1
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Pereira AF, Martínez L. Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A. J Chem Inf Model 2024; 64:3350-3359. [PMID: 38566451 DOI: 10.1021/acs.jcim.3c01822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The B domain of protein A (BdpA), a small three-helix bundle, folds on a time scale of a few microseconds with heterogeneous native and unfolded states. It is widely used as a model for understanding protein folding mechanisms. In this work, we use structure-based models (SBMs) and atomistic simulations to comprehensively investigate how BdpA folding is associated with the formation of its secondary structure. The energy landscape visualization method (ELViM) was used to characterize the pathways that connect the folded and unfolded states of BdpA as well as the sets of structures displaying specific ellipticity patterns. We show that the native state conformational diversity is due mainly to the conformational variability of helix I. Helices I, II, and III occur in a weakly correlated manner, with Spearman's rank correlation coefficients of 0.1539 (I and II), 0.1259 (I and III), and 0.2561 (II and III). These results, therefore, suggest the highest cooperativity between helices II and III. Our results allow the clustering of partially folded structures of folding of the B domain of protein A on the basis of its secondary structure, paving the way to an understanding of environmental factors in the relative stability of the basins of the folding ensemble, which are illustrated by the structural dependency of the protein hydration structures, as computed with minimum-distance distribution functions.
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Affiliation(s)
- Ander Francisco Pereira
- Institute of Chemistry and Center for Computing in Engineering & Science, Universidade Estadual de Campinas (UNICAMP), 13083-861 Campinas, SP, Brazil
| | - Leandro Martínez
- Institute of Chemistry and Center for Computing in Engineering & Science, Universidade Estadual de Campinas (UNICAMP), 13083-861 Campinas, SP, Brazil
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2
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Miranda-Quintana RA, Chen L, Craig VSJ, Smiatek J. Quantitative Solvation Energies from Gas-Phase Calculations: First-Principles Charge Transfer and Perturbation Approaches. J Phys Chem B 2023; 127:2546-2551. [PMID: 36917810 DOI: 10.1021/acs.jpcb.2c08907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
We present a first-principles approach for the calculation of solvation energies and enthalpies with respect to different ion pair combinations in various solvents. The method relies on the conceptual density functional theory (DFT) of solvation, from which detailed expressions for the solvation energies can be derived. In addition to fast and straightforward gas phase calculations, we also study the influence of modified chemical reactivity descriptors in terms of electronic perturbations. The corresponding phenomenological changes in molecular energy levels can be interpreted as the influence of continuum solvents. Our approach shows that the introduction of these modified expressions is essential for a quantitative agreement between the calculated and the experimental results.
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Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32603, United States
| | - Lexin Chen
- Department of Chemistry, University of Florida, Gainesville, Florida 32603, United States
| | - Vincent S J Craig
- Department of Applied Mathematics, Research School of Physics and Engineering, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
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3
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Oprzeska-Zingrebe EA, Smiatek J. Basket-type G-quadruplex with two tetrads in the presence of TMAO and urea: A molecular dynamics study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134375] [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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4
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Miranda-Quintana RA, Smiatek J. Application of Fundamental Chemical Principles for Solvation Effects: A Unified Perspective for Interaction Patterns in Solution. J Phys Chem B 2022; 126:8864-8872. [PMID: 36269164 DOI: 10.1021/acs.jpcb.2c06315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We demonstrate the utility of basic chemical principles like the "|Δμ| big is good" (DMB) rule for the study of solvation interactions between distinct solutes such as ions and solvents. The corresponding approach allows us to define relevant criteria for maximum solvation energies of ion pairs in different solvents in terms of electronegativities and chemical hardnesses. Our findings reveal that the DMB principle culminates into the strong and weak acids and bases concept as recently derived for specific ion effects in various solvents. The further application of the DMB approach highlights a similar condition for the chemical hardnesses with a reminiscence to the hard/soft acids and bases principle. Comparable conclusions can also be drawn with regard to the change of the solvent. We show that favorable solvent interactions are mainly driven by low chemical hardnesses as well as high electronegativity differences between the ions and the solvent. Our findings highlight that solvation interactions are governed by basic chemical principles, which demonstrates the close similarity between solvation mechanisms and chemical reactions.
