1
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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] [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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Lee PY, Singh O, Nanajkar N, Bermudez H, Matysiak S. Opposing roles of organic salts on mini-protein structure. Phys Chem Chem Phys 2024; 26:8973-8981. [PMID: 38436427 DOI: 10.1039/d3cp05607d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
We investigated the effects of 1-ethyl-3-methylimidazolium chloride ([EMIM][Cl]) and choline chloride ([Chol][Cl]) on the local environment and conformational landscapes of Trp-cage and Trpzip4 mini-proteins using experimental and computational approaches. Fluorescence experiments and computational simulations revealed distinct behaviors of the mini-proteins in the presence of these organic salts. [EMIM][Cl] showed a strong interaction with Trp-cage, leading to fluorescence quenching and destabilization of its native structural interactions. Conversely, [Chol][Cl] had a negligible impact on Trp-cage fluorescence at low concentrations but increased it at high concentrations, indicating a stabilizing role. Computational simulations elucidated that [EMIM][Cl] disrupted the hydrophobic core packing and decreased proline-aromatic residue contacts in Trp-cage, resulting in a more exposed environment for Trp residues. In contrast, [Chol][Cl] subtly influenced the hydrophobic core packing, creating a hydrophobic environment near the tryptophan residues. Circular dichroism experiments revealed that [Chol][Cl] stabilized the secondary structure of both mini-proteins, although computational simulations did not show significant changes in secondary content at the explored concentrations. The simulations also demonstrated a more rugged free energy landscape for Trp-cage and Trpzip4 in [EMIM][Cl], suggesting destabilization of the tertiary structure for Trp-cage and secondary structure for Trpzip4. Similar fluorescence trends were observed for Trpzip4, with [EMIM][Cl] quenching fluorescence and exhibiting stronger interaction, while [Chol][Cl] increased the fluorescence at high concentrations. These findings highlight the interplay between [EMIM][Cl] and [Chol][Cl] with the mini-proteins and provide a detailed molecular-level understanding of how these organic salts impact the nearby surroundings and structural variations. Understanding such interactions is valuable for diverse applications, from biochemistry to materials science.
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Affiliation(s)
- Pei-Yin Lee
- Chemical Physics Program, Institute for Physical Science and Technology, University of Maryland, College Park, USA
| | - Onkar Singh
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA, USA.
| | - Neha Nanajkar
- Department of Biology, University of Maryland, College Park, USA
| | - Harry Bermudez
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA, USA.
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.
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3
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Fiuza T, Sarkar M, Riedl JC, Beaughon M, Torres Bautista BE, Bhattacharya K, Cousin F, Barruet E, Demouchy G, Depeyrot J, Dubois E, Gélébart F, Geertsen V, Mériguet G, Michot L, Nakamae S, Perzynski R, Peyre V. Ion specific tuning of nanoparticle dispersion in an ionic liquid: a structural, thermoelectric and thermo-diffusive investigation. Phys Chem Chem Phys 2023; 25:28911-28924. [PMID: 37855156 DOI: 10.1039/d3cp02399k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Dispersions of charged maghemite nanoparticles (NPs) in EAN (ethylammonium nitrate) a reference Ionic Liquid (IL) are studied here using a number of static and dynamical experimental techniques; small angle scattering (SAS) of X-rays and of neutrons, dynamical light scattering and forced Rayleigh scattering. Particular insight is provided regarding the importance of tuning the ionic species present at the NP/IL interface. In this work we compare the effect of Li+, Na+ or Rb+ ions. Here, the nature of these species has a clear influence on the short-range spatial organisation of the ions at the interface and thus on the colloidal stability of the dispersions, governing both the NP/NP and NP/IL interactions, which are both evaluated here. The overall NP/NP interaction is either attractive or repulsive. It is characterised by determining, thanks to the SAS techniques, the second virial coefficient A2, which is found to be independent of temperature. The NP/IL interaction is featured by the dynamical effective charge ξeff0 of the NPs and by their entropy of transfer ŜNP (or equivalently their heat of transport ) determined here thanks to thermoelectric and thermodiffusive measurements. For repulsive systems, an activated process rules the temperature dependence of these two latter quantities.
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Affiliation(s)
- T Fiuza
- Sorbonne Université, CNRS, Lab. PHENIX, 4 Place Jussieu, F-75005 Paris, France.
- Grupo de Fluidos Complexos, Inst. de Fisíca, Univ. de Brasília, Brasília (DF), Brazil
| | - M Sarkar
- Sorbonne Université, CNRS, Lab. PHENIX, 4 Place Jussieu, F-75005 Paris, France.
| | - J C Riedl
- Sorbonne Université, CNRS, Lab. PHENIX, 4 Place Jussieu, F-75005 Paris, France.
| | - M Beaughon
- Service de Physique de l'état condensé, SPEC, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif sur Yvette, CEDEX, France
| | - B E Torres Bautista
- Service de Physique de l'état condensé, SPEC, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif sur Yvette, CEDEX, France
| | - K Bhattacharya
- Service de Physique de l'état condensé, SPEC, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif sur Yvette, CEDEX, France
| | - F Cousin
- Lab. Léon Brillouin-UMR 12 CNRS-CEA CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - E Barruet
- Univ. Paris-Saclay, CEA, CNRS, NIMBE-LIONS, 91191 Gif sur Yvette, CEDEX, France
| | - G Demouchy
- Sorbonne Université, CNRS, Lab. PHENIX, 4 Place Jussieu, F-75005 Paris, France.
- Univ. de Cergy Pontoise-Dpt de physique, 33 Bd du Port, 95011 Cergy-Pontoise, France
| | - J Depeyrot
- Grupo de Fluidos Complexos, Inst. de Fisíca, Univ. de Brasília, Brasília (DF), Brazil
| | - E Dubois
- Sorbonne Université, CNRS, Lab. PHENIX, 4 Place Jussieu, F-75005 Paris, France.
| | - F Gélébart
- Sorbonne Université, CNRS, Lab. PHENIX, 4 Place Jussieu, F-75005 Paris, France.
| | - V Geertsen
- Univ. Paris-Saclay, CEA, CNRS, NIMBE-LIONS, 91191 Gif sur Yvette, CEDEX, France
| | - G Mériguet
- Sorbonne Université, CNRS, Lab. PHENIX, 4 Place Jussieu, F-75005 Paris, France.
| | - L Michot
- Sorbonne Université, CNRS, Lab. PHENIX, 4 Place Jussieu, F-75005 Paris, France.
| | - S Nakamae
- Service de Physique de l'état condensé, SPEC, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif sur Yvette, CEDEX, France
| | - R Perzynski
- Sorbonne Université, CNRS, Lab. PHENIX, 4 Place Jussieu, F-75005 Paris, France.
| | - V Peyre
- Sorbonne Université, CNRS, Lab. PHENIX, 4 Place Jussieu, F-75005 Paris, France.
