151
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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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152
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153
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Yılmaz Topuzlu E, Okur HI, Ulgut B, Dag Ö. Role of Water in the Lyotropic Liquid Crystalline Mesophase of Lithium Salts and Non-ionic Surfactants. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:14443-14453. [PMID: 34856801 DOI: 10.1021/acs.langmuir.1c02411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The lyotropic liquid crystalline (LLC) mesophase forms upon evaporation of water from aqueous solutions of LiX salts (X is Cl-, Br-, NO3-, or SCN-) and a surfactant [C12H25(OCH2CH2)10OH, abbreviated as C12E10]. The LiX/C12E10/H2O aqueous solutions have been monitored (during evaporation of their excess water to obtain stable LLC mesophases) by gravimetric, spectroscopic, and conductivity measurements to elucidate the role of water in these mesophases. The water/salt molar ratio in stable mesophases changes from 1.5 to 8.0, depending on the counteranion of the salt and the ambient humidity of the laboratory. The LiX/C12E10/H2O LLC mesophases lose water at lower humidity levels and absorb water at higher humidity levels. The LiCl-containing mesophase holds as few as four structural water molecules per LiCl, whereas the LiNO3 mesophase holds 1.5 waters per salt (least among those assessed). This ratio strongly depends on the atmospheric humidity level; the water/LiX mole ratio increases by 0.08 ± 0.01 H2O in the LLC mesophases per percent humidity unit. Surprisingly, the LLC mesophases are stable (no salt leaching) in broad humidity (10-85%) and salt/surfactant mole ratio (2-10 LiX/C12E10) ranges. Attenuated total reflectance Fourier transform infrared spectroscopic data show that the water molecules in the mesophase interact with salt species more strongly in the LiCl mesophase and more weakly in the case of the nitrate ion, which is evident by the shift of the O-H stretching band of water. The O-H stretching peak position in the mesophases decreases in the order νLiCl > νLiBr > νLiSCN > νLiNO3 and accords well with the H2O/LiX mole ratio. The conductivity of the LLC mesophase also responds to the amount of water as well as the nature of the counteranion (X-). The conductivity decreases in the order σLiCl > σLiBr > σLiNO3 > σLiSCN at low salt mole ratios and in the order σLiBr > σLiCl > σLiNO3 > σLiSCN at higher ratios due to structural changes in the mesophase.
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Affiliation(s)
| | - Halil I Okur
- Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
- UNAM-National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Burak Ulgut
- Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
- UNAM-National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Ömer Dag
- Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
- UNAM-National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
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154
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Abstract
Photochemical reactions are increasingly being used for chemical and materials synthesis, for example, in photoredox catalysis, and generally involve photoexcitation of molecular chromophores dissolved in a liquid solvent. The choice of solvent influences the outcomes of the photochemistry because solute-solvent interactions modify the energies of and crossings between electronic states of the chromophores, and they affect the evolving structures of the photoexcited molecules. Ultrafast laser spectroscopy methods with femtosecond to picosecond time resolution can resolve the dynamics of these photoexcited molecules as they undergo structural and electronic changes, relax back to the ground state, dissipate their excess internal energy to the surrounding solvent, or undergo photochemical reactions. In this Account, we illustrate how experimental studies using ultrafast lasers can reveal the influences that different solvents or cosolutes exert on the photoinduced nonadiabatic dynamics of internal conversion and intersystem crossing in nonradiative relaxation pathways. Although the environment surrounding a solute molecule is rapidly changing, with fluctuations in the coordination to neighboring solvent molecules occurring on femtosecond or picosecond time scales, we show that it is possible to photoexcite selectively only those molecular chromophores transiently experiencing specific solute-solvent interactions such as intermolecular hydrogen bonding.The effects of different solvation environments on the photodynamics are illustrated using four selected examples of photochemical processes in which the solvent has a marked effect on the outcomes. We first consider two aromatic carbonyl compounds, benzophenone and acetophenone, which are known to undergo fast intersystem crossing to populate the first excited triplet state on time scales of a few picoseconds. We show that the nonadiabatic excited-state dynamics are modified by transient hydrogen bonding of the carbonyl group to a protic solvent or by coordination to a metal cation cosolute. We then examine how different solvents modify the competition between two alternative relaxation pathways in a photoexcited UVA-sunscreen molecule, diethylamino hydroxybenzoyl hexyl benzoate (DHHB). This relaxation back to the ground electronic state is an essential part of the effective operation of the sunscreen compound, but the dynamics are sensitive to the surrounding environment. Finally, we consider how solvents of different polarity affect the energies and lifetimes of excited states with locally excited or charge-transfer character in heterocyclic organic compounds used as excited-state electron donors for photoredox catalysis. With these and other examples, we seek to develop a molecular level understanding of how the choice of solution environment might be used to control the outcomes of photochemical reactions.
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Affiliation(s)
- Ravi Kumar Venkatraman
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Andrew J. Orr-Ewing
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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155
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Carré L, Girard É, Franzetti B. Experimental study of proteome halophilicity using nanoDSF: a proof of concept. Extremophiles 2021; 26:1. [PMID: 34878593 DOI: 10.1007/s00792-021-01250-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/30/2021] [Indexed: 10/19/2022]
Abstract
Adaption to environmental conditions is reflected by protein adaptation. In particular, proteins of extremophiles display distinctive traits ensuring functional, structural and dynamical properties under permanently extreme physical and chemical conditions. While it has mostly been studied with approaches focusing on specific proteins, biophysical approaches have also confirmed this link between environmental and protein adaptation at the more complex and diverse scale of the proteome. However, studies of this type remain challenging and often require large amounts of biological material. We report here the use of nanoDSF as a tool to study proteome stability and solubility in cell lysates of the model halophilic archaeon Haloarcula marismortui. Notably, our results show that, as with single halophilic protein studies, proteome stability was correlated to the concentration of NaCl or KCl under which the cells were lysed and hence the proteome exposed. This work highlights that adaptation to environmental conditions can be experimentally observed at the scale of the proteome. Still, we show that the biochemical properties of single halophilic proteins can only be partially extrapolated to the whole proteome.
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Affiliation(s)
- Lorenzo Carré
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Éric Girard
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
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156
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Brunori F, Padhi DK, Alshanski I, Freyse J, Dürig JN, Penk A, Vaccaro L, Hurevich M, Rademann J, Yitzchaik S. Sulfation Pattern Dependent Iron(III) Mediated Interleukin-8 Glycan Binding. Chembiochem 2021; 23:e202100552. [PMID: 34851004 DOI: 10.1002/cbic.202100552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/01/2021] [Indexed: 12/30/2022]
Abstract
Cytokines such as interleukin-8 activate the immune system during infection and interact with sulfated glycosaminoglycans with specific sulfation patterns. In some cases, these interactions are mediated by metal ion binding which can be used to tune surface-based glycan-protein interactions. We evaluated the effect of both hyaluronan sulfation degree and Fe3+ on interleukin-8 binding by electrochemical impedance spectroscopy and surface characterizations. Our results show that sulfation degree and metal ion interactions have a synergistic effect in tuning the electrochemical response of the glycated surfaces to the cytokine.
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Affiliation(s)
- Francesco Brunori
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel.,Laboratory of Green Synthetic Organic Chemistry, Dipartimento di Chimica, Biologiae Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Deepak Kumar Padhi
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Israel Alshanski
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Joanna Freyse
- Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, Berlin, 14195, Germany
| | - Jan-Niklas Dürig
- Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, Berlin, 14195, Germany
| | - Anja Penk
- Institute of Medical Physics and Biophysics, Leipzig University, Medical Faculty, Härtelstraße 16/18, 04107, Leipzig, Germany
| | - Luigi Vaccaro
- Laboratory of Green Synthetic Organic Chemistry, Dipartimento di Chimica, Biologiae Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Mattan Hurevich
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Jörg Rademann
- Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, Berlin, 14195, Germany
| | - Shlomo Yitzchaik
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
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157
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Carlsen A, Tabard-Cossa V. Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation. Proteomics 2021; 22:e2100068. [PMID: 34845853 DOI: 10.1002/pmic.202100068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/28/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]
Abstract
Solid-state nanopores have been used extensively in biomolecular studies involving DNA and proteins. However, the interpretation of signals generated by the translocation of proteins or protein-DNA complexes remains challenging. Here, we investigate the behavior of monovalent streptavidin and the complex it forms with short biotinylated DNA over a range of nanopore sizes, salts, and voltages. We describe a simple geometric model that is broadly applicable and employ it to explain observed variations in conductance blockage and dwell time with experimental conditions. The general approach developed here underscores the value of nanopore-based protein analysis and represents progress toward the interpretation of complex translocation signals.
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Affiliation(s)
- Autumn Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
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158
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Laurent H, Baker DL, Soper AK, Ries ME, Dougan L. Bridging Structure, Dynamics, and Thermodynamics: An Example Study on Aqueous Potassium Halides. J Phys Chem B 2021; 125:12774-12786. [PMID: 34757756 DOI: 10.1021/acs.jpcb.1c06728] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aqueous salt systems are ubiquitous in all areas of life. The ions in these solutions impose important structural and dynamic perturbations to water. In this study, we employ a combined neutron scattering, nuclear magnetic resonance, and computational modeling approach to deconstruct ion-specific perturbations to water structure and dynamics and shed light on the molecular origins of bulk thermodynamic properties of the solutions. Our approach uses the atomistic scale resolution offered to us by neutron scattering and computational modeling to investigate how the properties of particular short-ranged microenvironments within aqueous systems can be related to bulk properties of the system. We find that by considering only the water molecules in the first hydration shell of the ions that the enthalpy of hydration can be determined. We also quantify the range over which ions perturb water structure by calculating the average enthalpic interaction between a central halide anion and the surrounding water molecules as a function of distance and find that the favorable anion-water enthalpic interactions only extend to ∼4 Å. We further validate this by showing that ions induce structure in their solvating water molecules by examining the distribution of dipole angles in the first hydration shell of the ions but that this perturbation does not extend into the bulk water. We then use these structural findings to justify mathematical models that allow us to examine perturbations to rotational and diffusive dynamics in the first hydration shell around the potassium halide ions from NMR measurements. This shows that as one moves down the halide series from fluorine to iodine, and ionic charge density is therefore reduced, that the enthalpy of hydration becomes less negative. The first hydration shell also becomes less well structured, and rotational and diffusive motions of the hydrating water molecules are increased. This reduction in structure and increase in dynamics are likely the origin of the previously observed increased entropy of hydration as one moves down the halide series. These results also suggest that simple monovalent potassium halide ions induce mostly local perturbations to water structure and dynamics.