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Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida32611, United States
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, StuttgartD-70569, Germany
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5
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Pereira AF, Piccoli V, Martínez L. Trifluoroethanol direct interactions with protein backbones destabilize α-helices. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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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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Shmool T, Martin LK, Matthews RP, Hallett JP. Ionic Liquid-Based Strategy for Predicting Protein Aggregation Propensity and Thermodynamic Stability. JACS AU 2022; 2:2068-2080. [PMID: 36186557 PMCID: PMC9516703 DOI: 10.1021/jacsau.2c00356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 05/26/2023]
Abstract
Novel drug candidates are continuously being developed to combat the most life-threatening diseases; however, many promising protein therapeutics are dropped from the pipeline. During biological and industrial processes, protein therapeutics are exposed to various stresses such as fluctuations in temperature, solvent pH, and ionic strength. These can lead to enhanced protein aggregation propensity, one of the greatest challenges in drug development. Recently, ionic liquids (ILs), in particular, biocompatible choline chloride ([Cho]Cl)-based ILs, have been used to hinder stress-induced protein conformational changes. Herein, we develop an IL-based strategy to predict protein aggregation propensity and thermodynamic stability. We examine three key variables influencing protein misfolding: pH, ionic strength, and temperature. Using dynamic light scattering, zeta potential, and variable temperature circular dichroism measurements, we systematically evaluate the structural, thermal, and thermodynamic stability of fresh immunoglobin G4 (IgG4) antibody in water and 10, 30, and 50 wt % [Cho]Cl. Additionally, we conduct molecular dynamics simulations to examine IgG4 aggregation propensity in each system and the relative favorability of different [Cho]Cl-IgG4 packing interactions. We re-evaluate each system following 365 days of storage at 4 °C and demonstrate how to predict the thermodynamic properties and protein aggregation propensity over extended storage, even under stress conditions. We find that increasing [Cho]Cl concentration reduced IgG4 aggregation propensity both fresh and following 365 days of storage and demonstrate the potential of using our predictive IL-based strategy and formulations to radically increase protein stability and storage.
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Affiliation(s)
- Talia
A. Shmool
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
| | - Laura K. Martin
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, U.K.
| | - Richard P. Matthews
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
| | - Jason P. Hallett
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
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8
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Schwarz J, Kielgast F, Baev I, Reinwardt S, Trinter F, Klumpp S, Perry-Sassmannshausen A, Buhr T, Schippers S, Müller A, Bari S, Mondes V, Flesch R, Rühl E, Martins M. X-Ray absorption spectroscopy of H 3O . Phys Chem Chem Phys 2022; 24:23119-23127. [PMID: 36056691 DOI: 10.1039/d2cp02383k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the X-ray absorption of isolated H3O+ cations at the O 1s edge. The molecular ions were prepared in a flowing afterglow ion source which was designed for the production of small water clusters, protonated water clusters, and hydrated ions. Isolated H2O+ cations have been analyzed for comparison. The spectra show significant differences in resonance energies and widths compared to neutral H2O with resonances shifting to higher energies by as much as 10 eV and resonance widths increasing by as much as a factor of 5. The experimental results are supported by time-dependent density functional theory calculations performed for both molecular cations, showing a good agreement with the experimental data. The spectra reported here could enable the identification of the individual molecules in charged small water clusters or liquid water using X-ray absorption spectroscopy.
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Affiliation(s)
- Julius Schwarz
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, Hamburg, Germany.
| | - Fridtjof Kielgast
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, Hamburg, Germany.
| | - Ivan Baev
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, Hamburg, Germany.
| | - Simon Reinwardt
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, Hamburg, Germany.
| | - Florian Trinter
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, Germany.,Molecular Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Stephan Klumpp
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, Germany
| | | | - Ticia Buhr
- I. Physikalisches Institut, Justus-Liebig-Universität Gießen, Leihgesterner Weg 217, 35292 Gießen, Germany
| | - Stefan Schippers
- I. Physikalisches Institut, Justus-Liebig-Universität Gießen, Leihgesterner Weg 217, 35292 Gießen, Germany
| | - Alfred Müller
- I. Physikalisches Institut, Justus-Liebig-Universität Gießen, Leihgesterner Weg 217, 35292 Gießen, Germany
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, Germany.,Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Valerie Mondes
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Roman Flesch
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Eckart Rühl
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Michael Martins
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, Hamburg, Germany.
