1
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Yao Y, Feng J, Ao N, Zhang Y, Zhang J, Wang Y, Liu C, Wang M, Yu C. Natural agents derived Pickering emulsion enabled by silica nanoparticles with enhanced antibacterial activity against drug-resistant bacteria. J Colloid Interface Sci 2024; 678:1158-1168. [PMID: 39288711 DOI: 10.1016/j.jcis.2024.09.066] [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: 05/22/2024] [Revised: 08/19/2024] [Accepted: 09/07/2024] [Indexed: 09/19/2024]
Abstract
The emergence of antibiotic-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) has become a global health challenge due to the overuse of antibiotics. Natural substances including enzymes and essential oils have shown great potential as alternative treatment options. However, the combinational use of these natural agents remains challenging due to the denaturation of enzymes upon direct contact with oil. In this study, we report the design of a Pickering emulsion containing two natural antibacterial agents, lysozyme and tea tree oil, stabilized by fractal silica nanoparticles. In this design, the enzyme activity is kept and the volatility problem of tea tree oil is mitigated. Due to synergistic bacterial cell wall digestion and membrane disruption functions, potent bactericidal efficacy in vitro against drug-resistant bacteria is achieved. The therapeutic potential is further demonstrated in a wound healing model with drug-resistant bacteria infection, better than a synthetic antibiotic, Ampicillin. This study opens new avenues for the development of natural product-based antimicrobial treatments with promising application potential.
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Affiliation(s)
- Yining Yao
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Jiayou Feng
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Niqi Ao
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Ye Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Jun Zhang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Yue Wang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Chao Liu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.
| | - Meiyan Wang
- School of Medicine, Shanghai University, Shanghai 200444, China.
| | - Chengzhong Yu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia.
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2
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Melnikova D, Ranjan VV, Nesmelov YE, Skirda VD, Nesmelova IV. Translational Diffusion and Self-Association of an Intrinsically Disordered Protein κ-Casein Using NMR with Ultra-High Pulsed-Field Gradient and Time-Resolved FRET. J Phys Chem B 2024; 128:7781-7791. [PMID: 39106061 PMCID: PMC11331516 DOI: 10.1021/acs.jpcb.4c03625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/09/2024] [Accepted: 07/17/2024] [Indexed: 08/07/2024]
Abstract
Much attention has been given to studying the translational diffusion of globular proteins, whereas the translational diffusion of intrinsically disordered proteins (IDPs) is less studied. In this study, we investigate the translational diffusion and how it is affected by the self-association of an IDP, κ-casein, using pulsed-field gradient nuclear magnetic resonance and time-resolved Förster resonance energy transfer. Using the analysis of the shape of diffusion attenuation and the concentration dependence of κ-casein diffusion coefficients and intermolecular interactions, we demonstrate that κ-casein exhibits continuous self-association. When the volume fraction of κ-casein is below 0.08, we observe that κ-casein self-association results in a macroscopic phase separation upon storage at 4 °C. At κ-casein volume fractions above 0.08, self-association leads to the formation of labile gel-like networks without subsequent macroscopic phase separation. Unlike α-casein, which shows a strong concentration dependence and extensive gel-like network formation, only one-third of κ-casein molecules participate in the gel network at a time, resulting in a more dynamic and less extensive structure. These findings highlight the unique association properties of κ-casein, contributing to a better understanding of its behavior under various conditions and its potential role in casein micelle formation.
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Affiliation(s)
- Daria
L. Melnikova
- Department
of Physics of Molecular Systems, Kazan Federal
University, Kazan 420011, Russia
| | - Venkatesh V. Ranjan
- Department
of Chemistry, University of North Carolina, Charlotte, North Carolina 28223, United States
- Department
of Physics and Optical Sciences, University
of North Carolina, Charlotte, North Carolina 28223, United States
| | - Yuri E. Nesmelov
- Department
of Physics and Optical Sciences, University
of North Carolina, Charlotte, North Carolina 28223, United States
| | - Vladimir D. Skirda
- Department
of Physics of Molecular Systems, Kazan Federal
University, Kazan 420011, Russia
| | - Irina V. Nesmelova
- Department
of Physics and Optical Sciences, University
of North Carolina, Charlotte, North Carolina 28223, United States
- School
of Data Science, University of North Carolina, Charlotte, North Carolina 28223, United States
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3
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Nowag J, Brauser M, Steuernagel L, Wende RC, Schreiner PR, Thiele CM. Quantifying Intermolecular Interactions in Asymmetric Peptide Organocatalysis as a Key toward Understanding Selectivity. J Am Chem Soc 2024; 146:170-180. [PMID: 38117177 DOI: 10.1021/jacs.3c06378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The kinetic resolution of trans-cyclohexane-1,2-diol with a lipophilic oligopeptide catalyst shows extraordinary selectivities. To improve our understanding of the factors governing selectivity, we quantified the Gibbs free energies of interactions of the peptide with both enantiomers of trans-cyclohexane-1,2-diol using nuclear magnetic resonance (NMR) spectroscopy. For this, we use advanced methods such as transverse relaxation (R2), diffusion measurements, saturation transfer difference (STD), and chemical shift (δ) analysis of peptide-diol mixtures upon varying their composition (NMR titrations). The methods employed give comparable and consistent results. The molecular recognition by the catalyst is approximately 3 kJ mol-1 in favor of the preferentially acetylated (R,R)-enantiomer in the temperature range studied. Interestingly, the difference of 3 kJ mol-1 is also confirmed by results from reaction monitoring of the acylation step under catalytic conditions, indicating that this finding is true regardless of whether the investigation is performed on the acetylated species or on the free catalyst. To arrive at these conclusions, the self-association of both the catalyst and the substrate in toluene was found to play an important role and thus needs to be taken into account in reaction screening.