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Affiliation(s)
- Harrison Laurent
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Daniel L Baker
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Alan K Soper
- ISIS Facility, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, U.K
| | - Michael E Ries
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Lorna Dougan
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K.,Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
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159
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Gregory KP, Wanless EJ, Webber GB, Craig VSJ, Page AJ. The electrostatic origins of specific ion effects: quantifying the Hofmeister series for anions. Chem Sci 2021; 12:15007-15015. [PMID: 34976339 PMCID: PMC8612401 DOI: 10.1039/d1sc03568a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/15/2021] [Indexed: 12/23/2022] Open
Abstract
Life as we know it is dependent upon water, or more specifically salty water. Without dissolved ions, the interactions between biological molecules are insufficiently complex to support life. This complexity is intimately tied to the variation in properties induced by the presence of different ions. These specific ion effects, widely known as Hofmeister effects, have been known for more than 100 years. They are ubiquitous throughout the chemical, biological and physical sciences. The origin of these effects and their relative strengths is still hotly debated. Here we reconsider the origins of specific ion effects through the lens of Coulomb interactions and establish a foundation for anion effects in aqueous and non-aqueous environments. We show that, for anions, the Hofmeister series can be explained and quantified by consideration of site-specific electrostatic interactions. This can simply be approximated by the radial charge density of the anion, which we have calculated for commonly reported ions. This broadly quantifies previously unpredictable specific ion effects, including those known to influence solution properties, virus activities and reaction rates. Furthermore, in non-aqueous solvents, the relative magnitude of the anion series is dependent on the Lewis acidity of the solvent, as measured by the Gutmann Acceptor Number. Analogous SIEs for cations bear limited correlation with their radial charge density, highlighting a fundamental asymmetry in the origins of specific ion effects for anions and cations, due to competing non-Coulombic phenomena.
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Affiliation(s)
- Kasimir P Gregory
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle Callaghan New South Wales 2308 Australia
| | - Erica J Wanless
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle Callaghan New South Wales 2308 Australia
| | - Grant B Webber
- School of Engineering, The University of Newcastle Callaghan New South Wales 2308 Australia
| | - Vincent S J Craig
- Department of Applied Mathematics, Research School of Physics, Australian National University Canberra ACT 0200 Australia
| | - Alister J Page
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle Callaghan New South Wales 2308 Australia
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160
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Ribeiro SS, Castro TG, Gomes CM, Marcos JC. Hofmeister effects on protein stability are dependent on the nature of the unfolded state. Phys Chem Chem Phys 2021; 23:25210-25225. [PMID: 34730580 DOI: 10.1039/d1cp02477a] [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
The interpretation of a salt's effect on protein stability traditionally discriminates low concentration regimes (<0.3 M), dominated by electrostatic forces, and high concentration regimes, generally described by ion-specific Hofmeister effects. However, increased theoretical and experimental studies have highlighted observations of the Hofmeister phenomena at concentration ranges as low as 0.001 M. Reasonable quantitative predictions of such observations have been successfully achieved throughout the inclusion of ion dispersion forces in classical electrostatic theories. This molecular description is also on the basis of quantitative estimates obtained resorting to surface/bulk solvent partition models developed for ion-specific Hofmeister effects. However, the latter are limited by the availability of reliable structures representative of the unfolded state. Here, we use myoglobin as a model to explore how ion-dependency on the nature of the unfolded state affects protein stability, combining spectroscopic techniques with molecular dynamic simulations. To this end, the thermal and chemical stability of myoglobin was assessed in the presence of three different salts (NaCl, (NH4)2SO4 and Na2SO4), at physiologically relevant concentrations (0-0.3 M). We observed mild destabilization of the native state induced by each ion, attributed to unfavorable neutralization and hydrogen-bonding with the protein side-chains. Both effects, combined with binding of Na+, Cl- and SO42- to the thermally unfolded state, resulted in an overall destabilization of the protein. Contrastingly, ion binding was hindered in the chemically unfolded conformation, due to occupation of the binding sites by urea molecules. Such mechanistic action led to a lower degree of destabilization, promoting surface tension effects that stabilized myoglobin according to the Hofmeister series. Therefore, we demonstrate that Hofmeister effects on protein stability are modulated by the heterogeneous physico-chemical nature of the unfolded state. Altogether, our findings evidence the need to characterize the structure of the unfolded state when attempting to dissect the molecular mechanisms underlying the effects of salts on protein stability.
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Affiliation(s)
- Sara S Ribeiro
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Tarsila G Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências and Departamento de Química e Bioquímica, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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161
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162
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Walden K, Martin ME, LaBee L, Provorse Long M. Hydration and Charge-Transfer Effects of Alkaline Earth Metal Ions Binding to a Carboxylate Anion, Phosphate Anion, and Guanine Nucleobase. J Phys Chem B 2021; 125:12135-12146. [PMID: 34706195 DOI: 10.1021/acs.jpcb.1c05757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To investigate the ability of alkaline earth metal ions to tune ion-mediated DNA adsorption, hydrated Mg2+, Ca2+, Sr2+, and Ba2+ ions bound to a carboxylate anion, phosphate anion, and guanine nucleobase were modeled using density functional theory (DFT) and a combined explicit and continuum solvent model. The large first solvation shell of Ba2+ requires a larger solute cavity defined by a solvent-accessible surface, which is used to model all hydrated ions. Alkaline earth metal ions bind indirectly or directly to each binding site. DFT binding energies decrease with increasing ion size, which is likely due to ion size and hydration structure, rather than quantum effects such as charge transfer. However, charge transfer explains weaker ion binding to guanine compared to phosphate or carboxylate. Overall, carboxylate and phosphate anions are expected to compete equally for hydrated Mg2+, Ca2+, Sr2+, and Ba2+ ions and larger alkaline earth metal ions may induce weaker ion-mediated adsorption. The ion size and hydration structure of alkaline earth metal ions may effectively tune ion-mediated adsorption processes, such as DNA adsorption to functionalized surfaces.
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Affiliation(s)
- Kathryn Walden
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas 72035, United States
| | - Madison E Martin
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas 72035, United States
| | - Lacey LaBee
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas 72035, United States
| | - Makenzie Provorse Long
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas 72035, United States
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163
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Stamboroski S, Boateng K, Lierath J, Kowalik T, Thiel K, Köppen S, Noeske PLM, Brüggemann D. Influence of Divalent Metal Ions on the Precipitation of the Plasma Protein Fibrinogen. Biomacromolecules 2021; 22:4642-4658. [PMID: 34670087 DOI: 10.1021/acs.biomac.1c00930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fibrinogen nanofibers are very attractive biomaterials to mimic the native blood clot architecture. Previously, we reported the self-assembly of fibrinogen nanofibers in the presence of monovalent salts and have now studied how divalent salts influence fibrinogen precipitation. Although the secondary fibrinogen structure was significantly altered with divalent metal ions, morphological analysis revealed exclusively smooth fibrinogen precipitates. In situ monitoring of the surface roughness facilitated predicting the tendency of various salts to form fibrinogen fibers or smooth films. Analysis of the chemical composition revealed that divalent salts were removed from smooth fibrinogen films upon rinsing while monovalent Na+ species were still present in fibrinogen fibers. Therefore, we assume that the decisive factor controlling the morphology of fibrinogen precipitates is direct ion-protein contact, which requires disruption of the ion-surrounding hydration shells. We conclude that in fibrinogen aggregates, this mechanism is effective only for monovalent ions, whereas divalent ions are limited to indirect fibrinogen adsorption.