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4
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Shumilin I, Harries D. Enhanced solubilization in multi-component mixtures: mechanism of synergistic amplification of cyclodextrin solubility by urea and inorganic salts. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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5
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Pal T, Sahoo S, Prasad Ghanta K, Bandyopadhyay S. Computational Investigation of Conformational Fluctuations of Aβ42 Monomers in Aqueous Ionic Liquid Mixtures. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Piccoli V, Martínez L. Ionic liquid solvation of proteins in native and denatured states. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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7
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Solution behavior of native and denatured beta lactoglobulin in presence of pyridinium based ionic liquids: A biophysical perspective of folding and refolding pattern of the protein. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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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] [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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9
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Li R, Liu Z, Jiang F, Zhao Y, Yang G, Hong L. Enhancement of thermal stability of proteinase K by biocompatible cholinium-based ionic liquids. Phys Chem Chem Phys 2022; 24:13057-13065. [PMID: 35583879 DOI: 10.1039/d1cp04782e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteinase K (PK) is a proteolytic enzyme that has been widely used in nucleic acid purification, leather production, environmental protection, and other industrial applications. However, this biocatalyst cannot tolerate high temperatures which has severely restricted its wider application. As reported in previous studies, cholinium-based ionic liquids (ILs) have gained tremendous attention serving as a promising media to stabilize and preserve proteins, DNA, and other biomolecules due to their environmentally benign nature and biocompatibility. In this work, we chose 13 different kinds of cholinium-based ILs to examine their effects on the thermal stability and enzymatic activity of PK. We found that biocompatible cholinium-based ions with appropriately chosen anions can greatly improve the thermal stability of PK, whose melting temperature (Tm) is increased from ∼74.4 °C to 87.7 °C. However, the enzymatic activity is slightly reduced in the presence of ILs. Further comparison of our results with other literature findings suggests that kosmotropic anions of cholinium-based ILs are crucial to maintain the thermal stability of proteins. However, to achieve the best performance, the choice of IL anions is protein specific.
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Affiliation(s)
- Rui Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. .,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai National Center for Applied Mathematics (SJTU center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. .,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Zhao
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. .,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai National Center for Applied Mathematics (SJTU center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Miranda-Quintana RA, Smiatek J. Specific Ion Effects in Different Media: Current Status and Future Challenges. J Phys Chem B 2021; 125:13840-13849. [PMID: 34918938 DOI: 10.1021/acs.jpcb.1c07957] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We discuss the current state of research as well as the future challenges for a deeper understanding of specific ion effects in protic and aprotic solvents as well as various additional media. Despite recent interest in solute or interfacial effects, we focus exclusively on the specific properties of ions in bulk electrolyte solutions. Corresponding results show that many mechanisms remain unknown for these simple media, although theoretical, computational, and experimental studies have provided some insights into explaining individual observations. In particular, the importance of local interactions and electronic properties is emphasized, which enabled a more consistent interpretation of specific ion effects over the past years. Despite current insufficient knowledge, we also discuss future challenges in relation to dynamic properties as well as the influence of different concentrations, different solvents, and solute contributions to gain a deeper understanding of specific ion effects for technological applications.
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Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany.,Digitalization Development Biologicals CMC, Boehringer Ingelheim Pharma GmbH & Co. KG, D-88397 Biberach (Riss), Germany
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11
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Miranda-Quintana RA, Smiatek J. Electronic Properties of Protein Destabilizers and Stabilizers: Implications for Preferential Binding and Exclusion Mechanisms. J Phys Chem B 2021; 125:11857-11868. [PMID: 34672590 DOI: 10.1021/acs.jpcb.1c06295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We study the electronic properties of low-weight organic co-solutes by means of conceptual density functional theory calculations. Our results highlight the important role of certain chemical reactivity descriptors such as chemical hardness, electronegativity, nucleofugality, and the electrofugality as important criteria to classify protein stabilizers and destabilizers. Our results imply Lewis basic properties with lower chemical hardness for stabilizers, while destabilizers show higher Lewis acidity with higher chemical hardness. Further consideration of analytical calculations in terms of transfer energies reveals the crucial role of co-solute-protein interactions which significantly change the interaction pattern of the stabilizing or destabilizing species. The corresponding outcomes connect statistical thermodynamics with the electronic properties of co-solutes and also allow us to define general principles for strong stabilizers and destabilizers.
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Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
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12
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Keller F, Heuer A, Galla HJ, Smiatek J. Stabilization of DPPC lipid bilayers in the presence of co-solutes: molecular mechanisms and interaction patterns. Phys Chem Chem Phys 2021; 23:22936-22946. [PMID: 34622252 DOI: 10.1039/d1cp03052c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We study the interactions between dipalmitoylphosphatidylcholine (DPPC) lipid bilayers in the gel and the fluid phase with ectoine, amino ectoine and water molecules by means of atomistic molecular dynamics (MD) simulations and conceptual density functional theory (DFT) calculations. Our results reveal a pronounced preferential exclusion of both co-solutes from the DPPC lipid bilayer which is stronger for the fluid phase. The corresponding outcomes can be brought into relation with the Kirkwood-Buff theory of solutions in order to provide a thermodynamic rationale for the experimentally observed stabilization of the gel phase. Closely related to preferential exclusion of both co-solutes, our simulations also highlight a preferential hydration behavior as manifested by an increased number of hydrogen bonds between water and DPPC molecules. All results are rationalized by conceptual DFT calculations with regard to differences in the electronic properties between ectoine and amino ectoine.
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Affiliation(s)
- Fabian Keller
- Institute of Physical Chemistry, University of Münster, D-48149 Münster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Münster, D-48149 Münster, Germany
| | - Hans-Joachim Galla
- Institute of Biochemistry, University of Münster, D-48149 Münster, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany.