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Affiliation(s)
- Jens Nowag
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Peter-Grünberg-Straße 16, D-64287 Darmstadt, Germany
| | - Matthias Brauser
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Peter-Grünberg-Straße 16, D-64287 Darmstadt, Germany
| | - Lisa Steuernagel
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Peter-Grünberg-Straße 16, D-64287 Darmstadt, Germany
| | - Raffael C Wende
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Peter-Grünberg-Straße 16, D-64287 Darmstadt, Germany
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4
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Latreille PL, Rabanel JM, Le Goas M, Salimi S, Arlt J, Patten SA, Ramassamy C, Hildgen P, Martinez VA, Banquy X. In Situ Characterization of the Protein Corona of Nanoparticles In Vitro and In Vivo. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2203354. [PMID: 35901787 DOI: 10.1002/adma.202203354] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/23/2022] [Indexed: 06/15/2023]
Abstract
A new theoretical framework that enables the use of differential dynamic microscopy (DDM) in fluorescence imaging mode to quantify in situ protein adsorption onto nanoparticles (NP) while simultaneously monitoring for NP aggregation is proposed. This methodology is used to elucidate the thermodynamic and kinetic properties of the protein corona (PC) in vitro and in vivo. The results show that protein adsorption triggers particle aggregation over a wide concentration range and that the formed aggregate structures can be quantified using the proposed methodology. Protein affinity for polystyrene (PS) NPs is observed to be dependent on particle concentration. For complex protein mixtures, this methodology identifies that the PC composition changes with the dilution of serum proteins, demonstrating a Vroman effect never quantitatively assessed in situ on NPs. Finally, DDM allows monitoring of the evolution of the PC in vivo. This results show that the PC composition evolves significantly over time in zebrafish larvae, confirming the inherently dynamic nature of the PC. The performance of the developed methodology allows to obtain quantitative insights into nano-bio interactions in a vast array of physiologically relevant conditions that will serve to further improve the design of nanomedicine.
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Affiliation(s)
- Pierre-Luc Latreille
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Jean-Michel Rabanel
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
- INRS, Centre Armand Frappier Santé Biotechnologie, 531 Boul des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Marine Le Goas
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Sina Salimi
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Jochen Arlt
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Shunmoogum A Patten
- INRS, Centre Armand Frappier Santé Biotechnologie, 531 Boul des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Charles Ramassamy
- INRS, Centre Armand Frappier Santé Biotechnologie, 531 Boul des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Patrice Hildgen
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Vincent A Martinez
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Xavier Banquy
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
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5
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Tang B, Chong K, Massefski W, Evans R. Quantitative Interpretation of Protein Diffusion Coefficients in Mixed Protiated-Deuteriated Aqueous Solvents. J Phys Chem B 2022; 126:5887-5895. [PMID: 35917500 PMCID: PMC9376945 DOI: 10.1021/acs.jpcb.2c03554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Diffusion-ordered nuclear magnetic resonance (NMR) spectroscopy
is widely used for the analysis of mixtures, dispersing the signals
of different species in a two-dimensional spectrum according to their
diffusion coefficients. However, interpretation of these diffusion
coefficients is typically purely qualitative, for example, to deduce
which species are bigger or smaller. In studies of proteins in solution,
important questions concern the molecular weight of the proteins,
the presence or absence of aggregation, and the degree of folding.
The Stokes–Einstein Gierer–Wirtz estimation (SEGWE)
method has been previously developed to simplify the complex relationship
between diffusion coefficient and molecular mass, allowing the prediction
of a species’ diffusion coefficient in a pure solvent based
on its molecular weight. Here, we show that SEGWE can be extended
to successfully predict both peptide and protein diffusion coefficients
in mixed protiated–deuteriated water samples and, hence, distinguish
effectively between globular and disordered proteins.