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9
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Fadaei F, Tortora M, Gessini A, Masciovecchio C, Catalini S, Vigna J, Mancini I, Mele A, Vacek J, Reha D, Minofar B, Rossi B. Structural specificity of groove binding mechanism between imidazolium-based ionic liquids and DNA revealed by synchrotron-UV Resonance Raman spectroscopy and molecular dynamics simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Sevilla M, Cortes-Huerto R. Connecting density fluctuations and Kirkwood–Buff integrals for finite-size systems. J Chem Phys 2022; 156:044502. [DOI: 10.1063/5.0076744] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Mauricio Sevilla
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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11
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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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12
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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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13
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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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14
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Rossi B, Tortora M, Catalini S, Vigna J, Mancini I, Gessini A, Masciovecchio C, Mele A. Insight into the thermal stability of DNA in hydrated ionic liquids from multi-wavelength UV resonance Raman experiments. Phys Chem Chem Phys 2021; 23:15980-15988. [PMID: 34313275 DOI: 10.1039/d1cp01970h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The utility of ionic liquids (ILs) as alternative solvents for stabilizing and preserving the native structure of DNA over the long term may be envisaged for biotechnological and biomedical applications in the near future. The delicate balance between the stabilizing and destabilizing effects of IL-mediated interactions with the structure of DNA is complex and is still not well understood. This work reports a fundamental study dealing with the effect exerted by cations and anions in imidazolium-based ILs on the thermal structural stability of large nucleic acid molecules. Multi-wavelength UV resonance Raman spectroscopy is used for selectively detecting heat-induced structural transitions of DNA localized on specific base tracts. Our study reveals the establishment of preferential interactions between the imidazolium cations of ILs and the guanine bases in the DNA groove that lead to more effective stacking between the guanine bases even at high temperatures. Interestingly, we observe that this trend for ILs sharing the same chloride anion is further enhanced as the alkyl chain on the imidazolium cation gets shorter. The results from the present investigation lead to a more comprehensive view of the IL-mediated interactions with A-T and G-C base pairs during thermal unfolding.
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Affiliation(s)
- Barbara Rossi
- Elettra-Sincrotrone Trieste, S. S. 114 km 163.5, Basovizza, 34149, Trieste, Italy.
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15
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Beneficial properties of solvents and ions for lithium ion and post-lithium ion batteries: Implications from charge transfer models. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138418] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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16
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Yusof R, Jumbri K, Ahmad H, Abdulmalek E, Abdul Rahman MB. Binding of tetrabutylammonium bromide based deep eutectic solvent to DNA by spectroscopic analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 253:119543. [PMID: 33636491 DOI: 10.1016/j.saa.2021.119543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/24/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
The binding characteristics of DNA in deep eutectic solvents (DESs), particularly the binding energy and interaction mechanism, are not widely known. In this study, the binding of tetrabutylammonium bromide (TBABr) based DES of different hydrogen bond donors (HBD), including ethylene glycol (EG), glycerol (Gly), 1,3-propanediol (1,3-PD) and 1,5-pentanediol (1,5-PD), to calf thymus DNA was investigated using fluorescence spectroscopy. It was found that the shorter the alkyl chain length (2 carbons) and higher EG ratios of TBABr:EG (1:5) increased the binding constant (Kb) between DES and DNA up to 5.75 × 105 kJ mol-1 and decreased the binding of Gibbs energy (ΔGo) to 32.86 kJ mol-1. Through displacement studies, all synthesised DESs have been shown to displace DAPI (4',6-diamidino-2-phenylindole) and were able to bind on the minor groove of Adenine-Thymine (AT)-rich DNA. A higher number of hydroxyl (OH) groups caused the TBABr:Gly to form more hydrogen bonds with DNA bases and had the highest ability to quench DAPI from DNA, with Stern-Volmer constants (Ksv) of 115.16 M-1. This study demonstrated that the synthesised DESs were strongly bound to DNA through a combination of electrostatic, hydrophobic, and groove binding. Hence, DES has the potential to solvate and stabilise nucleic acid structures.