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13
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El Harrar T, Frieg B, Davari MD, Jaeger KE, Schwaneberg U, Gohlke H. Aqueous ionic liquids redistribute local enzyme stability via long-range perturbation pathways. Comput Struct Biotechnol J 2021; 19:4248-4264. [PMID: 34429845 PMCID: PMC8355836 DOI: 10.1016/j.csbj.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/25/2023] Open
Abstract
Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co-)solvents for biocatalysis due to their unique properties. On the other hand, the incubation of enzymes in IL or aIL often reduces enzyme activity. Recent studies proposed various aIL-induced effects to explain the reduction, classified as direct effects, e.g., local dehydration or competitive inhibition, and indirect effects, e.g., structural perturbations or disturbed catalytic site integrity. However, the molecular origin of indirect effects has largely remained elusive. Here we show by multi-μs long molecular dynamics simulations, free energy computations, and rigidity analyses that aIL favorably interact with specific residues of Bacillus subtilis Lipase A (BsLipA) and modify the local structural stability of this model enzyme by inducing long-range perturbations of noncovalent interactions. The perturbations percolate over neighboring residues and eventually affect the catalytic site and the buried protein core. Validation against a complete experimental site saturation mutagenesis library of BsLipA (3620 variants) reveals that the residues of the perturbation pathways are distinguished sequence positions where substitutions highly likely yield significantly improved residual activity. Our results demonstrate that identifying these perturbation pathways and specific IL ion-residue interactions there effectively predicts focused variant libraries with improved aIL tolerance.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Benedikt Frieg
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52428 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- DWI – Leibniz Institute for Interactive Materials e.V., 52074 Aachen, Germany
| | - Holger Gohlke
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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14
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Proteins maintain hydration at high [KCl] concentration regardless of content in acidic amino acids. Biophys J 2021; 120:2746-2762. [PMID: 34087206 PMCID: PMC8390907 DOI: 10.1016/j.bpj.2021.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/22/2021] [Accepted: 05/19/2021] [Indexed: 11/23/2022] Open
Abstract
Proteins of halophilic organisms, which accumulate molar concentrations of KCl in their cytoplasm, have a much higher content in acidic amino acids than proteins of mesophilic organisms. It has been proposed that this excess is necessary to maintain proteins hydrated in an environment with low water activity, either via direct interactions between water and the carboxylate groups of acidic amino acids or via cooperative interactions between acidic amino acids and hydrated cations. Our simulation study of five halophilic proteins and five mesophilic counterparts does not support either possibility. The simulations use the AMBER ff14SB force field with newly optimized Lennard-Jones parameters for the interactions between carboxylate groups and potassium ions. We find that proteins with a larger fraction of acidic amino acids indeed have higher hydration levels, as measured by the concentration of water in their hydration shell and the number of water/protein hydrogen bonds. However, the hydration level of each protein is identical at low (bKCl = 0.15 mol/kg) and high (bKCl = 2 mol/kg) KCl concentrations; excess acidic amino acids are clearly not necessary to maintain proteins hydrated at high salt concentration. It has also been proposed that cooperative interactions between acidic amino acids in halophilic proteins and hydrated cations stabilize the folded protein structure and would lead to slower dynamics of the solvation shell. We find that the translational dynamics of the solvation shell is barely distinguishable between halophilic and mesophilic proteins; if such a cooperative effect exists, it does not have that entropic signature.
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15
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Sarimov RM, Binhi VN, Matveeva TA, Penkov NV, Gudkov SV. Unfolding and Aggregation of Lysozyme under the Combined Action of Dithiothreitol and Guanidine Hydrochloride: Optical Studies. Int J Mol Sci 2021; 22:2710. [PMID: 33800175 PMCID: PMC7962454 DOI: 10.3390/ijms22052710] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
Using a number of optical techniques (interferometry, dynamic light scattering, and spectroscopy), denaturation of hen egg white lysozyme (HEWL) by treatment with a combination of dithiothreitol (DTT) and guanidine hydrochloride (GdnHCl) has been investigated. The denaturing solutions were selected so that protein denaturation occurred with aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM) or without aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM, GdnHCl 6 M) and can be evaluated after 60 min of treatment. It has been found that denatured by solution with 6 M GdnHCl lysozyme completely loses its enzymatic activity after 30 min and the size of the protein molecule increases by 1.5 times, from 3.8 nm to 5.7 nm. Denaturation without of GdnHCl led to aggregation with preserving about 50% of its enzymatic activity. Denaturation of HEWL was examined using interferometry. Previously, it has been shown that protein denaturation that occurs without subsequent aggregation leads to an increase in the refractive index (Δn ~ 4.5 × 10-5). This is most likely due to variations in the HEWL-solvent interface area. By applying modern optical techniques conjointly, it has been possible to obtain information on the nature of time-dependent changes that occur inside a protein and its hydration shell as it undergoes denaturation.
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Affiliation(s)
- Ruslan M. Sarimov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov St., 38, 119991 Moscow, Russia; (R.M.S.); (V.N.B.); (T.A.M.)
| | - Vladimir N. Binhi
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov St., 38, 119991 Moscow, Russia; (R.M.S.); (V.N.B.); (T.A.M.)
| | - Tatiana A. Matveeva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov St., 38, 119991 Moscow, Russia; (R.M.S.); (V.N.B.); (T.A.M.)
| | - Nikita V. Penkov
- Institute of Cell Biophysics of the Russian Academy of Sciences, PSCBR RAS, Institutskaya St., 3, Pushchino, 142290 Moscow, Russia;
| | - Sergey V. Gudkov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov St., 38, 119991 Moscow, Russia; (R.M.S.); (V.N.B.); (T.A.M.)
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16
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Oprzeska-Zingrebe EA, Smiatek J. Interactions of a DNA G-quadruplex with TMAO and urea: a molecular dynamics study on co-solute compensation mechanisms. Phys Chem Chem Phys 2021; 23:1254-1264. [PMID: 33355575 DOI: 10.1039/d0cp05356b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We study the individual and combined influence of TMAO and urea on a basket-type DNA G-quadruplex by means of atomistic molecular dynamics (MD) simulations. In combination with the Kirkwood-Buff theory of solutions, we propose a simple mechanism to elucidate the impact of TMAO and urea on the G-quadruplex. Our results reveal the importance of the molecular accumulation around the DNA in terms of stabilizing or destabilizing effects. The results for mixtures show only a weak interaction between both co-solutes, which highlights the additivity of contributions. Despite the fact, that TMAO can to some extent compensate the adverse impact of urea on the G-quadruplex structure, the destabilizing influence is not completely eliminated. This observation opens the door for further research on selective stabilization of DNA G-quadruplexes by modulating the concentrations of TMAO and urea in solution.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany.