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Affiliation(s)
- Bridget Tang
- Aston Institute of Materials Research, Aston University, Birmingham B4 7ET, U.K
| | - Katie Chong
- Energy and Bioproducts Research Institute (EBRI), Aston University, Birmingham B4 7ET, U.K
| | - Walter Massefski
- Department of Chemistry Instrumentation Facility, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Robert Evans
- Aston Institute of Materials Research, Aston University, Birmingham B4 7ET, U.K
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6
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Długosz M, Cichocki B, Szymczak P. Estimating near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules. Phys Rev E 2022; 106:014407. [PMID: 35974550 DOI: 10.1103/physreve.106.014407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
We developed a computationally efficient approach to approximate near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules. The proposed method relies on extremum principles for Stokes flows produced by the motion of rigid bodies. In the presence of the wall, the rate of energy dissipation is decreased relative to the unbounded fluid. In our approach, the position- and orientation-dependent mobility matrix of a body suspended near a no-slip plane is calculated numerically using a coarse-grained molecular model and the Rotne-Prager-Yamakawa description of hydrodynamics. Effects of the boundary are accounted for via Blake's image construction. The matrix components are scaled using ratios of the corresponding bulk values evaluated for the detailed representation of the molecule and its coarse-grained model, leading to accurate values of the near-wall diffusion coefficients. We assess the performance of the approach for two biomolecules at different levels of coarse-graining.
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Affiliation(s)
- Maciej Długosz
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
| | - Bogdan Cichocki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
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7
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Fillbrook LL, Nothling MD, Stenzel MH, Price WS, Beves JE. Rapid Online Analysis of Photopolymerization Kinetics and Molecular Weight Using Diffusion NMR. ACS Macro Lett 2022; 11:166-172. [PMID: 35574764 DOI: 10.1021/acsmacrolett.1c00719] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Online, high-throughput molecular weight analysis of polymerizations is rare, with most studies relying on tedious sampling techniques and batchwise postanalysis. The ability to track both monomer conversion and molecular weight evolution in real time could underpin precision polymer development and facilitate study of rapid polymerization reactions. Here, we use a single time-resolved diffusion nuclear magnetic resonance (NMR) experiment to simultaneously study the kinetics and molecular weight evolution during a photopolymerization, with in situ irradiation inside the NMR instrument. As a model system, we used a photoinduced electron transfer reversible addition-fragmentation chain transfer (PET-RAFT) polymerization. The data allow diffusion coefficients and intensities to be calculated every 14 s from which the polymer size and monomer conversion can be extracted. Key to this approach is (1) the use of shuffled gradient amplitudes in the diffusion NMR experiment to access reactions of any rate, (2) the addition of a relaxation agent to increase achievable time resolution and, (3) a sliding correction that accounts for viscosity changes during polymerization. Diffusion NMR offers a uniquely simple, translatable handle for online monitoring of polymerization reactions.
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Affiliation(s)
| | | | | | - William S. Price
- Nanoscale Group, School of Science, Western Sydney University, Penrith, NSW 2751, Australia
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8
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Ranjan R, Tiwari N, Kayastha AM, Sinha N. Biophysical Investigation of the Interplay between the Conformational Species of Domain-Swapped GB1 Amyloid Mutant through Real-Time Monitoring of Amyloid Fibrillation. ACS OMEGA 2021; 6:34359-34366. [PMID: 34963921 PMCID: PMC8697013 DOI: 10.1021/acsomega.1c04223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Mutant polypeptide GB1HS#124F26A, which is known to aggregate into amyloid-like fibrils, has been utilized as a model in this study for gaining insights into the mechanism of domain-swapped aggregation through real-time monitoring. Size exclusion with UV monitoring at 280 nm and dynamic light scattering (DLS) profiles through different time points of fibrillation reveal that the dimer transitions into monomeric intermediates during the aggregation, which could further facilitate domain swapping to form amyloid fibrils. The 1D 1H and 2D 1H-13C HSQC nuclear magnetic resonance (NMR) spectra profiling through different time points of fibrillation reveal that there may be some other species present along with the dimer during aggregation which contribute to different trends for the intensity of protons in the spectral peaks. Diffusion NMR reveals changes in the mobility of the dimeric species during the process of aggregation, indicating that the dimer gives rise to other lower molecular weight species midway during aggregation, which further add up to form the oligomers and amyloid fibrils successively. The present work is a preliminary study which explores the possibility of utilizing biophysical methods to gain atomistic level insights into the different stages of aggregation.