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Affiliation(s)
- Stephani Stamboroski
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Strasse 12, 28359 Bremen, Germany.,Institute for Biophysics, University of Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Kwasi Boateng
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Strasse 12, 28359 Bremen, Germany.,Institute for Biophysics, University of Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Jana Lierath
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Strasse 12, 28359 Bremen, Germany.,Institute for Biophysics, University of Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Thomas Kowalik
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Strasse 12, 28359 Bremen, Germany
| | - Karsten Thiel
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Strasse 12, 28359 Bremen, Germany
| | - Susan Köppen
- Hybrid Materials Interfaces Group, Faculty of Production Engineering and Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, 28359 Bremen, Germany.,MAPEX Center for Materials and Processes, University of Bremen, 28359 Bremen, Germany
| | - Paul-Ludwig Michael Noeske
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Strasse 12, 28359 Bremen, Germany
| | - Dorothea Brüggemann
- Institute for Biophysics, University of Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany.,MAPEX Center for Materials and Processes, University of Bremen, 28359 Bremen, Germany
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164
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Pasquier C, Pezennec S, Bouchoux A, Cabane B, Lechevalier V, Le Floch-Fouéré C, Paboeuf G, Pasco M, Dollet B, Lee LT, Beaufils S. Protein Transport upon Advection at the Air/Water Interface: When Charge Matters. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12278-12289. [PMID: 34636247 DOI: 10.1021/acs.langmuir.1c01591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of dense protein interfacial layers at a free air-water interface is known to result from both diffusion and advection. Furthermore, protein interactions in concentrated phases are strongly dependent on their overall positive or negative net charge, which is controlled by the solution pH. As a consequence, an interesting question is whether the presence of an advection flow of water toward the interface during protein adsorption produces different kinetics and interfacial structure of the adsorbed layer, depending on the net charge of the involved proteins and, possibly, on the sign of this charge. Here we test a combination of the following parameters using ovalbumin and lysozyme as model proteins: positive or negative net charge and the presence or absence of advection flow. The formation and the organization of the interfacial layers are studied by neutron reflectivity and null-ellipsometry measurements. We show that the combined effect of a positive charge of lysozyme and ovalbumin and the presence of advection flow does induce the formation of interfacial multilayers. Conversely, negatively charged ovalbumin forms monolayers, whether advection flow is present or not. We show that an advection/diffusion model cannot correctly describe the adsorption kinetics of multilayers, even in the hypothesis of a concentration-dependent diffusion coefficient as in colloidal filtration, for instance. Still, it is clear that advection is a necessary condition for making multilayers through a mechanism that remains to be determined, which paves the way for future research.
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Affiliation(s)
- Coralie Pasquier
- INRAE, Institut Agro, STLO, F-35042 Rennes, France
- IPR Institute of Physics, UMR UR1 CNRS 6251, Rennes, 1 University, France
| | | | - Antoine Bouchoux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | | | | | | | - Gilles Paboeuf
- IPR Institute of Physics, UMR UR1 CNRS 6251, Rennes, 1 University, France
- Université Rennes 1, CNRS, ScanMAT - UMS 2001, F-35042 Rennes, France
| | | | - Benjamin Dollet
- Université Grenoble Alpes, CNRS, LIPhy, 38000 Grenoble, France
| | - Lay-Theng Lee
- Laboratoire Léon Brillouin CEA - Saclay, Université Paris-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Sylvie Beaufils
- IPR Institute of Physics, UMR UR1 CNRS 6251, Rennes, 1 University, France
- Université Rennes 1, CNRS, ScanMAT - UMS 2001, F-35042 Rennes, France
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165
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Takács D, Katana B, Szerlauth A, Sebők D, Tomšič M, Szilágyi I. Influence of adsorption of ionic liquid constituents on the stability of layered double hydroxide colloids. SOFT MATTER 2021; 17:9116-9124. [PMID: 34569591 DOI: 10.1039/d1sm01074c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The influence of ionic liquid (IL) anions and cations on the charging and aggregation properties of layered double hydroxide (LDH) nanoparticles was systematically studied. Surface charge characteristics were explored using zeta potential measurements, while aggregation processes were followed in dynamic light scattering experiments in aqueous IL solutions. The results revealed that the aggregation rates of LDHs were sensitive to the composition of ILs leading to IL-dependent critical coagulation concentration (CCC) values being obtained. The origin of the interparticle forces was found to be electrostatic, in line with the classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, as the experimental aggregation kinetics were in good agreement with the predicted data. The ion specific adsorption of IL anions led to different surface charge densities for LDHs, which decreased in the order Cl- > Br- > DCA- > SCN- > NO3- for counterions and BMIM+ > BMPYR+ > BMPY+ > BMPIP+ in the case of coions resulting in weaker electrical double layer repulsion in these sequences. Since van der Waals forces are always present and their strength does not depend significantly on the ionic strength, the CCC values decreased in the above order. The present results shed light on the importance of the interfacial arrangement of the IL constituent ions on the colloidal stability of particle dispersions and provide important information on the design of stable or unstable particle-ionic liquid systems.
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Affiliation(s)
- Dóra Takács
- MTA-SZTE Lendület Biocolloids Research Group, Department of Physical Chemistry and Materials Science, University of Szeged, 1 Rerrich Béla tér, H-6720 Szeged, Hungary.
| | - Bojana Katana
- MTA-SZTE Lendület Biocolloids Research Group, Department of Physical Chemistry and Materials Science, University of Szeged, 1 Rerrich Béla tér, H-6720 Szeged, Hungary.
| | - Adél Szerlauth
- MTA-SZTE Lendület Biocolloids Research Group, Department of Physical Chemistry and Materials Science, University of Szeged, 1 Rerrich Béla tér, H-6720 Szeged, Hungary.
| | - Dániel Sebők
- Department of Applied and Environmental Chemistry, University of Szeged, 1 Rerrich Béla tér, H-6720 Szeged, Hungary
| | - Matija Tomšič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - István Szilágyi
- MTA-SZTE Lendület Biocolloids Research Group, Department of Physical Chemistry and Materials Science, University of Szeged, 1 Rerrich Béla tér, H-6720 Szeged, Hungary.
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166
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Spontaneous assembly of redox-active iron-sulfur clusters at low concentrations of cysteine. Nat Commun 2021; 12:5925. [PMID: 34635654 PMCID: PMC8505563 DOI: 10.1038/s41467-021-26158-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Iron-sulfur (FeS) proteins are ancient and fundamental to life, being involved in electron transfer and CO2 fixation. FeS clusters have structures similar to the unit-cell of FeS minerals such as greigite, found in hydrothermal systems linked with the origin of life. However, the prebiotic pathway from mineral surfaces to biological clusters is unknown. Here we show that FeS clusters form spontaneously through interactions of inorganic Fe2+/Fe3+ and S2- with micromolar concentrations of the amino acid cysteine in water at alkaline pH. Bicarbonate ions stabilize the clusters and even promote cluster formation alone at concentrations >10 mM, probably through salting-out effects. We demonstrate robust, concentration-dependent formation of [4Fe4S], [2Fe2S] and mononuclear iron clusters using UV-Vis spectroscopy, 57Fe-Mössbauer spectroscopy and 1H-NMR. Cyclic voltammetry shows that the clusters are redox-active. Our findings reveal that the structures responsible for biological electron transfer and CO2 reduction could have formed spontaneously from monomers at the origin of life.
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167
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Jin SA, Khan SA, Spontak RJ, Rojas OJ. Anion-Specific Water Interactions with Nanochitin: Donnan and Osmotic Pressure Effects as Revealed by Quartz Microgravimetry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11242-11250. [PMID: 34520662 PMCID: PMC8516332 DOI: 10.1021/acs.langmuir.1c01585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The development of new materials emphasizes greater use of sustainable and eco-friendly resources, including those that take advantage of the unique properties of nanopolysaccharides. Advances in this area, however, necessarily require a thorough understanding of interactions with water. Our contribution to this important topic pertains to the swelling behavior of partially deacetylated nanochitin (NCh), which has been studied here by quartz crystal microgravimetry. Ultrathin films of NCh supported on gold-coated resonators have been equilibrated in aqueous electrolyte solutions (containing NaF, NaCl, NaBr, NaNO3, Na2SO4, Na2SO3, or Na3PO4) at different ionic strengths. As anticipated, NCh displays contrasting swelling/deswelling responses, depending on the ionic affinities and valences of the counterions. The extent of water uptake induced by halide anions, for instance, follows a modified Hofmeister series with F- producing the highest swelling. In marked contrast, Cl- induces film dehydration. We conclude that larger anions promote deswelling such that water losses increase with increasing anion valence. Results such as the ones reported here are critical to ongoing efforts designed to dry chitin nanomaterials and develop bio-based and sustainable materials, including particles, films, coatings, and other nanostructured assemblies, for various devices and applications.
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Affiliation(s)
- Soo-Ah Jin
- Department
of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Saad A. Khan
- Department
of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Richard J. Spontak
- Department
of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department
of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Orlando J. Rojas
- Department
of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Bioproducts
Institute, Departments of Chemical & Biological Engineering, Chemistry and Wood Science University of British Columbia, Vancouver V6T 1Z3, Canada
- Department
of Bioproducts and Biosystems, Aalto University, Espoo 02150, Finland
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168
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Guo Y, Nishida N, Hoshino T. Quantifying the Separation of Positive and Negative Areas in Electrostatic Potential for Predicting Feasibility of Ammonium Sulfate for Protein Crystallization. J Chem Inf Model 2021; 61:4571-4581. [PMID: 34565151 DOI: 10.1021/acs.jcim.1c00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ammonium sulfate (AS) and poly(ethylene glycol) (PEG) are the most popular precipitants in protein crystallization. Some proteins are preferably crystallized by AS, while some are by PEG. The electrostatic potential is related to the preference of the precipitant agents. The iso-surfaces of the electrostatic potentials for the AS-crystallized proteins display a common shape and a distinct separation between the positive and negative areas. In contrast, the PEG-crystallized proteins show unclear positive and negative separation. In this work, we propose schemes to quantitatively evaluate the separation for predicting which precipitant is favorable for crystal growth between AS or PEG. Three methods were attempted to quantify the amplitude of the separation, separation distance, dipole moment, and shape regularity. The positive and negative areas are approximated to the spherical potentials caused by point charges. The first method is a measurement of the distance between the positive and negative point charges. The second one is an assessment including the quantity of electric charge into the distance. The last one is an approach monitoring the clarity of the positive and negative separation. The average value for 25 kinds of AS-preferring proteins was higher than that for the PEG-preferring ones in all three methods. Therefore, every method can distinguish the proteins preferring AS for crystal growth from those preferring PEG. These methods require an iso-surface of the electrostatic potential depicted at a certain contouring value. The shape of the iso-surface depends on the contouring value. The dependency on contour was examined by depicting the iso-surfaces of electrostatic potential with three values at ±0.8, ±0.5, and ±0.2 kT/e. While reducing the contouring value leads to the increase in separation distance and the decrease in shape regularity, dipole moment is independent of the alteration of contouring value. While the AS-preferring proteins are distinguishable from the PEG-preferring ones in any contouring values, the iso-surface at ±0.5 kT/e seems adequate for regular use. The dipole moment assessment is feasible for the choice of potent precipitants for crystal growth in experiments.