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17
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Shukla SK, Mikkola JP. Use of Ionic Liquids in Protein and DNA Chemistry. Front Chem 2020; 8:598662. [PMID: 33425856 PMCID: PMC7786294 DOI: 10.3389/fchem.2020.598662] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Ionic liquids (ILs) have been receiving much attention as solvents in various areas of biochemistry because of their various beneficial properties over the volatile solvents and ILs availability in myriad variants (perhaps as many as 108) owing to the possibility of paring one cation with several anions and vice-versa as well as formulations as zwitterions. Their potential as solvents lies in their tendency to offer both directional and non-directional forces toward a solute molecule. Because of these forces, ionic liquids easily undergo intermolecular interactions with a range of polar/non-polar solutes, including biomolecules such as proteins and DNA. The interaction of genomic species in aqueous/non-aqueous states assists in unraveling their structure and functioning, which have implications in various biomedical applications. The charge density of ionic liquids renders them hydrophilic and hydrophobic, which retain intact over long-range of temperatures. Their ability in stabilizing or destabilizing the 3D-structure of a protein or the double-helical structure of DNA has been assessed superior to the water and volatile organic solvents. The aptitude of an ion in influencing the structure and stability of a native protein depends on their ranking in the Hofmeister series. However, at several instances, a reverse Hofmeister ordering of ions and specific ion-solute interaction has been observed. The capability of an ionic liquid in terms of the tendency to promote the coiling/uncoiling of DNA structure is noted to rely on the basicity, electrostatic interaction, and hydrophobicity of the ionic liquid in question. Any change in the DNA's double-helical structure reflects a change in its melting temperature (T m), compared to a standard buffer solution. These changes in DNA structure have implications in biosensor design and targeted drug-delivery in biomedical applications. In the current review, we have attempted to highlight various aspects of ionic liquids that influence the structure and properties of proteins and DNA. In short, the review will address the issues related to the origin and strength of intermolecular interactions, the effect of structural components, their nature, and the influence of temperature, pH, and additives on them.
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Affiliation(s)
- Shashi Kant Shukla
- Technical Chemistry, Department of Chemistry, Chemical-Biological Centre, Umeå University, Umeå, Sweden
| | - Jyri-Pekka Mikkola
- Technical Chemistry, Department of Chemistry, Chemical-Biological Centre, Umeå University, Umeå, Sweden
- Industrial Chemistry and Reaction Engineering, Department of Chemical Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland
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18
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Miranda‐Quintana RA, Smiatek J. Theoretical Insights into Specific Ion Effects and Strong-Weak Acid-Base Rules for Ions in Solution: Deriving the Law of Matching Solvent Affinities from First Principles. Chemphyschem 2020; 21:2605-2617. [PMID: 32975891 PMCID: PMC7756232 DOI: 10.1002/cphc.202000644] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/21/2020] [Indexed: 12/02/2022]
Abstract
We present a detailed study of specific ion effects, volcano plots and the law of matching solvent affinities by means of a conceptual density functional theory (DFT) approach. Our results highlight that specific ion effects and the corresponding implications on the solvation energy are mainly due to differences in the electric chemical potentials and chemical hardnesses of the ions and the solvent. Our approach can be further used to identify reliable criteria for the validity of the law of matching solvent affinities. Basic expressions are derived, which allow us to study the limiting conditions for this empirical observation with regard to matching chemical reactivity indices. Moreover, we show that chaotropic and kosmotropic concepts and their implications for the stability of ion pairs are directly related to a generalized strong and weak acids and bases (SWAB) principle for ions in solution, which is also applicable to rationalize the shape of volcano plots for different solvents. In contrast to previous assumptions, all empirical findings can be explained by the properties of local solvent-ion complexes which dominate the specific global behavior of ion pairs in solution.
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Affiliation(s)
| | - Jens Smiatek
- Institut für ComputerphysikUniversität Stuttgart70569StuttgartGermany
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19
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Piccoli V, Martínez L. Correlated counterion effects on the solvation of proteins by ionic liquids. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Mestdagh JM, Poisson L. Excited State Dynamics of Isolated 6- and 8-Hydroxyquinoline Molecules. Chemphyschem 2020; 21:2605-2613. [PMID: 33022865 DOI: 10.1002/cphc.202000626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/05/2020] [Indexed: 11/09/2022]
Abstract
The photoinduced dynamics of isolated n-hydroxyquinoline (nHQ) molecules (n=6,8) was investigated in femtosecond pump-probe experiments. A qualitative difference was found between 8HQ and 6HQ. After an initial rapid decay corresponding to the departure of the initial wavepacket out of the Franck-Condon region of the excitation, the 8HQ probe signal decays to zero in 0.37 ps whereas a much longer time constant of 10.4 ps is observed in 6HQ. This interrogates on the role played by the intramolecular H-bond N · · · HO which is at play the 8HQ molecule. Ab-initio were performed at the MCSCF/aug-cc-pVDZ level on the 8HQ molecule to help the discussion. A complex energy landscape was found, which includes a conical intersection.
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Affiliation(s)
- Jean-Michel Mestdagh
- LIDYL, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - Lionel Poisson
- LIDYL, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
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21
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Bezerra-Neto JR, Bezerra LL, Sousa NG, Dos Santos LPM, Marinho ES, Monteiro NKV, Correia AN, de Lima-Neto P. Molecular approach about the effect of water on the electrochemical behaviour of Ag + ions in urea-choline chloride-water mixture. J Mol Model 2020; 26:339. [PMID: 33179132 DOI: 10.1007/s00894-020-04587-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/25/2020] [Indexed: 01/29/2023]
Abstract
The water influence on electrochemical behaviour of Ag+ ions in urea and choline chloride mixture was investigated by cyclic voltammetry technique, while the molecular insights about the investigated systems were obtained from molecular dynamic (MD) simulation. The water content was variated from 0 up to 10% (v/v). Cyclic voltammetry technique showed that the peak potential for Ag+/Ag redox couples shifted in direction to more positive potentials with the gradual increase of water content in solution, indicating that the addition of water electrocatalyses the kinetics of the reduction of Ag+ ions. The MD simulations demonstrated that water molecules do not interact strongly with Ag+ ions but induce a small reduction in the number of urea molecules around of the ion and that the water molecules adjust to free spaces in the mixture.
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Affiliation(s)
- João R Bezerra-Neto
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, Fortaleza, CE, 60440-900, Brazil
| | - Lucas L Bezerra
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, Fortaleza, CE, 60440-900, Brazil
| | - Natalia G Sousa
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, Fortaleza, CE, 60440-900, Brazil
| | - Luis P M Dos Santos
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, Fortaleza, CE, 60440-900, Brazil
| | - Emmanuel S Marinho
- Departamento de Química/FAFIDAM, Universidade Estadual do Ceará, Limoeiro do Norte, CE, 62930-000, Brazil
| | - Norberto K V Monteiro
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, Fortaleza, CE, 60440-900, Brazil
| | - Adriana N Correia
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, Fortaleza, CE, 60440-900, Brazil
| | - Pedro de Lima-Neto
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, Fortaleza, CE, 60440-900, Brazil.