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Affiliation(s)
- Renuka Ranjan
- Centre
of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar
Pradesh
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh
| | - Nidhi Tiwari
- Centre
of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar
Pradesh
- Department
of Chemistry, Institute of Science, Banaras
Hindu University, Varanasi 221005, Uttar Pradesh
| | - Arvind M. Kayastha
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh
| | - Neeraj Sinha
- Centre
of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar
Pradesh
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9
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Roeven E, Scheres L, Smulders MM, Zuilhof H. Zwitterionic dendrimer – Polymer hybrid copolymers for self-assembling antifouling coatings. Eur Polym J 2021. [DOI: 10.1016/j.eurpolymj.2021.110578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Barišić D, Cindro N, Vidović N, Bregović N, Tomišić V. Protonation and anion-binding properties of aromatic sulfonylurea derivatives. RSC Adv 2021; 11:23992-24000. [PMID: 35479025 PMCID: PMC9039416 DOI: 10.1039/d1ra04738h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
In this work the anion-binding properties of three aromatic sulfonylurea derivatives in acetonitrile and dimethyl sulfoxide were explored by means of NMR titrations. It was found that the studied receptors effectively bind anions of low basicity (Cl-, Br-, I-, NO3 - and HSO4 -). The stoichiometry of the complexes with receptors containing one binding site was 1 : 1 exclusively, whereas in the case of the receptor containing two sulfonylurea groups 1 : 2 (receptor : anion) complexes were also detected in some cases. The presence of strongly basic anions (acetate and dihydrogen phosphate) led to the deprotonation of the sulfonylurea moiety. This completely hindered its anion-binding properties in DMSO and only proton transfer occurred upon the addition of basic anions to the studied receptors. In MeCN, a complex system of equilibria including both ligand deprotonation and anion binding was established. Since ionisation of receptors was proven to be a decisive factor defining the behaviour of the sulfonylurea receptors, their pK a values were determined using several deprotonation agents in both solvents. The results were interpreted in the context of receptor structures and solvent properties and applied for the identification of the interactions with basic anions.
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Affiliation(s)
- D Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102/A 10000 Zagreb Croatia .,Division of Physical Chemistry, Ruđer Bošković Institute Bijenička cesta 54 10000 Zagreb Croatia
| | - N Cindro
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102/A 10000 Zagreb Croatia
| | - N Vidović
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102/A 10000 Zagreb Croatia .,Institute of Agriculture and Tourism K. Huguesa 8 52440 Poreč Croatia
| | - N Bregović
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102/A 10000 Zagreb Croatia
| | - V Tomišić
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102/A 10000 Zagreb Croatia
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11
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Markiewicz R, Klimaszyk A, Jarek M, Taube M, Florczak P, Kempka M, Fojud Z, Jurga S. Influence of Alkyl Chain Length on Thermal Properties, Structure, and Self-Diffusion Coefficients of Alkyltriethylammonium-Based Ionic Liquids. Int J Mol Sci 2021; 22:5935. [PMID: 34073046 PMCID: PMC8198313 DOI: 10.3390/ijms22115935] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
The application of ionic liquids (ILs) has grown enormously, from their use as simple solvents, catalysts, media in separation science, or electrolytes to that as task-specific, tunable molecular machines with appropriate properties. A thorough understanding of these properties and structure-property relationships is needed to fully exploit their potential, open new directions in IL-based research and, finally, properly implement the appropriate applications. In this work, we investigated the structure-properties relationships of a series of alkyltriethylammonium bis(trifluoromethanesulfonyl)imide [TEA-R][TFSI] ionic liquids in relation to their thermal behavior, structure organization, and self-diffusion coefficients in the bulk state using DSC, FT-IR, SAXS, and NMR diffusometry techniques. The phase transition temperatures were determined, indicating alkyl chain dependency. Fourier-transformed infrared spectroscopy studies revealed the structuration of the ionic liquids along with alkyl chain elongation. SAXS experiments clearly demonstrated the existence of polar/non-polar domains. The alkyl chain length influenced the expansion of the non-polar domains, leading to the expansion between cation heads in polar regions of the structured IL. 1H NMR self-diffusion coefficients indicated that alkyl chain elongation generally caused the lowering of the self-diffusion coefficients. Moreover, we show that the diffusion of anions and cations of ILs is similar, even though they vary in their size.
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Affiliation(s)
- Roksana Markiewicz
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej str. 3, 61-614 Poznań, Poland; (M.J.); (P.F.); (M.K.); (S.J.)
| | - Adam Klimaszyk
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej str. 3, 61-614 Poznań, Poland; (M.J.); (P.F.); (M.K.); (S.J.)
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego str. 2, 61-614 Poznań, Poland; (M.T.); (Z.F.)
| | - Marcin Jarek
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej str. 3, 61-614 Poznań, Poland; (M.J.); (P.F.); (M.K.); (S.J.)
| | - Michał Taube
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego str. 2, 61-614 Poznań, Poland; (M.T.); (Z.F.)
| | - Patryk Florczak
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej str. 3, 61-614 Poznań, Poland; (M.J.); (P.F.); (M.K.); (S.J.)
| | - Marek Kempka
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej str. 3, 61-614 Poznań, Poland; (M.J.); (P.F.); (M.K.); (S.J.)
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego str. 2, 61-614 Poznań, Poland; (M.T.); (Z.F.)
| | - Zbigniew Fojud
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego str. 2, 61-614 Poznań, Poland; (M.T.); (Z.F.)
| | - Stefan Jurga
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej str. 3, 61-614 Poznań, Poland; (M.J.); (P.F.); (M.K.); (S.J.)
