liquids. In the present work, we applied all-atom molecular dynamics (MD) simulations to characterize diffusive and ballistic energy transfer mechanisms within nanodiamonds (NDs), carbon nanotubes (CNTs), and N-butylpyridinium tetrafluoroborate ionic liquid (IL). We showed that heat transfer within both NDs and CNTs is orders of magnitude faster than that in the surrounding IL, whereas diffusion of all particles in the considered NF is similar. Intramolecular heat transfer in NPs is a key factor determining the difference of NFs from base liquids. Solvation free energy of NDs and CNTs in ILs was estimated from MD simulations. The geometric dimensions of NPs were shown to be a major source of entropic penalty. Temperature adjusts the entropic factor substantially by modifying a genuine local structure of the bulk base liquid. Our work contributes to engineering more stable and productive suspensions of NPs in ILs, which are necessary for essential progress in the field of NFs.
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Tarannum A, Rao JR, Fathima NN. Choline-Based Amino Acid ILs-Collagen Interaction: Enunciating Its Role in Stabilization/Destabilization Phenomena. J Phys Chem B 2018; 122:1145-1151. [PMID: 29239608 DOI: 10.1021/acs.jpcb.7b10645] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Given the potential of productive interaction between choline-based amino acid ionic liquids (CAAILs) and collagen, we investigated the role of four CAAILs, viz., choline serinate, threoninate, lysinate, and phenylalaninate, and the changes mediated by them in the structure of collagen at different hierarchical orderings, that is, at molecular and fibrillar levels. The rheological, dielectric behavior and the secondary structural changes signify the alteration in the triple helical structure of collagen at higher concentrations of CAAILs. A marginal swelling and slight decrease in the thermal stability of rat tail tendon collagen fibers were observed for choline serinate and threoninate, albeit distortions in banding patterns were noticed for choline lysinate and phenylalaninate, suggesting chaotropicity of the ions at the fibrillar level. This signifies the changes in the hydrogen-bonding environment of collagen with increasing concentrations of CAAILs, which could be due to competitive hydrogen bonding between the carbonyl group of amino acid ionic liquids and the hydroxyl groups of collagen.
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Affiliation(s)
- Aafiya Tarannum
- Chemical Laboratory, CSIR-Central Leather Research Institute , Adyar, Chennai 600020, India
| | - J Raghava Rao
- Chemical Laboratory, CSIR-Central Leather Research Institute , Adyar, Chennai 600020, India
| | - N Nishad Fathima
- Chemical Laboratory, CSIR-Central Leather Research Institute , Adyar, Chennai 600020, India
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Násztor Z, Dér A, Bogár F. Ion-induced alterations of the local hydration environment elucidate Hofmeister effect in a simple classical model of Trp-cage miniprotein. J Mol Model 2017; 23:298. [PMID: 28956172 DOI: 10.1007/s00894-017-3471-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 09/10/2017] [Indexed: 10/18/2022]
Abstract
Protein stability is known to be influenced by the presence of Hofmeister active ions in the solution. In addition to direct ion-protein interactions, this influence manifests through the local alterations of the interfacial water structure induced by the anions and cations present in this region. In our earlier works it was pointed out that the effects of Hofmeister active salts on the stability of Trp-cage miniprotein can be modeled qualitatively using non-polarizable force fields. These simulations reproduced the structure-stabilization and structure-destabilization effects of selected kosmotropic and chaotropic salts, respectively. In the present study we use the same model system to elucidate atomic processes behind the chaotropic destabilization and kosmotropic stabilization of the miniprotein. We focus on changes of the local hydration environment of the miniprotein upon addition of NaClO4 and NaF salts to the solution. The process is separated into two parts. In the first, 'promotion' phase, the protein structure is fixed, and the local hydration properties induced by the simultaneous presence of protein and ions are investigated, with a special focus on the interaction of Hofmeister active anions with the charged and polar sites. In the second, 'rearrangement' phase we follow changes of the hydration of ions and the protein, accompanying the conformational relaxation of the protein. We identify significant factors of an enthalpic and entropic nature behind the ion-induced free energy changes of the protein-water system, and also propose a possible atomic mechanism consistent with the Collins's rule, for the chaotropic destabilization and kosmotropic stabilization of protein conformation.