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22
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Mező E, Páger C, Makszin L, Kilár F. Capillary zone electrophoresis of proteins applying ionic liquids for dynamic coating and as background electrolyte component. Electrophoresis 2020; 41:2083-2091. [PMID: 33022798 DOI: 10.1002/elps.202000204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/07/2022]
Abstract
The use of ionic liquids in capillary electrophoresis, either as coating material or as components of the background electrolyte needs systematic standardization to set up optimal conditions. Excellent separation of the proteins was achieved using 1-ethyl-3-methylimidazolium tetrafluoroborate ([emim][BF4 ]) or 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4 ]) ionic liquids using the properly made ionic-liquid-water binary mixtures for the experiments. The binary mixture has a distinctly stable and well perceptible low pH, which depends on the concentration of the ionic liquid, and on the preparation time of the mixture. Optimal conditions for the electrophoretic separation were obtained upon a multivariate analysis of the experimental parameters (applied voltage, migration time, concentration, and type of the ionic liquid). The standardized condition provides a low electroendosmotic flow toward the anode, which, however, did not hinder the proteins to migrate toward the cathode. The migration of cytochrome c, lysozyme, myoglobin, trypsin, and apo-transferrin at a pH around 2, far below the isoelectric points of the proteins, showed RSD values of the migration times less than 7.5% and less than 6.5% when using [emim][BF4 ] or [bmim][BF4 ], respectively, either in run-to-run or day-to-day experiments. The determination of the extent of the EOF is not possible with the commonly used EOF markers, due to interaction with the ionic-liquid constituents. The interaction of the ionic liquids with the proteins influences the migration order in zone electrophoresis. This method has been applied successfully for the analyses of real biological samples such as proteins from egg whites and human tears.
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Affiliation(s)
- Emerencia Mező
- Institute of Bioanalysis, Medical School, and Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Csilla Páger
- Institute of Bioanalysis, Medical School, and Szentágothai Research Center, University of Pécs, Pécs, Hungary
- Department of Analytical and Environmental Chemistry, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Lilla Makszin
- Institute of Bioanalysis, Medical School, and Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Ferenc Kilár
- Institute of Bioanalysis, Medical School, and Szentágothai Research Center, University of Pécs, Pécs, Hungary
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Miercurea Ciuc, Romania
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23
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Smiatek J, Jung A, Bluhmki E. Towards a Digital Bioprocess Replica: Computational Approaches in Biopharmaceutical Development and Manufacturing. Trends Biotechnol 2020; 38:1141-1153. [DOI: 10.1016/j.tibtech.2020.05.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022]
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24
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Chen M, Feng G, Qiao R. Water-in-salt electrolytes: An interfacial perspective. Curr Opin Colloid Interface Sci 2020. [DOI: 10.1016/j.cocis.2019.12.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Smiatek J. Specific Ion Effects and the Law of Matching Solvent Affinities: A Conceptual Density Functional Theory Approach. J Phys Chem B 2020; 124:2191-2197. [PMID: 32105071 DOI: 10.1021/acs.jpcb.9b10886] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We study the principles behind specific ion effects of alkali and halide ions in various protic and aprotic solvents by means of a conceptual density functional theory (DFT) approach. The results of our calculations are in good agreement with experimental data and underline the crucial role of frontier molecular orbital energies. Further analysis reveals that the electronegativities and chemical hardness values of the considered ion and solvent species provide a molecular rationale for specific ion effects and the law of matching water affinities. Based on the analytical expressions and DFT calculations, we show that solvent affinities and the occurrence of specific ion effects, among other molecular mechanisms and interactions, are mainly due to electronegativity differences between the ions and the surrounding solvent molecules.
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Affiliation(s)
- Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
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26
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Morimitsu Y, Matsuno H, Ohta N, Sekiguchi H, Takahara A, Tanaka K. Mechanical Stabilization of Deoxyribonucleic Acid Solid Films Based on Hydrated Ionic Liquid. Biomacromolecules 2020; 21:464-471. [PMID: 31800230 DOI: 10.1021/acs.biomac.9b01207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solid films of deoxyribonucleic acid (DNA) containing a hydrated ionic liquid, choline dihydrogen phosphate (CDP), were prepared by a solvent-casting method. Thermal properties, aggregation structure, thermal molecular motion, and tensile properties of CDP-containing DNA films were examined by thermogravimetry (TG), wide-angle X-ray diffraction (WAXD) measurement, dynamic mechanical analysis (DMA), and tensile tests, respectively. The water retentivity of the films at room temperature was much improved with CDP. The packing density of DNA helical chains clearly depended on the amount of CDP in the film. A small amount of CDP contributed to the suppression of the BI → BII conformational transition and the cooperative motion of the DNA duplex in the film. The tensile properties of the film drastically changed in the presence of CDP. When the amount of hydrated CDP in the film increased, the mechanical response of the film changed from glassy-like to rubbery-like via a semicrystalline-like state. The above results make it clear that CDP plays two major roles as a water absorber and plasticizer in the DNA film. Thus, it can be concluded that the use of an ionic liquid as an additive significantly increases the possibility of using a DNA solid film as a structural material.