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12
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Young P, Mills T, Norton I. Influence of pH on fluid gels produced from egg and whey protein isolate. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Kusova AM, Sitnitsky AE, Zuev YF. Impact of intermolecular attraction and repulsion on molecular diffusion and virial coefficients of spheroidal and rod-shaped proteins. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Kirk KA, Vasilescu A, Andreescu D, Senarathna D, Mondal S, Andreescu S. Collision-Based Electrochemical Detection of Lysozyme Aggregation. Anal Chem 2021; 93:2026-2037. [PMID: 33416307 DOI: 10.1021/acs.analchem.0c03578] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proteins are utilized across many biomedical and pharmaceutical industries; therefore, methods for rapid and accurate monitoring of protein aggregation are needed to ensure proper product quality. Although these processes have been previously studied, it is difficult to comprehensively evaluate protein folding and aggregation by traditional characterization techniques such as atomic force microscopy (AFM), electron microscopy, or X-ray diffraction, which require sample pre-treatment and do not represent native state proteins in solution. Herein, we report early tracking of lysozyme (Lyz) aggregation states by using single-particle collision electrochemistry (SPCE) of silver nanoparticle (AgNP) redox probes. The method relies on monitoring the rapid interaction of Lyz with AgNPs, which decreases the number of single AgNPs available for collisions and ultimately the frequency of oxidative impacts in the chronoamperometric profile. When Lyz is in a non-aggregated monomeric form, the protein forms a homogeneous coverage onto the surface of AgNPs, stabilizing the particles. When Lyz is aggregated, part of the AgNP surface remains uncoated, promoting the agglomeration of Lyz-AgNP conjugates. The frequency of AgNP impacts decreases with increasing aggregation time, providing a metric to track protein aggregation. Visualizations of integrated oxidation charge-transfer data displayed significant differences between the charge transfer per impact for AgNP samples alone and in the presence of non-aggregated and aggregated Lyz with 99% confidence using parametric ANOVA tests. Electrochemical results revealed meaningful associations with UV-vis, circular dichroism, and AFM, demonstrating that SPCE can be used as an alternative method for studying protein aggregation. This electrochemical technique could serve as a powerful tool to indirectly evaluate protein stability and screen protein samples for formation of aggregates.
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Affiliation(s)
- Kevin A Kirk
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699-5810, United States
| | - Alina Vasilescu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, Sector 6, 060101 Bucharest, Romania
| | - Daniel Andreescu
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699-5810, United States
| | - Dinushani Senarathna
- Department of Mathematics, Clarkson University, Potsdam, New York 13699-5810, United States
| | - Sumona Mondal
- Department of Mathematics, Clarkson University, Potsdam, New York 13699-5810, United States
| | - Silvana Andreescu
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699-5810, United States
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15
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Ghosh R, Raveendranath R, Kishore N. Unraveling diverse action of triton X-100 and methimazole on lysozyme fibrillation/aggregation: Physicochemical insights. Int J Biol Macromol 2020; 167:736-745. [PMID: 33278448 DOI: 10.1016/j.ijbiomac.2020.11.210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/19/2020] [Accepted: 11/30/2020] [Indexed: 01/18/2023]
Abstract
Identification of functionalities responsible for prevention of fibrillation in proteins is important to design effective drugs in addressing neurodegenerative diseases. We have used nonionic surfactant triton X-100 (TX-100) and antithyroid drug methimazole (MMI) to understand mechanistic aspects of action of these molecules having different functionalities on hen egg-white lysozyme at different stages of fibrillation. After establishing the nucleation, elongation and maturation stages of fibrillation of protein at 57 °C, energetics of interactions with these molecules have been determined by using isothermal titration calorimetry. Differential scanning calorimetry has permitted assessment of thermal stability of the protein at these stages, with or without these molecular entities. The enthalpies of interaction of TX-100 and MMI with protein fibrils suggest importance of hydrogen bonding and polar interactions in their effectiveness towards prevention of fibrils. TX-100, in spite of several polar centres, is unable to prevent fibrillation, rather it promotes. MMI is able to establish polar interactions with interacting strands of the protein and disintegrate fibrils. A rigorous comparison with inhibitors reported in literature highlights importance -OH and >CO functionalities in fibrillation prevention. Even though MMI has hydrogen bonding centres, its efficiency as inhibitor falls after the inhibited lysozyme fibrils further interact and form amorphous aggregates.
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Affiliation(s)
- Ritutama Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Revathy Raveendranath
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India.
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16
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Temperature dependent aggregation mechanism and pathway of lysozyme: By all atom and coarse grained molecular dynamics simulation. J Mol Graph Model 2020; 103:107816. [PMID: 33291026 DOI: 10.1016/j.jmgm.2020.107816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 11/21/2022]
Abstract
Aggregation of protein causes various diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. It was found that aggregation of protein depends on many factors like temperature, pH, salt type, salt concentration, ionic strength, protein concentration, co solutes. Here we have tried to capture the aggregation mechanism and pathway of hen egg white lysozyme using molecular dynamics simulations at two different temperatures; 300 K and 340 K. Along with the all atom simulations to get the atomistic details of aggregation mechanism, we have used coarse grained simulation with MARTINI force field to monitor the aggregation for longer duration. Our results suggest that due to the aggregation, changes in the conformation of lysozyme are more at 340 K than at 300 K. The change in the conformation of the lysozyme at 300 K is mainly due to aggregation where at 340 K change in conformation of lysozyme is due to both aggregation and temperature. Also, a more compact aggregated system is formed at 340 K.