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Affiliation(s)
- Yan Guo
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
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169
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Gentile K, Bhide A, Kauffman J, Ghosh S, Maiti S, Adair J, Lee TH, Sen A. Enzyme aggregation and fragmentation induced by catalysis relevant species. Phys Chem Chem Phys 2021; 23:20709-20717. [PMID: 34516596 DOI: 10.1039/d1cp02966e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
It is usually assumed that enzymes retain their native structure during catalysis. However, the aggregation and fragmentation of proteins can be difficult to detect and sometimes conclusions are drawn based on the assumption that the protein is in its native form. We have examined three model enzymes, alkaline phosphatase (AkP), hexokinase (HK) and glucose oxidase (GOx). We find that these enzymes aggregate or fragment after addition of chemical species directly related to their catalysis. We used several independent techniques to study this behavior. Specifically, we found that glucose oxidase and hexokinase fragment in the presence of D-glucose but not L-glucose, while hexokinase aggregates in the presence of Mg2+ ion and either ATP or ADP at low pH. Alkaline phosphatase aggregates in the presence of Zn2+ ion and inorganic phosphate. The aggregation of hexokinase and alkaline phosphatase does not appear to attenuate their catalytic activity. Our study indicates that specific multimeric structures of native enzymes may not be retained during catalysis and suggests pathways for different enzymes to associate or separate over the course of substrate turnover.
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Affiliation(s)
- Kayla Gentile
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Ashlesha Bhide
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Joshua Kauffman
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Subhadip Ghosh
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Subhabrata Maiti
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - James Adair
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Ayusman Sen
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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170
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Fries MR, Skoda MWA, Conzelmann NF, Jacobs RMJ, Maier R, Scheffczyk N, Zhang F, Schreiber F. Bulk phase behaviour vs interface adsorption: Effects of anions and isotopes on β-lactoglobulin (BLG) interactions. J Colloid Interface Sci 2021; 598:430-443. [PMID: 33930747 DOI: 10.1016/j.jcis.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 01/17/2023]
Abstract
HYPOTHESIS Protein adsorption is highly relevant in numerous applications ranging from food processing to medical implants. In this context, it is important to gain a deeper understanding of protein-protein and protein-surface interactions. Thus, the focus of this investigation is on the interplay of bulk properties and surface properties on protein adsorption. It was hypothesised that the type of solvent and ions in solution should significantly influence the protein's bulk and interface behaviour, which has been observed in literature and previous work for other net negatively charged, globular proteins such as bovine serum albumin (BSA). EXPERIMENTS The phase behaviour of β-lactoglobulin (BLG) with lanthanum chloride (LaCl3) and iodide (LaI3) in normal water H2O(l) and heavy water (D2O(l)) was established via optical microscopy and ultraviolet-visible spectroscopy. The formation of an adsorption layer and its properties such as thickness, density, structure, and hydration was investigated via neutron reflectivity, quartz-crystal microbalance with dissipation, and infra-red measurements. FINDINGS β-lactoglobulin does not show significant anion-induced or isotope-induced effects - neither in bulk nor at the solid-liquid interface, which deviates strongly from the behaviour of bovine serum albumin. We also provide a comprehensive discussion and comparison of protein-specific bulk and interface behaviour between bovine serum albumin and β-lactoglobulin dependent on anion, cation, solvent, and substrate properties. These findings pave the way for understanding the transition from adsorption to crystallisation.
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Affiliation(s)
- Madeleine R Fries
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Maximilian W A Skoda
- ISIS Facility, STFC, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom.
| | - Nina F Conzelmann
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Robert M J Jacobs
- Department for Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom.
| | - Ralph Maier
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Niels Scheffczyk
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Fajun Zhang
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Frank Schreiber
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
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171
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Nomoto D, Nagase K, Nakamura Y, Kanazawa H, Citterio D, Hiruta Y. Anion species-triggered antibody separation system utilizing a thermo-responsive polymer column under optimized constant temperature. Colloids Surf B Biointerfaces 2021; 205:111890. [DOI: 10.1016/j.colsurfb.2021.111890] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/29/2021] [Accepted: 05/28/2021] [Indexed: 01/08/2023]
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172
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Interfacial properties of milk proteins: A review. Adv Colloid Interface Sci 2021; 295:102347. [PMID: 33541692 DOI: 10.1016/j.cis.2020.102347] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022]
Abstract
The interfacial properties of dairy proteins are of great interest to the food industry. Food manufacturing involves various environmental conditions and multiple processes that significantly alter the structure and colloidal stability of food materials. The effects of concentration, pH, heat treatment, addition of salts etc., have considerable influence on the surface activity of proteins and the mechanical properties of the interfacial protein films. Studies to date have established some understanding of the links between environmental and processing related parameters and their impacts on interfacial behavior. Improvement in knowledge may allow better design of interfacial protein structures for different food applications. This review examines the effects of environmental and processing conditions on the interfacial properties of dairy proteins with emphasis on interfacial tension dynamics, dilatational and surface shear rheological properties. The most commonly used surface analytical techniques along with relevant methods are also addressed.
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173
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Gault S, Jaworek MW, Winter R, Cockell CS. Perchlorate salts confer psychrophilic characteristics in α-chymotrypsin. Sci Rep 2021; 11:16523. [PMID: 34400699 PMCID: PMC8367967 DOI: 10.1038/s41598-021-95997-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Studies of salt effects on enzyme activity have typically been conducted at standard temperatures and pressures, thus missing effects which only become apparent under non-standard conditions. Here we show that perchlorate salts, which are found pervasively on Mars, increase the activity of α-chymotrypsin at low temperatures. The low temperature activation is facilitated by a reduced enthalpy of activation owing to the destabilising effects of perchlorate salts. By destabilising α-chymotrypsin, the perchlorate salts also cause an increasingly negative entropy of activation, which drives the reduction of enzyme activity at higher temperatures. We have also shown that α-chymotrypsin activity appears to exhibit an altered pressure response at low temperatures while also maintaining stability at high pressures and sub-zero temperatures. As the effects of perchlorate salts on the thermodynamics of α-chymotrypsin's activity closely resemble those of psychrophilic adaptations, it suggests that the presence of chaotropic molecules may be beneficial to life operating in low temperature environments.
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Affiliation(s)
- Stewart Gault
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Michel W Jaworek
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227, Dortmund, Germany
| | - Charles S Cockell
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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174
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Manoj KM, Bazhin N, Tamagawa H. The murburn precepts for cellular ionic homeostasis and electrophysiology. J Cell Physiol 2021; 237:804-814. [PMID: 34378795 DOI: 10.1002/jcp.30547] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 12/20/2022]
Abstract
Starting from the basic molecular structure and redox properties of its components, we build a macroscopic cellular electrophysiological model. We first present a murburn purview that could explain ion distribution in bulk-milieu/membrane-interface and support the origin of trans-membrane potential (TMP) in cells. In particular, the discussion focuses on how cells achieve disparity in the distribution of monovalent and divalent cations within (K+ > Na+ > Mg2+ > Ca2+ ) and outside (Na+ > K+ > Ca2+ > Mg2+ ). We explore how TMP could vary for resting/graded/action potentials generation and project a model for impulse conduction in neurons. Outcomes based on murburn bioenergetic equilibriums leading to solubilization of ion-pairs, membrane's permittivity, protein channels' fluxes, and proteins' innate ability to bind/adsorb ions selectively are projected as the integral rationale. We also provide experimental modalities to ratify the projections.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Palakkad, Kerala, India
| | - Nikolai Bazhin
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, Russia
| | - Hirohisa Tamagawa
- Department of Mechanical Engineering, Gifu University, Yanagido, Gifu, Japan
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175
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Ríos de Anda I, Coutable-Pennarun A, Brasnett C, Whitelam S, Seddon A, Russo J, Anderson JLR, Royall CP. Decorated networks of native proteins: nanomaterials with tunable mesoscopic domain size. SOFT MATTER 2021; 17:6873-6883. [PMID: 34231559 PMCID: PMC8294043 DOI: 10.1039/d0sm02269a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Natural and artificial proteins with designer properties and functionalities offer unparalleled opportunity for functional nanoarchitectures formed through self-assembly. However, to exploit this potential we need to design the system such that assembly results in desired architecture forms while avoiding denaturation and therefore retaining protein functionality. Here we address this challenge with a model system of fluorescent proteins. By manipulating self-assembly using techniques inspired by soft matter where interactions between the components are controlled to yield the desired structure, we have developed a methodology to assemble networks of proteins of one species which we can decorate with another, whose coverage we can tune. Consequently, the interfaces between domains of each component can also be tuned, with potential applications for example in energy - or electron - transfer. Our model system of eGFP and mCherry with tuneable interactions reveals control over domain sizes in the resulting networks.