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Affiliation(s)
| | | | - Noboru Ohta
- Japan Synchrotron Radiation Research Institute (JASRI) , Sayo-cho , Hyogo 679-5198 , Japan
| | - Hiroshi Sekiguchi
- Japan Synchrotron Radiation Research Institute (JASRI) , Sayo-cho , Hyogo 679-5198 , Japan
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27
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Aggregation selectivity of amyloid
β
1‐11
peptide in aqueous ionic liquid solutions. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Smiatek J. Enthalpic contributions to solvent–solute and solvent–ion interactions: Electronic perturbation as key to the understanding of molecular attraction. J Chem Phys 2019; 150:174112. [PMID: 31067894 DOI: 10.1063/1.5092567] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jens Smiatek
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
- Helmholtz Institut Münster (HI MS–IEK 12): Ionenleiter in Energiespeichern, Forschungszentrum Jülich GmbH, Corrensstrasse 46, D-48149 Münster, Germany
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29
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Oprzeska-Zingrebe EA, Smiatek J. Preferential Binding of Urea to Single-Stranded DNA Structures: A Molecular Dynamics Study. Biophys J 2019; 114:1551-1562. [PMID: 29642026 DOI: 10.1016/j.bpj.2018.02.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/12/2018] [Accepted: 02/12/2018] [Indexed: 01/06/2023] Open
Abstract
In nature, a wide range of biological processes such as transcription termination and intermolecular binding depend on the formation of specific DNA secondary and tertiary structures. These structures can be both stabilized or destabilized by different cosolutes coexisting with nucleic acids in the cellular environment. In our molecular dynamics simulation study, we investigate the binding of urea at different concentrations to short 7-nucleotide single-stranded DNA structures in aqueous solution. The local concentration of urea around a native DNA hairpin in comparison to an unfolded DNA conformation is analyzed by a preferential binding model in light of the Kirkwood-Buff theory. All our findings indicate a pronounced accumulation of urea around DNA that is driven by a combination of electrostatic and dispersion interactions and accomplished by a significant replacement of hydrating water molecules. The outcomes of our study can be regarded as a first step into a deeper mechanistic understanding toward cosolute-induced effects on nucleotide structures in general.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany; Helmholtz Institute Münster: Ionics in Energy Storage, Forschungszentrum Jülich, Münster, Germany.
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30
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Wiedemann C, Hempel G, Bordusa F. Reorientation dynamics and ion diffusivity of neat dimethylimidazolium dimethylphosphate probed by NMR spectroscopy. RSC Adv 2019; 9:35735-35750. [PMID: 35528082 PMCID: PMC9074696 DOI: 10.1039/c9ra07731f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/28/2019] [Indexed: 11/21/2022] Open
Abstract
NMR spectroscopy at two magnetic field strengths was employed to investigate the dynamics of dimethylimidazolium dimethylphosphate ([C1C1IM][(CH3)2PO4]). [C1C1IM][(CH3)2PO4] is a low-melting, halogen-free ionic liquid comprising of only methyl groups. 13C spin–lattice relaxation rates as well as self-diffusion coefficients were measured for [C1C1IM][(CH3)2PO4] as a function of temperature. The rotational correlation times, τc, for the cation and the anion were obtained from the 13C spin–lattice relaxation rates. Although from a theoretical point of view cations and anions are similar in size, they show different reorientation mobilities and diffusivities. The self-diffusion coefficients and the rotational correlation times were related to the radii of the diffusing spheres. The analysis reveals that the radii of the cation and the anion, respectively, are different from each other but constant at temperatures ranging from 293 to 353 K. The experimental results are rationalised by a discrete and individual cation and anion diffusion. The [(CH3)2PO4]− anion reorients faster compared to the cation but diffuses significantly slower indicating the formation of anionic aggregates. Relaxation data were acquired with standard liquid and magic-angle-spinning NMR probes to estimate residual dipolar interactions, chemical shift anisotropy or differences in magnetic susceptibility within the sample. Liquid and HR-MAS NMR spectroscopy at two magnetic field strengths was employed to investigate the dynamics of ([C1C1IM][(CH3)2PO4]).![]()
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Affiliation(s)
- Christoph Wiedemann
- Institute of Biochemistry and Biotechnology
- Charles Tanford Protein Center
- Martin Luther University Halle-Wittenberg
- D-06120 Halle (Saale)
- Germany
| | - Günter Hempel
- Institute of Physics
- Martin Luther University Halle-Wittenberg
- D-06120 Halle (Saale)
- Germany
| | - Frank Bordusa
- Institute of Biochemistry and Biotechnology
- Charles Tanford Protein Center
- Martin Luther University Halle-Wittenberg
- D-06120 Halle (Saale)
- Germany
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31
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Egorova KS, Ananikov VP. Fundamental importance of ionic interactions in the liquid phase: A review of recent studies of ionic liquids in biomedical and pharmaceutical applications. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.09.025] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Zeindlhofer V, Berger M, Steinhauser O, Schröder C. A shell-resolved analysis of preferential solvation of coffee ingredients in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate. J Chem Phys 2018; 148:193819. [PMID: 30307218 DOI: 10.1063/1.5009802] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Ionic liquids increase the solubility of various coffee ingredients in aqueous solution but little is known about the underlying mechanism. Kirkwood-Buff integrals as well as the potential of mean force indicate that the imidazolium cations are accumulated at the surface of the solutes, removing water molecules from the solute surface. Although hydrogen bonding of the anions to hydroxy groups of the solutes can be detected, their concentration at the surface is less enhanced compared to the cations. The decomposition into solvation shells by Voronoi tessellation reveals that structural features are only observed in the first solvation shell. Nevertheless, the depletion of water and the excess concentration of the ions and, in particular, of the cations are visible in the next solvation shells as well. Therefore, classical arguments of hydrotropic theory fail to explain this behavior.
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Affiliation(s)
- Veronika Zeindlhofer
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Vienna A-1090, Austria
| | - Magdalena Berger
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Vienna A-1090, Austria
| | - Othmar Steinhauser
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Vienna A-1090, Austria
| | - Christian Schröder
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Vienna A-1090, Austria
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33
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Lim GS, Klähn M. On the Stability of Proteins Solvated in Imidazolium-Based Ionic Liquids Studied with Replica Exchange Molecular Dynamics. J Phys Chem B 2018; 122:9274-9288. [DOI: 10.1021/acs.jpcb.8b06452] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Geraldine S. Lim
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16, Connexis, Singapore 138632, Republic of Singapore
| | - Marco Klähn
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore
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34
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Narayanan Krishnamoorthy A, Holm C, Smiatek J. Specific ion effects for polyelectrolytes in aqueous and non-aqueous media: the importance of the ion solvation behavior. SOFT MATTER 2018; 14:6243-6255. [PMID: 30009285 DOI: 10.1039/c8sm00600h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present the results of atomistic molecular dynamics simulations with regard to specific ion effects in water, methanol and N,N-dimethylacetamide (DMAc). As a reference system, we introduce rigid and rod-like models of polyanions and polycations in combination with alkali metal cations and halide anions as counterions. Pronounced specific ion effects can be observed in terms of the individual anion and cation condensation behavior. The outcomes of our simulations thus reveal significant deviations from standard electrostatic mean-field theories. A detailed investigation of the individual energy contributions shows that ion-dipole interactions play a pivotal role in rationalizing the findings. The corresponding deviations in terms of the cation and anion distribution can be brought into agreement with the donor and acceptor numbers of the solvents, which thus highlights the importance of solvent-ion interactions in addition to electrostatic attraction.