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17
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MacDonald TC, Feringa BL, Price WS, Wezenberg SJ, Beves JE. Controlled Diffusion of Photoswitchable Receptors by Binding Anti-electrostatic Hydrogen-Bonded Phosphate Oligomers. J Am Chem Soc 2020; 142:20014-20020. [PMID: 33180496 PMCID: PMC7735709 DOI: 10.1021/jacs.0c09072] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 12/12/2022]
Abstract
Dihydrogen phosphate anions are found to spontaneously associate into anti-electrostatic oligomers via hydrogen bonding interactions at millimolar concentrations in DMSO. Diffusion NMR measurements supported formation of these oligomers, which can be bound by photoswitchable anion receptors to form large bridged assemblies of approximately three times the volume of the unbound receptor. Photoisomerization of the oligomer-bound receptor causes a decrease in diffusion coefficient of up to 16%, corresponding to a 70% increase in effective volume. This new approach to external control of diffusion opens prospects in controlling molecular transport using light.
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Affiliation(s)
| | - Ben L. Feringa
- Stratingh Institute for Chemistry, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - William S. Price
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Sander J. Wezenberg
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Jonathon E. Beves
- School of Chemistry, University of New South Wales Sydney, NSW 2052, Australia
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18
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Keiffer S, Carneiro MG, Hollander J, Kobayashi M, Pogoryelev D, Ab E, Theisgen S, Müller G, Siegal G. NMR in target driven drug discovery: why not? JOURNAL OF BIOMOLECULAR NMR 2020; 74:521-529. [PMID: 32901320 PMCID: PMC7683447 DOI: 10.1007/s10858-020-00343-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/17/2020] [Indexed: 05/09/2023]
Abstract
No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophysical binding assays such as TR-FRET, SPR, thermophoresis and many others. Each method has its strengths and weaknesses, but none is as information rich and broadly applicable as NMR. Here we provide a number of examples of the utility of NMR for enabling and providing ongoing support for the early pre-clinical phase of small molecule drug discovery efforts. The examples have been selected for their usefulness in a commercial setting, with full understanding of the need for speed, cost-effectiveness and ease of implementation.
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Affiliation(s)
| | | | | | | | | | - Eiso Ab
- ZoBio, JH Oortweg 19, 2333CH, Leiden, Netherlands
| | | | - Gerhard Müller
- Gotham GmbH, Am Klopferspitz 19a, 82152, Martinsried, Germany
| | - Gregg Siegal
- ZoBio, JH Oortweg 19, 2333CH, Leiden, Netherlands.
- Amsterdam Institute of Molecular and Life Sciences, Free University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
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19
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Roeven E, Kuzmyn AR, Scheres L, Baggerman J, Smulders MMJ, Zuilhof H. PLL-Poly(HPMA) Bottlebrush-Based Antifouling Coatings: Three Grafting Routes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10187-10199. [PMID: 32820926 PMCID: PMC7498161 DOI: 10.1021/acs.langmuir.0c01675] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/30/2020] [Indexed: 06/11/2023]
Abstract
In this work, we compare three routes to prepare antifouling coatings that consist of poly(l-lysine)-poly(N-(2-hydroxypropyl)methacrylamide) bottlebrushes. The poly(l-lysine) (PLL) backbone is self-assembled onto the surface by charged-based interactions between the lysine groups and the negatively charged silicon oxide surface, whereas the poly(N-(2-hydroxypropyl)methacrylamide) [poly(HPMA)] side chains, grown by reversible addition-fragmentation chain-transfer (RAFT) polymerization, provide antifouling properties to the surface. First, the PLL-poly(HPMA) coatings are synthesized in a bottom-up fashion through a grafting-from approach. In this route, the PLL is self-assembled onto a surface, after which a polymerization agent is immobilized, and finally HPMA is polymerized from the surface. In the second explored route, the PLL is modified in solution by a RAFT agent to create a macroinitiator. After self-assembly of this macroinitiator onto the surface, poly(HPMA) is polymerized from the surface by RAFT. In the third and last route, the whole PLL-poly(HPMA) bottlebrush is initially synthesized in solution. To this end, HPMA is polymerized from the macroinitiator in solution and the PLL-poly(HPMA) bottlebrush is then self-assembled onto the surface in just one step (grafting-to approach). Additionally, in this third route, we also design and synthesize a bottlebrush polymer with a PLL backbone and poly(HPMA) side chains, with the latter containing 5% carboxybetaine (CB) monomers that eventually allow for additional (bio)functionalization in solution or after surface immobilization. These three routes are evaluated in terms of ease of synthesis, scalability, ease of characterization, and a preliminary investigation of their antifouling performance. All three coating procedures result in coatings that show antifouling properties in single-protein antifouling tests. This method thus presents a new, simple, versatile, and highly scalable approach for the manufacturing of PLL-based bottlebrush coatings that can be synthesized partly or completely on the surface or in solution, depending on the desired production process and/or application.