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Smiatek J. Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results. J Phys Condens Matter 2017; 29:233001. [PMID: 28398214 DOI: 10.1088/1361-648x/aa6c9d] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ionic liquids (ILs) are used in a variety of technological and biological applications. Recent experimental and simulation results reveal the influence of aqueous ionic liquids on the stability of protein and enzyme structures. Depending on different parameters like the concentration and the ion composition, one can observe distinct stabilization or denaturation mechanisms for various ILs. In this review, we summarize the main findings and discuss the implications with regard to molecular theories of solutions and specific ion effects. A preferential binding model is introduced in order to discuss protein-IL effects from a statistical mechanics perspective. The value of the preferential binding coefficient determines the strength of the ion influence and indicates a shift of the chemical equilibrium either to the native or the denatured state of the protein. We highlight the role of water in order to explain the self-association behavior of the IL species and discuss recent experimental and simulation results in the light of the observed binding effects.
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Affiliation(s)
- Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
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Munje RD, Muthukumar S, Jagannath B, Prasad S. A new paradigm in sweat based wearable diagnostics biosensors using Room Temperature Ionic Liquids (RTILs). Sci Rep 2017; 7:1950. [PMID: 28512341 PMCID: PMC5434046 DOI: 10.1038/s41598-017-02133-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/05/2017] [Indexed: 11/09/2022] Open
Abstract
Successful commercialization of wearable diagnostic sensors necessitates stability in detection of analytes over prolonged and continuous exposure to sweat. Challenges are primarily in ensuring target disease specific small analytes (i.e. metabolites, proteins, etc.) stability in complex sweat buffer with varying pH levels and composition over time. We present a facile approach to address these challenges using RTILs with antibody functionalized sensors on nanoporous, flexible polymer membranes. Temporal studies were performed using both infrared spectroscopic, dynamic light scattering, and impedimetric spectroscopy to demonstrate stability in detection of analytes, Interleukin-6 (IL-6) and Cortisol, from human sweat in RTILs. Temporal stability in sensor performance was performed as follows: (a) detection of target analytes after 0, 24, 48, 96, and 168 hours post-antibody sensor functionalization; and (b) continuous detection of target analytes post-antibody sensor functionalization. Limit of detection of IL-6 in human sweat was 0.2 pg/mL for 0-24 hours and 2 pg/mL for 24-48 hours post-antibody sensor functionalization. Continuous detection of IL-6 over 0.2-200 pg/mL in human sweat was demonstrated for a period of 10 hours post-antibody sensor functionalization. Furthermore, combinatorial detection of IL-6 and Cortisol in human sweat was established with minimal cross-talk for 0-48 hours post-antibody sensor functionalization.
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Affiliation(s)
- Rujuta D Munje
- Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas, 75080, USA
| | | | - Badrinath Jagannath
- Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas, 75080, USA
| | - Shalini Prasad
- Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas, 75080, USA.
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Caudle MR, Cox CE, Ley RT, Paluch AS. A molecular study of the wastewater contaminants atenolol and atrazine in 1-n-butyl-3-methylimidazolium based ionic liquids for potential treatment applications. Mol Phys 2017. [DOI: 10.1080/00268976.2016.1278478] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Miranda R. Caudle
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Courtney E. Cox
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Ran T. Ley
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Andrew S. Paluch
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
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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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Umapathi R, Mkhize TY, Venkatesu P, Deenadayalu N. The influence of various alkylammonium-based ionic liquids on the hydration state of temperature-responsive polymer. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.11.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Unanticipated high thermal stability and sustained activity of CT was found in the presence of [Ch][Ac], [Ch][Cl] and [Ch][Dhp], while [Ch][Cit] and [Ch][OH] act as strong destabilizers for the CT structure.
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Affiliation(s)
- Meena Bisht
- Department of Chemistry, University of Delhi
- Delhi-110 007
- India
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Jabbari M, Khosravi N, Feizabadi M, Ajloo D. Solubility temperature and solvent dependence and preferential solvation of citrus flavonoid naringin in aqueous DMSO mixtures: an experimental and molecular dynamics simulation study. RSC Adv 2017. [DOI: 10.1039/c7ra00038c] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This study describes the thermodynamics of dissolution of flavonoid naringin in different aqueous solutions of dimethyl sulfoxide (DMSO) containing 0–100% (w/w) under atmospheric pressure and over a temperature range of 298.15 to 325.15 K.