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Affiliation(s)
- Ioatzin Ríos de Anda
- H.H. Wills Physics LaboratoryTyndall AvenueBristolBS8 1TLUK
- School of Mathematics, University WalkBristolBS8 1TWUK
| | - Angélique Coutable-Pennarun
- BrisSynBio Synthetic Biology Research Centre, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
- School of Biochemistry, University of BristolBristolBS8 1TDUK
| | | | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National LaboratoryBerkeleyCalifornia 94720USA
| | - Annela Seddon
- H.H. Wills Physics LaboratoryTyndall AvenueBristolBS8 1TLUK
- Bristol Centre for Functional Nanomaterials, University of BristolBristolBS8 1TLUK
| | - John Russo
- School of Mathematics, University WalkBristolBS8 1TWUK
- Dipartimento di Fisica and CNR-ISC, Sapienza-Università di RomaPiazzale A. Moro 200185 RomaItaly
| | - J. L. Ross Anderson
- School of Biochemistry, University of BristolBristolBS8 1TDUK
- School of Cellular and Molecular Medicine, University WalkBristolBS8 1TDUK
| | - C. Patrick Royall
- H.H. Wills Physics LaboratoryTyndall AvenueBristolBS8 1TLUK
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL75005 ParisFrance
- School of Chemistry, University of BristolCantock's CloseBristolBS8 1TSUK
- Centre for Nanoscience and Quantum InformationTyndall AvenueBristolBS8 1FDUK
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176
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Drexler CI, Cracchiolo OM, Myers RL, Okur HI, Serrano AL, Corcelli SA, Cremer PS. Local Electric Fields in Aqueous Electrolytes. J Phys Chem B 2021; 125:8484-8493. [PMID: 34313130 DOI: 10.1021/acs.jpcb.1c03257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vibrational Stark shifts were explored in aqueous solutions of organic molecules with carbonyl- and nitrile-containing constituents. In many cases, the vibrational resonances from these moieties shifted toward lower frequency as salt was introduced into solution. This is in contrast to the blue-shift that would be expected based upon Onsager's reaction field theory. Salts containing well-hydrated cations like Mg2+ or Li+ led to the most pronounced Stark shift for the carbonyl group, while poorly hydrated cations like Cs+ had the greatest impact on nitriles. Moreover, salts containing I- gave rise to larger Stark shifts than those containing Cl-. Molecular dynamics simulations indicated that cations and anions both accumulate around the probe in an ion- and probe-dependent manner. An electric field was generated by the ion pair, which pointed from the cation to the anion through the vibrational chromophore. This resulted from solvent-shared binding of the ions to the probes, consistent with their positions in the Hofmeister series. The "anti-Onsager" Stark shifts occur in both vibrational spectroscopy and fluorescence measurements.
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Affiliation(s)
| | - Olivia M Cracchiolo
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | | | - Halil I Okur
- Department of Chemistry and National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey
| | - Arnaldo L Serrano
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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177
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Cao Y, Ren L, Zhang Y, Lu X, Zhang X, Yan J, Li W, Masuda T, Zhang A. Remarkable Effects of Anions on the Chirality of Thermoresponsive Helical Dendronized Poly(phenylacetylene)s. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuexin Cao
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Materials Building Room 447, Nanchen Street 333, Shanghai 200444, China
| | - Liangxuan Ren
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Materials Building Room 447, Nanchen Street 333, Shanghai 200444, China
| | - Yangwen Zhang
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Materials Building Room 447, Nanchen Street 333, Shanghai 200444, China
| | - Xueting Lu
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Materials Building Room 447, Nanchen Street 333, Shanghai 200444, China
| | - Xiacong Zhang
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Materials Building Room 447, Nanchen Street 333, Shanghai 200444, China
| | - Jiatao Yan
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Materials Building Room 447, Nanchen Street 333, Shanghai 200444, China
| | - Wen Li
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Materials Building Room 447, Nanchen Street 333, Shanghai 200444, China
| | - Toshio Masuda
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Materials Building Room 447, Nanchen Street 333, Shanghai 200444, China
| | - Afang Zhang
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Materials Building Room 447, Nanchen Street 333, Shanghai 200444, China
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178
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Chemo-Enzymatic Baeyer-Villiger Oxidation Facilitated with Lipases Immobilized in the Supported Ionic Liquid Phase. MATERIALS 2021; 14:ma14133443. [PMID: 34206178 PMCID: PMC8269471 DOI: 10.3390/ma14133443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/27/2022]
Abstract
A novel method for chemo-enzymatic Baeyer–Villiger oxidation of cyclic ketones in the presence of supported ionic liquid-like phase biocatalyst was designed. In this work, multi-walled carbon nanotubes were applied as a support for ionic liquids which were anchored to nanotubes covalently by amide or imine bonds. Next, lipases B from Candida antarctica, Candida rugosa, or Aspergillus oryzae were immobilized on the prepared materials. The biocatalysts were characterized using various techniques, like thermogravimetry, IR spectroscopy, XPS, elemental analysis, and SEM-EDS microscopy. In the proposed approach, a biocatalyst consisting of a lipase as an active phase allowed the generation of peracid in situ from the corresponding precursor and a green oxidant–hydrogen peroxide. The activity and stability of the obtained biocatalysts in the model oxidation of 2-adamantanone were demonstrated. High conversion of substrate (92%) was achieved under favorable conditions (toluene: n-octanoic acid ratio 1:1 = v:v, 35% aq. H2O2 2 eq., 0.080 g of biocatalyst per 1 mmol of ketone at 20 °C, reaction time 4 h) with four reaction cycles without a drop in its activity. Our ‘properties-by-design’ approach is distinguished by its short reaction time at low temperature and higher thermal stability in comparison with other biocatalysts presented in the literature reports.
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179
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Katsuto H, Okamoto R, Sumi T, Koga K. Ion Size Dependences of the Salting-Out Effect: Reversed Order of Sodium and Lithium Ions. J Phys Chem B 2021; 125:6296-6305. [PMID: 34102058 DOI: 10.1021/acs.jpcb.1c03388] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general trend of the salting-out effect on hydrophobic solutes in aqueous solution is that the smaller the size of a dissolved ion, the larger the effect of reducing the solubility of a hydrophobe. An exception is that Li+, the smallest in alkali metal ions, has a notably weaker effect than Na+. To understand the reversed order in the cation series, we performed molecular dynamics simulations of aqueous solutions of salt ions and calculated the Setschenow coefficient of methane with the ionic radius of either a cation or an anion varied in a wide range. It is confirmed that the Setschenow coefficient is correlated with the packing fraction of salt solution, as observed in earlier studies, and also correlated with the partial molar volume of an ion. Analyses of correlation function integrals, packing fractions of solvation spheres, and orientations of water molecules surrounding an ion reveal the key differences in microscopic properties between the cation and anion series, which give rise to the reversed order in the cation series of the partial molar volumes of ions and ultimately that of the Setschenow coefficients.
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Affiliation(s)
- Hiroyuki Katsuto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Ryuichi Okamoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Kenichiro Koga
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
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180
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Pusara S, Yamin P, Wenzel W, Krstić M, Kozlowska M. A coarse-grained xDLVO model for colloidal protein-protein interactions. Phys Chem Chem Phys 2021; 23:12780-12794. [PMID: 34048523 DOI: 10.1039/d1cp01573g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Colloidal protein-protein interactions (PPIs) of attractive and repulsive nature modulate the solubility of proteins, their aggregation, precipitation and crystallization. Such interactions are very important for many biotechnological processes, but are complex and hard to control, therefore, difficult to be understood in terms of measurements alone. In diluted protein solutions, PPIs can be estimated from the osmotic second virial coefficient, B22, which has been calculated using different methods and levels of theory. The most popular approach is based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory and its extended versions, i.e. xDLVO. Despite much efforts, these models are not fully quantitative and must be fitted to experiments, which limits their predictive value. Here, we report an extended xDLVO-CG model, which extends existing models by a coarse-grained representation of proteins and the inclusion of an additional ion-protein dispersion interaction term. We demonstrate for four proteins, i.e. lysozyme (LYZ), subtilisin (Subs), bovine serum albumin (BSA) and immunoglobulin (IgG1), that semi-quantitative agreement with experimental values without the need to fit to experimental B22 values. While most likely not the final step in the nearly hundred years of research in PPIs, xDLVO-CG is a step towards predictive PPIs calculations that are transferable to different proteins.
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Affiliation(s)
- Srdjan Pusara
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Peyman Yamin
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Marjan Krstić
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. and Institute of Theoretical Solid State Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Mariana Kozlowska
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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181
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Maryskova M, Linhartova L, Novotny V, Rysova M, Cajthaml T, Sevcu A. Laccase and horseradish peroxidase for green treatment of phenolic micropollutants in real drinking water and wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:31566-31574. [PMID: 33606164 DOI: 10.1007/s11356-021-12910-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Biologically active micropollutants that contain diverse phenolic/aromatic structures are regularly present in wastewater effluents and are even found in drinking water. Advanced green technologies utilizing immobilized laccase and/or peroxidase, which target these micropollutants directly, may provide a reasonable alternative to standard treatments. Nevertheless, the use of these enzymes is associated with several issues that may prevent their application, such as the low activity of laccase at neutral and basic pH or the necessity of hydrogen peroxide addition as a co-substrate for peroxidases. In this study, the activity of laccase from Trametes versicolor and horseradish peroxidase was evaluated across a range of commonly used substrates (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), syringaldazine, and guaiacol). Moreover, conditions for their optimal performance were explored along with an assessment of whether these conditions accurately reflect the effectivity of both enzymes in the degradation of a mixture of bisphenol A, 17α-ethinylestradiol, triclosan, and diclofenac in tap drinking water and secondary wastewater effluent. Laccase and horseradish peroxidase showed optimal activity at strongly acidic pH if ABTS was used as a substrate. Correspondingly, the activities of both enzymes detected using ABTS in real waters were significantly enhanced by adding approximately 2.5% (v/v) of McIlvaine's buffer. Degradation of a mixture of micropollutants in wastewater with 2.5% McIlvaine's buffer (pH 7) resulted in a substantial decrease in estrogenic activity. Low degradation efficiency of micropollutants by laccase was observed in pure McIlvaine's buffer of pH 3 and 7, compared with efficient degradation in tap water of pH 7.5 without buffer. This study clearly shows that enzyme activity needs to be evaluated on micropollutants in real waters as the assessment of optimal conditions based on commonly used substrates in pure buffer or deionized water can be misleading.