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Affiliation(s)
- Rizana Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Chemistry, Faculty of Applied Sciences, Universiti Teknologi MARA, Perlis Branch, Arau Campus, 02600 Arau, Perlis, Malaysia
| | - Khairulazhar Jumbri
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Centre of Research in Ionic Liquids, Universiti Teknologi PETRONAS, 32610 Bandar Seri Iskandar, Perak, Malaysia
| | - Haslina Ahmad
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Integrated Chemical BioPhysics Research Centre, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Emilia Abdulmalek
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Integrated Chemical BioPhysics Research Centre, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Basyaruddin Abdul Rahman
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Integrated Chemical BioPhysics Research Centre, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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17
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Kobayashi T, Smiatek J, Fyta M. Energetic Arguments on the Microstructural Analysis in Ionic Liquids. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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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18
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Rasteniene A, Gruskiene R, Sereikaite J. Interaction of ectoine and hydroxyectoine with protein: fluorescence study. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01527-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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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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20
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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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21
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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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22
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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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23
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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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24
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Theoretical and experimental studies of ionic liquid-urea mixtures on chitosan dissolution: Effect of cationic structure. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113918] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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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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26
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Solomun T, Hahn MB, Smiatek J. Raman Spectroscopic Signature of Ectoine Conformations in Bulk Solution and Crystalline State. Chemphyschem 2020; 21:1945-1950. [PMID: 32628316 PMCID: PMC7540454 DOI: 10.1002/cphc.202000457] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/06/2020] [Indexed: 01/29/2023]
Abstract
Recent crystallographic results revealed conformational changes of zwitterionic ectoine upon hydration. By means of confocal Raman spectroscopy and density functional theory calculations, we present a detailed study of this transformation process as part of a Fermi resonance analysis. The corresponding findings highlight that all resonant couplings are lifted upon exposure to water vapor as a consequence of molecular binding processes. The importance of the involved molecular groups for water binding and conformational changes upon hydration is discussed. Our approach further shows that the underlying rapid process can be reversed by carbon dioxide saturated atmospheres. For the first time, we also confirm that the conformational state of ectoine in aqueous bulk solution coincides with crystalline ectoine in its dihydrate state, thereby highlighting the important role of a few bound water molecules.
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Affiliation(s)
- Tihomir Solomun
- Bundesanstalt für Materialforschung und -prüfung (BAM)12205BerlinGermany
| | - Marc Benjamin Hahn
- Bundesanstalt für Materialforschung und -prüfung (BAM)12205BerlinGermany
- Freie Universität BerlinInstitut für Experimentalphysik14195BerlinGermany
| | - Jens Smiatek
- Institut für ComputerphysikUniversität Stuttgart70569StuttgartGermany
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27
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Dasari S, Mallik BS. Conformational Free-Energy Landscapes of Alanine Dipeptide in Hydrated Ionic Liquids from Enhanced Sampling Methods. J Phys Chem B 2020; 124:6728-6737. [PMID: 32666802 DOI: 10.1021/acs.jpcb.0c05629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Understanding the interaction of the ionic liquid (IL) with protein is vital to find the origin of the conformational changes of proteins in these alternative solvents. Here, we performed biased molecular dynamics simulations of alanine dipeptide (ADP), a widely used model for protein backbone structure, in water and two hydrated ionic liquids (ILs): 80% (w/w) 1-ethyl-3-methylimidazolium acetate ([EMIm][Ac]) and 80% (w/w) choline dihydrogen phosphate ([Cho][DHP]). We employed three different biasing methods, metadynamics (metaD), well-tempered metadynamics (WT-metaD), and adaptive biasing force (ABF), to construct the free-energy landscapes of the ADP conformations using the backbone dihedral angles (ϕ and ψ) as the collective variables. The calculations were also performed in water; the free-energy landscapes of ADP in water obtained from three methods are similar and agree well with the previously reported results. In hydrated [EMIm][Ac], α-planar conformation emerges as a minimum, which is comparable to that of α and β conformations corresponding to α-helix and β-sheet-like conformations of proteins. Investigation of corresponding conformations suggests that the imidazolium ring of [EMIm] cation is stacked with the amide bonds of ADP. Acetate anion makes hydrogen bonds with the amide hydrogens of the ADP. The amide-π stacking interaction is the driving force for α-planar conformation to become one of the minimum energy conformations in this IL, which destabilizes the protein conformation. However, α and β conformations are more stable in hydrated [Cho][DHP] compared to α-planar and β-planar conformations; therefore, this IL stabilizes the protein conformation. These findings are in good correlation with the previous study of proteins in these ILs. Our study helps to understand the interaction of proteins with the ionic entities and their stability in ILs.