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Affiliation(s)
- Esther Roeven
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Surfix
BV, Bronland 12 B-1, 6708 WH Wageningen, The Netherlands
| | - Andriy R. Kuzmyn
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Aquamarijn
Micro Filtration BV, IJsselkade 7, 7201 HB Zutphen, The Netherlands
| | - Luc Scheres
- Surfix
BV, Bronland 12 B-1, 6708 WH Wageningen, The Netherlands
| | - Jacob Baggerman
- Aquamarijn
Micro Filtration BV, IJsselkade 7, 7201 HB Zutphen, The Netherlands
| | - Maarten M. J. Smulders
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- School
of Pharmaceutical Sciences and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, People’s Republic of China
- Department
of Chemical and Materials Engineering, King
Abdulaziz University, 21589 Jeddah, Saudi Arabia
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20
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Richter Ł, Albrycht P, Księżopolska-Gocalska M, Poboży E, Bachliński R, Sashuk V, Paczesny J, Hołyst R. Fast and efficient deposition of broad range of analytes on substrates for surface enhanced Raman spectroscopy. Biosens Bioelectron 2020; 156:112124. [DOI: 10.1016/j.bios.2020.112124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/18/2020] [Accepted: 02/22/2020] [Indexed: 12/14/2022]
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21
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Silva NHCS, Figueira P, Fabre E, Pinto RJB, Pereira ME, Silvestre AJD, Marrucho IM, Vilela C, Freire CSR. Dual nanofibrillar-based bio-sorbent films composed of nanocellulose and lysozyme nanofibrils for mercury removal from spring waters. Carbohydr Polym 2020; 238:116210. [PMID: 32299563 DOI: 10.1016/j.carbpol.2020.116210] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 01/01/2023]
Abstract
The present study explores the preparation of dual nanofibrillar-based bio-sorbent films composed of cellulose nanofibrils (CNFs) and lysozyme nanofibrils (LNFs) for application in the removal of Hg(II) from aqueous solutions. The free-standing films were fabricated via simple vacuum filtration of water suspensions of CNFs and LNFs and disclose good mechanical and thermal properties. The Hg(II) removal efficiency was evaluated by atomic fluorescence spectroscopy in ultra-pure and natural spring waters contaminated with environmental realistic levels of mercury (50 μg L-1). The removal efficiency is pH-dependent reaching a maximum of 99 % after 24 h at a pH value close to the isoelectric point of the protein. Under the experimental conditions, the sorption kinetics are well described by the pseudo-second-order and Elovich models, suggesting a chemisorption mechanism. These results demonstrate the ability of the dual nanofibrillar-based films to remove Hg(II) from water samples reaching a residual concentration lower than the guideline value for water intended for human consumption (1 μg L-1). Therefore, the CNFs/LNFs bio-sorbents might be a solution to treat low-concentrated mercury-contaminated waters.
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Affiliation(s)
- Nuno H C S Silva
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Paula Figueira
- CESAM and LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal
| | - Elaine Fabre
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; CESAM and LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Ricardo J B Pinto
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Maria Eduarda Pereira
- CESAM and LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Armando J D Silvestre
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Isabel M Marrucho
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Carla Vilela
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carmen S R Freire
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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22
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Ramanujam V, Alderson TR, Pritišanac I, Ying J, Bax A. Protein structural changes characterized by high-pressure, pulsed field gradient diffusion NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 312:106701. [PMID: 32113145 PMCID: PMC7153785 DOI: 10.1016/j.jmr.2020.106701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Pulsed-field gradient NMR spectroscopy is widely used to measure the translational diffusion and hydrodynamic radius (Rh) of biomolecules in solution. For unfolded proteins, the Rh provides a sensitive reporter on the ensemble-averaged conformation and the extent of polypeptide chain expansion as a function of added denaturant. Hydrostatic pressure is a convenient and reversible alternative to chemical denaturants for the study of protein folding, and enables NMR measurements to be performed on a single sample. While the impact of pressure on the viscosity of water is well known, and our water diffusivity measurements agree closely with theoretical expectations, we find that elevated pressures increase the Rh of dioxane and other small molecules by amounts that correlate with their hydrophobicity, with parallel increases in rotational friction indicated by 13C longitudinal relaxation times. These data point to a tighter coupling with water for hydrophobic surfaces at elevated pressures. Translational diffusion measurement of the unfolded state of a pressure-sensitized ubiquitin mutant (VA2-ubiquitin) as a function of hydrostatic pressure or urea concentration shows that Rh values of both the folded and the unfolded states remain nearly invariant. At ca 23 Å, the Rh of the fully pressure-denatured state is essentially indistinguishable from the urea-denatured state, and close to the value expected for an idealized random coil of 76 residues. The intrinsically disordered protein (IDP) α-synuclein shows slight compaction at pressures above 2 kbar. Diffusion of unfolded ubiquitin and α-synuclein is significantly impacted by sample concentration, indicating that quantitative measurements need to be carried out under dilute conditions.