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35
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Jeong KB, Luo K, Lim MC, Jung JY, Yu JS, Kim KB, Kim YR. Reduction of DNA Folding by Ionic Liquids and Its Effects on the Analysis of DNA-Protein Interaction Using Solid-State Nanopore. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1801375. [PMID: 29971919 DOI: 10.1002/smll.201801375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/28/2018] [Indexed: 06/08/2023]
Abstract
DNA folding is not desirable for solid-state nanopore techniques when analyzing the interaction of a biomolecule with its specific binding sites on DNA since the signal derived from the binding site could be buried by a large signal from the folding of DNA nearby. To resolve the problems associated with DNA folding, ionic liquids (ILs), which are known to interact with DNA through charge-charge and hydrophobic interactions are employed. 1-n-butyl-3-methylimidazolium chloride (C4 mim) is found to be the most effective in lowering the incident of DNA folding during its translocation through solid-state nanopores (4-5 nm diameter). The rate of folding signals from the translocation of DNA-C4 mim is decreased by half in comparison to that from the control bare DNA. The conformational changes of DNA upon complexation with C4 mim are further examined using atomic force microscopy, showing that the entanglement of DNA which is common in bare DNA is not observed when treated with C4 mim. The stretching effect of C4 mim on DNA strands improves the detection accuracy of nanopore for identifying the location of zinc finger protein bound to its specific binding site in DNA by lowering the incident of DNA folding.
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Affiliation(s)
- Ki-Baek Jeong
- Institute of Life Sciences and Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Ke Luo
- Institute of Life Sciences and Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Min-Cheol Lim
- Food Safety Research Group, Korea Food Research Institute, Sungnam, 13539, South Korea
| | - Jong-Yoon Jung
- Institute of Life Sciences and Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Korea
| | - Young-Rok Kim
- Institute of Life Sciences and Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
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36
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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] [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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37
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Oprzeska-Zingrebe EA, Smiatek J. Aqueous ionic liquids in comparison with standard co-solutes : Differences and common principles in their interaction with protein and DNA structures. Biophys Rev 2018; 10:809-824. [PMID: 29611033 DOI: 10.1007/s12551-018-0414-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/12/2018] [Indexed: 12/29/2022] Open
Abstract
Ionic liquids (ILs) are versatile solvents for a broad range of biotechnological applications. Recent experimental and simulation results highlight the potential benefits of dilute ILs in aqueous solution (aqueous ILs) in order to modify protein and DNA structures systematically. In contrast to a limited number of standard co-solutes like urea, ectoine, trimethylamine-N-oxide (TMAO), or guanidinium chloride, the large amount of possible cation and anion combinations in aqueous ILs can be used to develop tailor-made stabilizers or destabilizers for specific purposes. In this review article, we highlight common principles and differences between aqueous ILs and standard co-solutes with a specific focus on their underlying macromolecular stabilization or destabilization behavior. In combination with statistical thermodynamics theories, we present an efficient framework, which is used to classify structure modification effects consistently. The crucial importance of enthalpic and entropic contributions to the free energy change upon IL-assisted macromolecular unfolding in combination with a complex destabilization mechanism is described in detail. A special focus is also set on aqueous IL-DNA interactions, for which experimental and simulation outcomes are summarized and discussed in the context of previous findings.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569, Stuttgart, Germany. .,Helmholtz Institute Münster: Ionics in Energy Storage (HI MS - IEK 12), Forschungszentrum Jülich GmbH, Corrensstrasse 46, 48149, Münster, Germany.
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38
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Effect of water and ionic liquids on biomolecules. Biophys Rev 2018; 10:795-808. [PMID: 29423700 DOI: 10.1007/s12551-018-0399-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/23/2018] [Indexed: 12/23/2022] Open
Abstract
The remarkable progress in the field of ionic liquids (ILs) in the last two decades has involved investigations on different aspects of ILs in various conditions. The nontoxic and biocompatible nature of ILs makes them a suitable substance for the storage and application of biomolecules. In this regard, the aqueous IL solutions have attracted a large number of studies to comprehend the role of water in modulating various properties of biomolecules. Here, we review some of the recent studies on aqueous ILs that concern the role of water in altering the behavior of ILs in general and in case of biomolecules solvated in ILs. The different structural and dynamic effects caused by water have been highlighted. We discuss the different modes of IL interaction that are responsible for stabilization and destabilization of proteins and enzymes followed by examples of water effect on this. The role of water in the case of nucleic acid storage in ILs, an area which has mostly been underrated, also has been emphasized. Our discussions highlight the fact that the effects of water on IL behavior are not general and are highly dependent on the nature of the IL under consideration. Overall, we aim to draw attention to the significance of water dynamics in the aqueous IL solutions, a better understanding of which can help in developing superior storage materials for application purposes.
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39
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Aqueous ionic liquids influence the disulfide bond isoform equilibrium in conotoxin AuIB: a consequence of the Hofmeister effect? Biophys Rev 2018; 10:769-780. [PMID: 29294259 DOI: 10.1007/s12551-017-0391-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/13/2017] [Indexed: 12/13/2022] Open
Abstract
The appearance of several disulfide bond isoforms in multiple cysteine containing venom peptides poses a significant challenge in their synthesis and purification under laboratory conditions. Recent experiments suggest that careful tuning of solvent and temperature conditions can propel the disulfide bond isoform equilibrium in favor of the most potent, native form. Certain aqueous ionic liquids (ILs) have proven significantly useful as solvents for this purpose, while exceptions have also been noted. To elucidate the molecular level origin behind such a preference, we report a detailed explicit solvent replica exchange molecular dynamics study of a conotoxin, AuIB, in pure water and four different aqueous IL solutions (~45-60% v/v). The ILs studied here are comprised of cations like 1-ethyl-3-methyl-imidazolium (Im21+) or 1-butyl-3-methyl-imidazolium (Im41+) coupled with either acetate (OAc-) or chloride (Cl-) as the counter anion. Our simulations unfold interesting features of the conformational spaces sampled by the peptide and its solvation in pure water and aqueous IL solutions. Detailed investigation into populations of the globular disulfide bond isoform of AuIB in aqueous IL solutions reveal distinct trends which might be related to the Hofmeister effect of the cation and anion of the IL and of specific interactions of the aqueous IL solutions with the peptide. In accordance with experimental observations, the aqueous [Im21][OAc] solution is found to promote the highest globular isoform population in AuIB.