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Affiliation(s)
- Sathish Dasari
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, Telangana, India
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28
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PDADMAC/PSS Oligoelectrolyte Multilayers: Internal Structure and Hydration Properties at Early Growth Stages from Atomistic Simulations. Molecules 2020; 25:molecules25081848. [PMID: 32316422 PMCID: PMC7222011 DOI: 10.3390/molecules25081848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022] Open
Abstract
We analyze the internal structure and hydration properties of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) oligoelectrolyte multilayers at early stages of their layer-by-layer growth process. Our study is based on large-scale molecular dynamics simulations with atomistic resolution that we presented recently [Sánchez et al., Soft Matter2019, 15, 9437], in which we produced the first four deposition cycles of a multilayer obtained by alternate exposure of a flat silica substrate to aqueous electrolyte solutions of such polymers at 0.1M of NaCl. In contrast to any previous work, here we perform a local structural analysis that allows us to determine the dependence of the multilayer properties on the distance to the substrate. We prove that the large accumulation of water and ions next to the substrate observed in previous overall measurements actually decreases the degree of intrinsic charge compensation, but this remains as the main mechanism within the interface region. We show that the range of influence of the substrate reaches approximately 3 nm, whereas the structure of the outer region is rather independent from the position. This detailed characterization is essential for the development of accurate mesoscale models able to reach length and time scales of technological interest.
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29
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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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30
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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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31
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Tuning Water Networks via Ionic Liquid/Water Mixtures. Int J Mol Sci 2020; 21:ijms21020403. [PMID: 31936347 PMCID: PMC7013630 DOI: 10.3390/ijms21020403] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/19/2019] [Accepted: 01/03/2020] [Indexed: 11/17/2022] Open
Abstract
Water in nanoconfinement is ubiquitous in biological systems and membrane materials, with altered properties that significantly influence the surrounding system. In this work, we show how ionic liquid (IL)/water mixtures can be tuned to create water environments that resemble nanoconfined systems. We utilize molecular dynamics simulations employing ab initio force fields to extensively characterize the water structure within five different IL/water mixtures: [BMIM+][BF4−], [BMIM+][PF6−], [BMIM+][OTf−], [BMIM+][NO3−] and [BMIM+][TFSI−] ILs at varying water fraction. We characterize water clustering, hydrogen bonding, water orientation, pairwise correlation functions and percolation networks as a function of water content and IL type. The nature of the water nanostructure is significantly tuned by changing the hydrophobicity of the IL and sensitively depends on water content. In hydrophobic ILs such as [BMIM+][PF6−], significant water clustering leads to dynamic formation of water pockets that can appear similar to those formed within reverse micelles. Furthermore, rotational relaxation times of water molecules in supersaturated hydrophobic IL/water mixtures indicate the close-connection with nanoconfined systems, as they are quantitatively similar to water relaxation in previously characterized lyotropic liquid crystals. We expect that this physical insight will lead to better design principles for incorporation of ILs into membrane materials to tune water nanostructure.
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32
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de Oliveira IP, Martínez L. The shift in urea orientation at protein surfaces at low pH is compatible with a direct mechanism of protein denaturation. Phys Chem Chem Phys 2020; 22:354-367. [DOI: 10.1039/c9cp05196a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protonation of acidic side-chains promotes a orientational shift of urea molecules, but only locally, with the interactions with other protein moieties being preserved.