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Affiliation(s)
- Milena Maryskova
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 1409/7, 461 17, Liberec, Czech Republic.
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentska 1402/2, 461 17, Liberec, Czech Republic.
| | - Lucie Linhartova
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Czech Republic
| | - Vit Novotny
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 1409/7, 461 17, Liberec, Czech Republic
| | - Miroslava Rysova
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 1409/7, 461 17, Liberec, Czech Republic
| | - Tomas Cajthaml
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Czech Republic
| | - Alena Sevcu
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 1409/7, 461 17, Liberec, Czech Republic.
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182
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Gong SY, Wang P, Wei ZY, Xu HG, Xu XL, Zheng WJ. Structures of (NaSCN) 2(H 2O) n -/0 (n = 0-7) and solvation induced ion pair separation: Gas phase anion photoelectron spectroscopy and theoretical calculations. J Chem Phys 2021; 154:204301. [PMID: 34241176 DOI: 10.1063/5.0049567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We studied (NaSCN)2(H2O)n - clusters in the gas phase using size-selected anion photoelectron spectroscopy. The photoelectron spectra and vertical detachment energies of (NaSCN)2(H2O)n - (n = 0-5) were obtained in the experiment. The structures of (NaSCN)2(H2O)n -/0 up to n = 7 were investigated with density functional theory calculations. Two series of peaks are observed in the spectra, indicating that two types of structures coexist, the high electron binding energy peaks correspond to the chain style structures, and the low electron binding energy peaks correspond to the Na-N-Na-N rhombic structures or their derivatives. For the (NaSCN)2(H2O)n - clusters at n = 3-5, the Na-N-Na-N rhombic structures are the dominant structures, the rhombic four-membered rings start to open at n = 4, and the solvent separated ion pair (SSIP) type of structures start to appear at n = 6. For the neutral (NaSCN)2(H2O)n clusters, the Na-N-Na-N rhombic isomers become the dominant starting at n = 3, and the SSIP type of structures start to appear at n = 5 and become dominant at n = 6. The structural evolution of (NaSCN)2(H2O)n -/0 (n = 0-7) confirms the possible existence of ionic clusters such as Na(SCN)2 - and Na2(SCN)+ in NaSCN aqueous solutions.
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Affiliation(s)
- Shi-Yan Gong
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-You Wei
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Guang Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi-Ling Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Jun Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
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183
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Dhabal D, Jiang Z, Pallath A, Patel AJ. Characterizing the Interplay between Polymer Solvation and Conformation. J Phys Chem B 2021; 125:5434-5442. [PMID: 33978411 DOI: 10.1021/acs.jpcb.1c02191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and extended states can be quantified by the strength of the requisite potential. Our results also provide mechanistic insights into the collapse transition, highlighting that the bottleneck to polymer collapse is the formation of a sufficiently large cluster, and the collective dewetting of such a cluster. We also study the collapse of the hydrophobic polymer in octane, a nonpolar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhitong Jiang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Akash Pallath
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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184
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Babu CS, Lim C. Influence of solution ionic strength on the stabilities of M20 loop conformations in apo E. coli dihydrofolate reductase. J Chem Phys 2021; 154:195103. [PMID: 34240890 DOI: 10.1063/5.0048968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interactions among ions and their specific interactions with macromolecular solutes are known to play a central role in biomolecular stability. However, similar effects in the conformational stability of protein loops that play functional roles, such as binding ligands, proteins, and DNA/RNA molecules, remain relatively unexplored. A well-characterized enzyme that has such a functional loop is Escherichia coli dihydrofolate reductase (ecDHFR), whose so-called M20 loop has been observed in three ordered conformations in crystal structures. To explore how solution ionic strengths may affect the M20 loop conformation, we proposed a reaction coordinate that could quantitatively describe the loop conformation and used it to classify the loop conformations in representative ecDHFR x-ray structures crystallized in varying ionic strengths. The Protein Data Bank survey indicates that at ionic strengths (I) below the intracellular ion concentration-derived ionic strength in E. coli (I ≤ 0.237M), the ecDHFR M20 loop tends to adopt open/closed conformations, and rarely an occluded loop state, but when I is >0.237M, the loop tends to adopt closed/occluded conformations. Distance-dependent electrostatic potentials around the most mobile M20 loop region from molecular dynamics simulations of ecDHFR in equilibrated CaCl2 solutions of varying ionic strengths show that high ionic strengths (I = 0.75/1.5M) can preferentially stabilize the loop in closed/occluded conformations. These results nicely correlate with conformations derived from ecDHFR structures crystallized in varying ionic strengths. Altogether, our results suggest caution in linking M20 loop conformations derived from crystal structures solved at ionic strengths beyond that tolerated by E. coli to the ecDHFR function.
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Affiliation(s)
- C Satheesan Babu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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185
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Gomez DT, Pratt LR, Rogers DM, Rempe SB. Free Energies of Hydrated Halide Anions: High Through-Put Computations on Clusters to Treat Rough Energy-Landscapes. Molecules 2021; 26:molecules26113087. [PMID: 34064203 PMCID: PMC8196753 DOI: 10.3390/molecules26113087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022] Open
Abstract
With a longer-term goal of addressing the comparative behavior of the aqueous halides F−, Cl−, Br−, and I− on the basis of quasi-chemical theory (QCT), here we study structures and free energies of hydration clusters for those anions. We confirm that energetically optimal (H2O)nX clusters, with X = Cl−, Br−, and I−, exhibit surface hydration structures. Computed free energies, based on optimized surface hydration structures utilizing a harmonic approximation, typically (but not always) disagree with experimental free energies. To remedy the harmonic approximation, we utilize single-point electronic structure calculations on cluster geometries sampled from an AIMD (ab initio molecular dynamics) simulation stream. This rough-landscape procedure is broadly satisfactory and suggests unfavorable ligand crowding as the physical effect addressed. Nevertheless, this procedure can break down when n≳4, with the characteristic discrepancy resulting from a relaxed definition of clustering in the identification of (H2O)nX clusters, including ramified structures natural in physical cluster theories. With ramified structures, the central equation for the present rough-landscape approach can acquire some inconsistency. Extension of these physical cluster theories in the direction of QCT should remedy that issue, and should be the next step in this research direction.
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Affiliation(s)
- Diego T. Gomez
- Department of Chemical & Biomolecular Engineering, Tulane University, New Orleans, LA 70118, USA; (D.T.G.); (L.R.P.)
| | - Lawrence R. Pratt
- Department of Chemical & Biomolecular Engineering, Tulane University, New Orleans, LA 70118, USA; (D.T.G.); (L.R.P.)
| | - David M. Rogers
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA;
| | - Susan B. Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
- Correspondence: ; Tel.: +1-505-845-0253
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186
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Zeng Y, Jia Y, Yan T, Zhuang W. Binary structure and dynamics of the hydrogen bonds in the hydration shells of ions. Phys Chem Chem Phys 2021; 23:11400-11410. [PMID: 33949400 DOI: 10.1039/d0cp06397e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ion-specific effects of cations (Li+, Na+, K+, Mg2+, Ca2+) and anions (F-, Cl-) on the hydrogen bond structure and dynamics of the coordination waters in the hydration shells have been studied using molecular dynamics simulations. Our simulations indicate that the hydrogen bonds between the first and second hydration shell waters show binary structural and dynamic properties. The hydrogen bond with a first shell water as the donor (HD) is strengthened, while those with a first shell water as the acceptor (HA) are weakened. For a hydrated anion, this binary effect reverses, but is less significant. This ion-specific binary effect correlates with the size and the valence of the ion, and is more significant for the strong kosmotropic ions of high charge density.
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Affiliation(s)
- Yonghui Zeng
- Institute of New Energy Material Chemistry, School of Materials Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Yunzhe Jia
- Institute of New Energy Material Chemistry, School of Materials Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Tianying Yan
- Institute of New Energy Material Chemistry, School of Materials Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China.
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187
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Abstract
The molecular properties of proteins are influenced by various ions present in the same solution. While site-specific strong interactions between multivalent metal ions and proteins are well characterized, the behavior of other ions that are only weakly interacting with proteins remains elusive. In the current study, using NMR spectroscopy, we have investigated anion-protein interactions for three proteins that are similar in size but differ in overall charge. Using a unique NMR-based approach, we quantified anions accumulated around the proteins. The determined numbers of anions that are electrostatically attracted to the charged proteins were notably smaller than the overall charge valences and were consistent with predictions from the Poisson-Boltzmann theory. This NMR-based approach also allowed us to measure ionic diffusion and characterize the anions interacting with the positively charged proteins. Our data show that these anions rapidly diffuse while bound to the proteins. Using the same experimental approach, we observed the release of the anions from the protein surface upon the formation of the Antp homeodomain-DNA complex. Using paramagnetic relaxation enhancement (PRE), we visualized the spatial distribution of anions around the free proteins and the Antp homeodomain-DNA complex. The obtained PRE data revealed the localization of anions in the vicinity of the highly positively charged regions of the free Antp homeodomain and provided further evidence of the release of anions from the protein surface upon the protein-DNA association. This study sheds light on the dynamic behavior of anions that electrostatically interact with proteins.