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40
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Oprzeska-Zingrebe EA, Meyer S, Roloff A, Kunte HJ, Smiatek J. Influence of compatible solute ectoine on distinct DNA structures: thermodynamic insights into molecular binding mechanisms and destabilization effects. Phys Chem Chem Phys 2018; 20:25861-25874. [DOI: 10.1039/c8cp03543a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study ectoine-induced destabilization effects on DNA hairpins by a combination of atomistic molecular dynamics simulations, experiments, and theoretical approaches.
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Affiliation(s)
| | - Susann Meyer
- Federal Institute for Materials Research and Testing (BAM)
- D-12205 Berlin
- Germany
- Institute of Biochemistry and Biology
- University of Potsdam
| | - Alexander Roloff
- Federal Institute for Materials Research and Testing (BAM)
- D-12489 Berlin
- Germany
| | - Hans-Jörg Kunte
- Federal Institute for Materials Research and Testing (BAM)
- D-12205 Berlin
- Germany
| | - Jens Smiatek
- Institute for Computational Physics
- University of Stuttgart
- D-70569 Stuttgart
- Germany
- Helmholtz Institute Münster: Ionics in Energy Storage (HI MS IEK-12)
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41
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Bezerra-Neto JR, Sousa NG, dos Santos LPM, Correia AN, de Lima-Neto P. The effect of water on the physicochemical properties of an ethylene glycol and choline chloride mixture containing Cu2+ ions: electrochemical results and dynamic molecular simulation approach. Phys Chem Chem Phys 2018; 20:9321-9327. [DOI: 10.1039/c7cp05911f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular dynamic indicated that the water molecules replace the ethylene glycol molecules that are coordinated with Cu2+ ions.
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Affiliation(s)
- João R. Bezerra-Neto
- Universidade Federal do Ceará
- Centro de Ciências
- Departamento de Química Analítica e Físico-Química
- Campus do Pici
- bloco 940
| | - Natalia G. Sousa
- Universidade Federal do Ceará
- Centro de Ciências
- Departamento de Química Analítica e Físico-Química
- Campus do Pici
- bloco 940
| | - Luis P. M. dos Santos
- Universidade Federal do Ceará
- Centro de Ciências
- Departamento de Química Analítica e Físico-Química
- Campus do Pici
- bloco 940
| | - Adriana N. Correia
- Universidade Federal do Ceará
- Centro de Ciências
- Departamento de Química Analítica e Físico-Química
- Campus do Pici
- bloco 940
| | - Pedro de Lima-Neto
- Universidade Federal do Ceará
- Centro de Ciências
- Departamento de Química Analítica e Físico-Química
- Campus do Pici
- bloco 940
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42
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Narayanan Kirshnamoorthy A, Oldiges K, Winter M, Heuer A, Cekic-Laskovic I, Holm C, Smiatek J. Electrolyte solvents for high voltage lithium ion batteries: ion correlation and specific anion effects in adiponitrile. Phys Chem Chem Phys 2018; 20:25701-25715. [DOI: 10.1039/c8cp04102d] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Combined atomistic molecular dynamics, quantum chemical, and experimental study regarding the properties of two lithium conducting salts in high voltage electrolyte solvent adiponitrile.
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Affiliation(s)
| | - Kristina Oldiges
- Helmholtz Institute Münster (HI MS): Ionics in Energy Storage
- Forschungszentrum Jülich GmbH
- 48149 Münster
- Germany
| | - Martin Winter
- Helmholtz Institute Münster (HI MS): Ionics in Energy Storage
- Forschungszentrum Jülich GmbH
- 48149 Münster
- Germany
- MEET Battery Research Centre
| | - Andreas Heuer
- Institute of Physical Chemistry
- University of Münster
- 48149 Münster
- Germany
| | - Isidora Cekic-Laskovic
- Helmholtz Institute Münster (HI MS): Ionics in Energy Storage
- Forschungszentrum Jülich GmbH
- 48149 Münster
- Germany
| | - Christian Holm
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Jens Smiatek
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
- Helmholtz Institute Münster (HI MS): Ionics in Energy Storage
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43
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Umapathi R, Reddy PM, Rani A, Venkatesu P. Influence of additives on thermoresponsive polymers in aqueous media: a case study of poly(N-isopropylacrylamide). Phys Chem Chem Phys 2018; 20:9717-9744. [DOI: 10.1039/c7cp08172c] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Thermoresponsive polymers (TRPs) in different solvent media have been studied over a long period and are important from both scientific and technical points of view.
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Affiliation(s)
| | - P. Madhusudhana Reddy
- Department of Chemistry
- University of Delhi
- Delhi-110 007
- India
- Department of Chemical Engineering
| | - Anjeeta Rani
- Department of Chemistry
- University of Delhi
- Delhi-110 007
- India
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44
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Martínez L, Shimizu S. Molecular Interpretation of Preferential Interactions in Protein Solvation: A Solvent-Shell Perspective by Means of Minimum-Distance Distribution Functions. J Chem Theory Comput 2017; 13:6358-6372. [DOI: 10.1021/acs.jctc.7b00599] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leandro Martínez
- Institute of Chemistry and Center for Computational Engineering & Science, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Seishi Shimizu
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10
5DD, U.K
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45
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Nicol TWJ, Isobe N, Clark JH, Shimizu S. Statistical thermodynamics unveils the dissolution mechanism of cellobiose. Phys Chem Chem Phys 2017; 19:23106-23112. [DOI: 10.1039/c7cp04647b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Statistical thermodynamic analysis of cellobiose solubility in aqueous salts sheds light on the mechanism of cellulose solubilization on a molecular scale.
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Affiliation(s)
- Thomas W. J. Nicol
- York Structural Biology Laboratory
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
| | - Noriyuki Isobe
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
- Yokosuka
- Japan
| | - James H. Clark
- Green Chemistry Centre of Excellence
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
| | - Seishi Shimizu
- York Structural Biology Laboratory
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
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46
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Kobayashi T, Reid JESJ, Shimizu S, Fyta M, Smiatek J. The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches. Phys Chem Chem Phys 2017; 19:18924-18937. [DOI: 10.1039/c7cp03717a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Atomistic molecular dynamics simulations of aqueous ionic liquid mixtures were performed in order to compare the resulting Kirkwood–Buff integrals with experimental data and the corresponding integrals derived by an inverse Kirkwood–Buff approach.
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Affiliation(s)
- Takeshi Kobayashi
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Joshua E. S. J. Reid
- York Structural Biology Laboratory
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
| | - Seishi Shimizu
- York Structural Biology Laboratory
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
| | - Maria Fyta
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Jens Smiatek
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
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