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Affiliation(s)
- Ivan Pires de Oliveira
- Institute of Chemistry and Center for Computing in Engineering & Science
- University of Campinas
- Campinas
- Brazil
- Department of Pharmacology
| | - Leandro Martínez
- Institute of Chemistry and Center for Computing in Engineering & Science
- University of Campinas
- Campinas
- Brazil
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33
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Oprzeska-Zingrebe EA, Smiatek J. Some Notes on the Thermodynamic Accuracy of Coarse-Grained Models. Front Mol Biosci 2019; 6:87. [PMID: 31552269 PMCID: PMC6746972 DOI: 10.3389/fmolb.2019.00087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/27/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ewa Anna Oprzeska-Zingrebe
- Institute for Computational Physics, Theoretical Chemical Physics, University of Stuttgart, Stuttgart, Germany
| | - Jens Smiatek
- Institute for Computational Physics, Theoretical Chemical Physics, University of Stuttgart, Stuttgart, Germany
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34
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Oprzeska-Zingrebe EA, Smiatek J. Aqueous Mixtures of Urea and Trimethylamine-N-oxide: Evidence for Kosmotropic or Chaotropic Behavior? J Phys Chem B 2019; 123:4415-4424. [PMID: 31046272 DOI: 10.1021/acs.jpcb.9b02598] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Trimethylamine-N-oxide (TMAO) and urea are commonly produced in many extremophilic microorganisms that live in harsh environments. In view of high temperature, high pressure, or high salt content, TMAO is known as a protein structure stabilizer, whereas urea destabilizes protein structures even under ambient conditions. Despite clear evidence, destabilizers are often regarded as chaotropes, meaning water-structure breakers, whereas kosmotropes as water-structure makers are classified as stabilizers. Using atomistic molecular dynamics simulations, we study aqueous mixtures of TMAO and urea in various biologically relevant concentrations to gain insight into the molecular details of their mutual cross-interactions and their influence on water dynamics and structure. Our results for binary and ternary solutions in combination with different mixing ratios show that both co-solutes strengthen the water network in terms of dynamic and structural aspects. Slight differences in the water binding behavior between both species result in only negligible compensation effects. The outcomes of our simulations thus question the validity and the ill-considered use of attributes like kosmotropic or chaotropic substances for stabilizers and destabilizers.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics , University of Stuttgart , D-70569 Stuttgart , Germany.,Helmholtz-Institute Münster: Ionics in Energy Storage (HIMS-IEK 12) , Forschungszentrum Jülich GmbH , D-48149 Münster , Germany
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35
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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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36
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Carter EE, Heyert AJ, De Souza M, Baker JL, Lindberg GE. The ionic liquid [C4mpy][Tf2N] induces bound-like structure in the intrinsically disordered protein FlgM. Phys Chem Chem Phys 2019; 21:17950-17958. [DOI: 10.1039/c9cp01882d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide is shown to induce secondary structure similar to a bioactive state in the protein FlgM.
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Affiliation(s)
- Erin E. Carter
- Department of Chemistry and Biochemistry
- Northern Arizona University
- Flagstaff
- USA
| | | | | | | | - Gerrick E. Lindberg
- Department of Chemistry and Biochemistry
- Northern Arizona University
- Flagstaff
- USA
- Center for Materials Interfaces in Research and Applications
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37
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Michalowsky J, Zeman J, Holm C, Smiatek J. A polarizable MARTINI model for monovalent ions in aqueous solution. J Chem Phys 2018; 149:163319. [PMID: 30384758 DOI: 10.1063/1.5028354] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a new polarizable coarse-grained martini force field for monovalent ions, called refIon, which is developed mainly for the accurate reproduction of electrostatic properties in aqueous electrolyte solutions. The ion model relies on full long-range Coulomb interactions and introduces satellite charges around the central interaction site in order to model molecular polarization effects. All force field parameters are matched to reproduce the mass density and the static dielectric permittivity of aqueous NaCl solutions, such that experimental values are well-reproduced up to moderate salt concentrations of 2 m o l / l . In addition, an improved agreement with experimentally measured ionic conductivities is observed. Our model is validated with regard to analytic solutions for the ion distribution around highly charged rod-like polyelectrolytes in combination with atomistic simulations and experimental results concerning structural properties of lipid bilayers in the presence of distinct salt concentrations. Further results regarding the coordination numbers of counterions around dilute poly(styrene sulfonate) and poly(diallyldimethylammonium) polyelectrolyte chains also highlight the applicability of our approach. The introduction of our force field allows us to eliminate heuristic scaling factors, as reported for previous martini ion models in terms of effective salt concentrations, and in consequence provides a better agreement between simulation and experimental results. The presented approach is specifically useful for recent martini attempts that focus on highly charged systems-such as models of DNA, polyelectrolytes or polyelectrolyte complexes-where precise studies of electrostatic effects and charge transport processes are essential.
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Affiliation(s)
- Julian Michalowsky
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Johannes Zeman
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Christian Holm
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Jens Smiatek
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
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38
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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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39
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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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40
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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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