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188
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Baryiames CP, Garrett P, Baiz CR. Bursting the bubble: A molecular understanding of surfactant-water interfaces. J Chem Phys 2021; 154:170901. [PMID: 34241044 DOI: 10.1063/5.0047377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Surfactant science has historically emphasized bulk, thermodynamic measurements to understand the microemulsion properties of greatest industrial significance, such as interfacial tensions, phase behavior, and thermal stability. Recently, interest in the molecular properties of surfactants has grown among the physical chemistry community. This has led to the application of cutting-edge spectroscopic methods and advanced simulations to understand the specific interactions that give rise to the previously studied bulk characteristics. In this Perspective, we catalog key findings that describe the surfactant-oil and surfactant-water interfaces in molecular detail. We emphasize the role of ultrafast spectroscopic methods, including two-dimensional infrared spectroscopy and sum-frequency-generation spectroscopy, in conjunction with molecular dynamics simulations, and the role these techniques have played in advancing our understanding of interfacial properties in surfactant microemulsions.
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Affiliation(s)
- Christopher P Baryiames
- Department of Chemistry, University of Texas at Austin, 105 E 24th St. Stop A5300, Austin, Texas 78712-1224, USA
| | - Paul Garrett
- Department of Chemistry, University of Texas at Austin, 105 E 24th St. Stop A5300, Austin, Texas 78712-1224, USA
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, 105 E 24th St. Stop A5300, Austin, Texas 78712-1224, USA
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189
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Schwidetzky R, Lukas M, YazdanYar A, Kunert AT, Pöschl U, Domke KF, Fröhlich-Nowoisky J, Bonn M, Koop T, Nagata Y, Meister K. Specific Ion-Protein Interactions Influence Bacterial Ice Nucleation. Chemistry 2021; 27:7402-7407. [PMID: 33464680 PMCID: PMC8251952 DOI: 10.1002/chem.202004630] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Indexed: 11/12/2022]
Abstract
Ice nucleation‐active bacteria are the most efficient ice nucleators known, enabling the crystallization of water at temperatures close to 0 °C, thereby overcoming the kinetically hindered phase transition process at these conditions. Using highly specialized ice‐nucleating proteins (INPs), they can cause frost damage to plants and influence the formation of clouds and precipitation in the atmosphere. In nature, the bacteria are usually found in aqueous environments containing ions. The impact of ions on bacterial ice nucleation efficiency, however, has remained elusive. Here, we demonstrate that ions can profoundly influence the efficiency of bacterial ice nucleators in a manner that follows the Hofmeister series. Weakly hydrated ions inhibit bacterial ice nucleation whereas strongly hydrated ions apparently facilitate ice nucleation. Surface‐specific sum‐frequency generation spectroscopy and molecular dynamics simulations reveal that the different effects are due to specific interactions of the ions with the INPs on the surface of the bacteria. Our results demonstrate that heterogeneous ice nucleation facilitated by bacteria strongly depends upon the nature of the ions, and specific ion–protein interactions are essential for the complete description of heterogeneous ice nucleation by bacteria.
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Affiliation(s)
| | - Max Lukas
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Azade YazdanYar
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Anna T Kunert
- Max Planck Institute for Chemistry, 55128, Mainz, Germany
| | - Ulrich Pöschl
- Max Planck Institute for Chemistry, 55128, Mainz, Germany
| | - Katrin F Domke
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | | | - Mischa Bonn
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Thomas Koop
- Bielefeld University, 33615, Bielefeld, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Konrad Meister
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany.,University of Alaska Southeast, 99801, Juneau, AK, USA
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190
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191
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Travers W, Kelleher F. Studies of the highly potent lantibiotic peptide nisin Z in aqueous solutions of salts and biological buffer components. Biophys Chem 2021; 274:106603. [PMID: 33945991 DOI: 10.1016/j.bpc.2021.106603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 12/20/2022]
Abstract
The lantibiotic nisin, usually used as a 2.5%w/w in NaCl and milk solids, has activity against a wide range of Gram-positive bacteria, especially food-borne pathogens, and has been used as a food preservative for decades without the development of significant resistance. It has been reported that the high purity (>95%) nisin Z form has activity against the Gram-negative speciesE. coli, which is significantly reduced in the presence of NaCl. This current study examined, by1H NMR spectroscopy, the effects of NaCl, and a range of other salts, on the observed aqueous solution1H NMR spectra of nisin Z in the pH 3-4 range, where nisin Z has its maximum stability. Nisin's mechanism of action involves binding to the polyoxygenated pyrophosphate moiety of lipid II, and in acidic solution the positively charged C-terminus region is reported to interact with the negative sulfate groups of SDS micelles, so the study was extended to include a number of polyoxygenated anions commonly used as buffers in many biological assays. In general, the biggest changes found were in the chemical shifts of protons in the hydrophobic N-terminus region, rather than the more polar C-terminus region. The effects seen on the addition of the salts (cations and anions) were not just an overall non-specific ionic strength effect, as different salts caused different effects, in an unpredictive manner. Similarly, the polyoxygenated anions behaved differently and not predictably, and neither the cations/anions, or polyoxygenated anions, constitute a Hofmeister or inverse Hofmeister series.
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Affiliation(s)
- Wayne Travers
- Molecular Design & Synthesis Group, Centre of Applied Science for Health, TU Dublin Tallaght, Dublin D24 FKT9, Ireland
| | - Fintan Kelleher
- Molecular Design & Synthesis Group, Centre of Applied Science for Health, TU Dublin Tallaght, Dublin D24 FKT9, Ireland.
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192
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Herman KM, Heindel JP, Xantheas SS. The many-body expansion for aqueous systems revisited: III. Hofmeister ion-water interactions. Phys Chem Chem Phys 2021; 23:11196-11210. [PMID: 33899854 DOI: 10.1039/d1cp00409c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a Many Body Energy (MBE) analysis of aqueous ionic clusters containing anions and cations at the two opposite ends of the Hofmeister series, viz. the kosmotropes Ca2+ and SO42- and the chaotropes NH4+ and ClO4-, with 9 water molecules to quantify how these ions alter the interaction between the water molecules in their immediate surroundings. We specifically aim at quantifying how various ions (depending on their position in the Hofmeister series) affect the interaction between the surrounding water molecules and probe whether there is a qualitatively different behavior between kosmotropic vs. chaotropic ions. The current results when compared to the ones reported earlier for water clusters [J. P. Heindel and S. S. Xantheas, J. Chem. Theor. Comput., 2020, 16, 6843-6855] as well as for alkali metal and halide ion aqueous clusters of the same size [J. P. Heindel and S. S. Xantheas, J. Chem. Theor. Comput., 2021, 17, 2200-2216], which lie in the middle of the Hofmeister series, offer a complete account of the effect an ion across the Hofmeister series from "kosmotropes" to "chaotropes" has on the interaction between the neighboring water molecules. Through this analysis, noteworthy differences between the MBE of kosmotropes and chaotropes were identified. The MBE of kosmotropes is dominated by ion-water interactions that extend beyond the 4-body term, the rank at which the MBE of pure water converges. The percentage contribution of the 2-B term to the total cluster binding energy is noticeably larger. The disruption of the hydrogen bonded network due to the dominant ion-water interactions results in weak, unfavorable water-water interactions. The MBE for chaotropes, on the other hand, was found to converge more quickly as it more closely resembles that of pure water clusters. Chaotropes exhibit weaker overall binding energies and weaker ion-water interactions in favor of water-water interactions, somewhat recovering the pattern of the 2-4 body terms exemplified by pure water clusters. A remarkable anti-correlation between the 2-B ion-water (I-W) and water-water (W-W) interactions as well as between the 3-B (I-W-W) and (I-W) interactions was found for both kosmotropic and chaotropic ions. This anti-correlation is linear for both monatomic anions and monatomic cations, suggesting the existence of underlying physical mechanisms that were previously unexplored. The consideration of two different structural arrangements (ion inside and outside of a water cluster) suggests that fully solvated (ion inside) chaotropes disrupt the hydrogen bonding network in a similar manner to partially solvated (ion outside) kosmotropes and offers useful insights into the modeling requirements of bulk vs. interfacial ion solvation. It is noteworthy that the 2-B contribution to the total Basis Set Superposition Error (BSSE) correction for both kosmotropic and chaotropic ions follows the universal erf profile vs. intermolecular distance previously reported for pure water, halide ion-water and alkali metal ion-water clusters. When scaled for the corresponding dimer energies and distances, a single profile fits the current results together with all previously reported ones for pure water and halide water clusters. This finding lends further support to schemes for accurately estimating the 2-B BSSE correction in condensed environments.
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Affiliation(s)
- Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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193
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Kinetic Methods of Deducing Binding Mechanisms Involving Intrinsically Disordered Proteins. Methods Mol Biol 2021. [PMID: 33877595 DOI: 10.1007/978-1-0716-1197-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
There are multiple examples of protein-protein interactions involving one intrinsically disordered protein region binding to an ordered protein domain in a coupled binding and folding reaction. Similarly to protein folding studies, much effort has been devoted to understanding the mechanisms of such coupled binding and folding reactions. In this chapter, we describe how kinetics can be used to assess binding mechanisms with focus on fluorescence-monitored stopped-flow experiments. The approach can be applied more generally to any protein interaction with or without a coupled conformational change and to other kinetic techniques. Determining binding mechanisms is a great challenge and while "proving" a mechanism may be futile, it is possible to deduce the simplest scenarios, which are consistent with experimental data.