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Affiliation(s)
- Morteza Jabbari
- School of Chemistry
- Damghan University
- 36716-41167 Damghan
- Iran
| | - Negar Khosravi
- School of Chemistry
- Damghan University
- 36716-41167 Damghan
- Iran
| | - Mina Feizabadi
- School of Chemistry
- Damghan University
- 36716-41167 Damghan
- Iran
| | - Davood Ajloo
- School of Chemistry
- Damghan University
- 36716-41167 Damghan
- Iran
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Sajeevan KA, Roy D. Temperature-dependent molecular dynamics study reveals an ionic liquid induced 3 10 - to α-helical switch in a neurotoxin. Biopolymers 2016; 108. [PMID: 28009043 DOI: 10.1002/bip.23009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/29/2016] [Accepted: 12/06/2016] [Indexed: 02/01/2023]
Abstract
Thermal melting and recooling of AuIB, a neurotoxic conopeptide and a highly potent nonaddictive pain reliever is investigated thoroughly in water and an ionic liquid (IL) 1-butyl-3-methylimidazolium Chloride, [Im41 ][Cl] by classical molecular dynamics simulations. Structural evolution of AuIB in water and the IL is observed at different temperatures between 305 and 400 K, to explore how highly viscous ionic solvents affect the peptide structure as compared to conventional solvent water. At 305 K, unlike water, the coercive effect of IL frustrates AuIB secondary structural motifs significantly. As the temperature is raised, a very interesting IL induced conformational transition from 310 - to α-helix is noticed in the peptide, presumably triggered by a significant restructuring of the peptide H-bond network. The backbone length distributions of the peptide indicate that the IL induced conformational switching is accompanied by a reduction of the axial rise of the helical region, encompassing the residues Pro-6 to Ala-10. Further, we estimated the void space available to the peptide for its structural relaxation within the first solvation shell of ∼5 Å in water as well as in IL. A temperature increase by 100 K, opens up an estimated void volume of ∼70 Å3 , equivalent to the volume of approximately six water molecules, around the peptide in IL. Cooling simulations of AuIB point to the crucial interplay between thermodynamically favored AuIB conformers and their kinetic control. This study provides a comprehensive understanding of the ionic solvation of biomolecules reinforcing previous experimental findings.
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Affiliation(s)
- Karuna Anna Sajeevan
- Department of Chemistry, Birla Institute of Technology and Science-Pilani, Hyderabad, Campus, Jawahar Nagar, Shameerpet Mandal, Hyderabad, Telangana, 500078, India
| | - Durba Roy
- Department of Chemistry, Birla Institute of Technology and Science-Pilani, Hyderabad, Campus, Jawahar Nagar, Shameerpet Mandal, Hyderabad, Telangana, 500078, India
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Chevrot G, Fileti EE, Chaban VV. Protein remains stable at unusually high temperatures when solvated in aqueous mixtures of amino acid based ionic liquids. J Mol Model 2016; 22. [DOI: 10.1007/s00894-016-3123-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 09/08/2016] [Indexed: 10/20/2022]
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Bisht M, Jha I, Venkatesu P. Comprehensive Evaluation of Biomolecular Interactions between Protein and Amino Acid Based-Ionic Liquids: A Comparable Study between [Bmim][Br] and [Bmim][Gly] Ionic Liquids. ChemistrySelect 2016. [DOI: 10.1002/slct.201600524] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Meena Bisht
- Department of Chemistry; University of Delhi; Delhi- 110007 India, Tel:+91-11-27666646-142, Fax: +91-11-2766 6605
| | - Indrani Jha
- Department of Chemistry; University of Delhi; Delhi- 110007 India, Tel:+91-11-27666646-142, Fax: +91-11-2766 6605
| | - Pannuru Venkatesu
- Department of Chemistry; University of Delhi; Delhi- 110007 India, Tel:+91-11-27666646-142, Fax: +91-11-2766 6605
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