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194
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Song WW, Qian ZG, Liu H, Chen HF, Kaplan DL, Xia XX. On-Demand Regulation of Dual Thermosensitive Protein Hydrogels. ACS Macro Lett 2021; 10:395-400. [PMID: 35549223 DOI: 10.1021/acsmacrolett.1c00062] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Despite considerable progress having been made in thermosensitive protein hydrogels, regulating their thermal transitions remains a challenge due to the intricate molecular structures and interactions of the underlying protein polymers. Here we report a genetic fusion strategy to tune the unique dual thermal transitions of the C-terminal domain (CTD) of spider major ampullate spidroin 1, and explore the regulation mechanism by biophysical characterization and molecular dynamics simulations. We found that the fusion of elastin-like polypeptides (ELPs) tuned the dual transition temperatures of CTD to a physiologically relevant window, by introducing extra hydrogen bonding at low temperatures and hydrophobic interactions at high temperatures. The resulting hydrogels constructed from the fusion proteins were demonstrated to be a promising vehicle for cell preservation and delivery. This study provides insights on the regulation of the dual thermosensitive protein hydrogels and suggests a potential application of the hydrogels for consolidated cell storage and delivery.
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Affiliation(s)
- Wen-Wen Song
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhi-Gang Qian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Xiao-Xia Xia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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195
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Wang Y, Wang X, Montclare JK. Effect of Divalent Metal Cations on the Conformation, Elastic Behavior, and Controlled Release of a Photocrosslinked Protein Engineered Hydrogel. ACS APPLIED BIO MATERIALS 2021; 4:3587-3597. [PMID: 35014444 DOI: 10.1021/acsabm.1c00091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We investigate the effect of Zn2+, Cu2+, and Ni2+ coordination on the conformation, mechanical properties, contraction, and small-molecule drug encapsulation and release of a photocrosslinked protein-engineered hydrogel, CEC-D. The treatment of the CEC-D hydrogel with divalent metal (M2+) results in significant conformational changes where a loss in structure is observed with Zn2+, while both Cu2+ and Ni2+ induce a blueshift. The relationship of M2+ to mechanical properties illustrates a trend, while the CEC-D hydrogel in the presence of 2 mM Cu2+ reveals the highest increase in G' to 14.4 ± 0.7 kPa followed by 9.7 ± 0.9 kPa by addition of 2 mM Zn2+, and a decrease to 1.1 ± 0.2 kPa is demonstrated in the presence of 2 mM Ni2+. A similar observation in M2+ responsiveness emerges where CEC-D hydrogels contract into a condensed state of 2.6-fold for Cu2+, 2.4-fold for Zn2+, and 1.6-fold for Ni2+. Furthermore, CEC-D hydrogels coordinated with M2+ demonstrate control over the encapsulation and release of the small molecule curcumin. The trend of release is opposite of the mechanical and contraction properties with a 70.0 ± 5.3% release with Ni2+, 64.2 ± 1.2% release with Zn2+, and 42.3 ± 11.3 release with Cu2+. Taken together, these results indicate that the CEC-D hydrogel tuned by M2+ is a promising drug delivery platform with tunable physicochemical properties.
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Affiliation(s)
- Yao Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Xiaole Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States.,Department of Chemistry, New York University, New York, New York 10003, United States.,Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States.,Department of Radiology, New York University Langone Health, New York, New York 10016, United States
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196
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Yu B, Iwahara J. Experimental approaches for investigating ion atmospheres around nucleic acids and proteins. Comput Struct Biotechnol J 2021; 19:2279-2285. [PMID: 33995919 PMCID: PMC8102144 DOI: 10.1016/j.csbj.2021.04.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 01/26/2023] Open
Abstract
Ionic interactions are crucial to biological functions of DNA, RNA, and proteins. Experimental research on how ions behave around biological macromolecules has lagged behind corresponding theoretical and computational research. In the 21st century, quantitative experimental approaches for investigating ionic interactions of biomolecules have become available and greatly facilitated examinations of theoretical electrostatic models. These approaches utilize anomalous small-angle X-ray scattering, atomic emission spectroscopy, mass spectrometry, or nuclear magnetic resonance (NMR) spectroscopy. We provide an overview on the experimental methodologies that can quantify and characterize ions within the ion atmospheres around nucleic acids, proteins, and their complexes.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
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197
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Abstract
Bioelectrocatalysis using redox enzymes appears as a sustainable way for biosensing, electricity production, or biosynthesis of fine products. Despite advances in the knowledge of parameters that drive the efficiency of enzymatic electrocatalysis, the weak stability of bioelectrodes prevents large scale development of bioelectrocatalysis. In this review, starting from the understanding of the parameters that drive protein instability, we will discuss the main strategies available to improve all enzyme stability, including use of chemicals, protein engineering and immobilization. Considering in a second step the additional requirements for use of redox enzymes, we will evaluate how far these general strategies can be applied to bioelectrocatalysis.
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198
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Bharadwaj S, Nayar D, Dalgicdir C, van der Vegt NFA. An interplay of excluded-volume and polymer-(co)solvent attractive interactions regulates polymer collapse in mixed solvents. J Chem Phys 2021; 154:134903. [PMID: 33832270 DOI: 10.1063/5.0046746] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Cosolvent effects on the coil-globule transitions in aqueous polymer solutions are not well understood, especially in the case of amphiphilic cosolvents that preferentially adsorb on the polymer and lead to both polymer swelling and collapse. Although a predominant focus in the literature has been placed on the role of polymer-cosolvent attractive interactions, our recent work has shown that excluded-volume interactions (repulsive interactions) can drive both preferential adsorption of the cosolvent and polymer collapse via a surfactant-like mechanism. Here, we further study the role of polymer-(co)solvent attractive interactions in two kinds of polymer solutions, namely, good solvent (water)-good cosolvent (alcohol) (GSGC) and poor solvent-good cosolvent (PSGC) solutions, both of which exhibit preferential adsorption of the cosolvent and a non-monotonic change in the polymer radius of gyration with the addition of the cosolvent. Interestingly, at low concentrations, the polymer-(co)solvent energetic interactions oppose polymer collapse in the GSGC solutions and contrarily support polymer collapse in the PSGC solutions, indicating the importance of the underlying polymer chemistry. Even though the alcohol molecules are preferentially adsorbed on the polymer, the trends of the energetic interactions at low cosolvent concentrations are dominated by the polymer-water energetic interactions in both the cases. Therefore, polymer-(co)solvent energetic interactions can either reinforce or compensate the surfactant-like mechanism, and it is this interplay that drives coil-to-globule transitions in polymer solutions. These results have implications for rationalizing the cononsolvency transitions in real systems such as polyacrylamides in aqueous alcohol solutions where the understanding of microscopic driving forces is still debatable.
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Affiliation(s)
- Swaminath Bharadwaj
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Divya Nayar
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Cahit Dalgicdir
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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199
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Fang Y, Furó I. Weak Anion Binding to Poly( N-isopropylacrylamide) Detected by Electrophoretic NMR. J Phys Chem B 2021; 125:3710-3716. [PMID: 33821651 PMCID: PMC8154593 DOI: 10.1021/acs.jpcb.1c00642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ion specific effects are ubiquitous in solutions and govern a large number of colloidal phenomena. To date, a substantial and sustained effort has been directed at understanding the underlying molecular interactions. As a new approach, we address this issue by sensitive 1H NMR methods that measure the electrophoretic mobility and the self-diffusion coefficient of poly(N-isopropylacrylamide) (PNIPAM) chains in bulk aqueous solution in the presence of salts with the anion component varied from kosmotropes to chaotropes along the Hofmeister series. The accuracy of the applied electrophoretic NMR experiments is exceptionally high, on the order of 10-10 m2/(V s), corresponding to roughly 10-4 elementary charges per monomer effectively associated with the neutral polymer. We find that chaotropic anions associate to PNIPAM with an apparent Langmuir-type saturation behavior. The polymer chains remain extended upon ion association, and momentum transfer from anion to polymer is only partial which indicates weak attractive short-range forces between anion and polymer and, thereby and in contrast to some other ion-polymer systems, the lack of well-defined binding sites.
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Affiliation(s)
- Yuan Fang
- Division of Applied Physical Chemistry, Department of Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - István Furó
- Division of Applied Physical Chemistry, Department of Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
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200
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Souza PCT, Alessandri R, Barnoud J, Thallmair S, Faustino I, Grünewald F, Patmanidis I, Abdizadeh H, Bruininks BMH, Wassenaar TA, Kroon PC, Melcr J, Nieto V, Corradi V, Khan HM, Domański J, Javanainen M, Martinez-Seara H, Reuter N, Best RB, Vattulainen I, Monticelli L, Periole X, Tieleman DP, de Vries AH, Marrink SJ. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat Methods 2021; 18:382-388. [PMID: 33782607 DOI: 10.1038/s41592-021-01098-3] [Citation(s) in RCA: 414] [Impact Index Per Article: 138.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/22/2021] [Indexed: 01/31/2023]
Abstract
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 ( http://cgmartini.nl ), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein-protein and protein-lipid interactions and material science applications as ionic liquids and aedamers.
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Affiliation(s)
- Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands. .,Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon, France.
| | - Riccardo Alessandri
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Jonathan Barnoud
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands.,Intangible Realities Laboratory, University of Bristol, School of Chemistry, Bristol, UK
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands.,Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
| | - Ignacio Faustino
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Bart M H Bruininks
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Peter C Kroon
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Vincent Nieto
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon, France
| | - Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hanif M Khan
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.,Department of Chemistry and Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Jan Domański
- Department of Biochemistry, University of Oxford, Oxford, UK.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Nathalie Reuter
- Department of Chemistry and Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ilpo Vattulainen
- Computational Physics Laboratory, Tampere University, Tampere, Finland.,Department of Physics, University of Helsinki, Helsinki, Finland
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon, France
| | - Xavier Periole
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands.
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