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Affiliation(s)
- Venkatraman Ramanujam
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - T Reid Alderson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Iva Pritišanac
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany.
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23
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Stradner A, Schurtenberger P. Potential and limits of a colloid approach to protein solutions. SOFT MATTER 2020; 16:307-323. [PMID: 31830196 DOI: 10.1039/c9sm01953g] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Looking at globular proteins with the eyes of a colloid scientist has a long tradition, in fact a significant part of the early colloid literature was focused on protein solutions. However, it has also been recognized that proteins are much more complex than the typical hard sphere-like synthetic model colloids. Proteins are not perfect spheres, their interaction potentials are in general not isotropic, and using theories developed for such particles are thus clearly inadequate in many cases. In this perspective article, we now take a closer look at the field. In particular, we reflect on the fact that modern colloid science has been undergoing a tremendous development, where a multitude of novel systems have been developed in the lab and in silico. During the last decade we have seen a rapidly increasing number of reports on the synthesis of anisotropic, patchy and/or responsive synthetic colloids, that start to resemble their complex biological counterparts. This experimental development is also reflected in a corresponding theoretical and simulation effort. The experimental and theoretical toolbox of colloid science has thus rapidly expanded, and there is obviously an enormous potential for an application of these new concepts to protein solutions, which has already been realized and harvested in recent years. In this perspective article we make an attempt to critically discuss the exploitation of colloid science concepts to better understand protein solutions. We not only consider classical applications such as the attempt to understand and predict solution stability and phase behaviour, but also discuss new challenges related to the dynamics, flow behaviour and liquid-solid transitions found in concentrated or crowded protein solutions. It not only aims to provide an overview on the progress in experimental and theoretical (bio)colloid science, but also discusses current shortcomings in our ability to correctly reproduce and predict the structural and dynamic properties of protein solutions based on such a colloid approach.
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Affiliation(s)
- Anna Stradner
- Division of Physical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-221 00 Lund, Sweden.
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24
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Probst C. Characterization of Protein Aggregates, Silicone Oil Droplets, and Protein-Silicone Interactions Using Imaging Flow Cytometry. J Pharm Sci 2020; 109:364-374. [DOI: 10.1016/j.xphs.2019.05.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/10/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
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25
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Lysozyme encapsulated gold nanoclusters for probing the early stage of lysozyme aggregation under acidic conditions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 197:111540. [DOI: 10.1016/j.jphotobiol.2019.111540] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 06/02/2019] [Accepted: 06/21/2019] [Indexed: 12/22/2022]
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26
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Kadam R, Maas M, Rezwan K. Selective, Agglomerate-Free Separation of Bacteria Using Biofunctionalized, Magnetic Janus Nanoparticles. ACS APPLIED BIO MATERIALS 2019; 2:3520-3531. [DOI: 10.1021/acsabm.9b00415] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Reshma Kadam
- Advanced Ceramics, University of Bremen, Am Biologischen Garten 2, 28359 Bremen, Germany
| | - Michael Maas
- Advanced Ceramics, University of Bremen, Am Biologischen Garten 2, 28359 Bremen, Germany
- MAPEX Centre of Materials and Processes, University of Bremen, 28359 Bremen, Germany
| | - Kurosch Rezwan
- Advanced Ceramics, University of Bremen, Am Biologischen Garten 2, 28359 Bremen, Germany
- MAPEX Centre of Materials and Processes, University of Bremen, 28359 Bremen, Germany
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27
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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28
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Golubev VA, Gurina DL. The self-diffusion of parabens (methyl-, propylparaben) and tetramethylsilane in the binary solvent carbon tetrachloride – Co-solvent (methanol‑d4, acetone‑d6) at 278, 298 and 318 K. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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von Bülow S, Siggel M, Linke M, Hummer G. Dynamic cluster formation determines viscosity and diffusion in dense protein solutions. Proc Natl Acad Sci U S A 2019; 116:9843-9852. [PMID: 31036655 PMCID: PMC6525548 DOI: 10.1073/pnas.1817564116] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We develop a detailed description of protein translational and rotational diffusion in concentrated solution on the basis of all-atom molecular dynamics simulations in explicit solvent. Our systems contain up to 540 fully flexible proteins with 3.6 million atoms. In concentrated protein solutions (100 mg/mL and higher), the proteins ubiquitin and lysozyme, as well as the protein domains third IgG-binding domain of protein G and villin headpiece, diffuse not as isolated particles, but as members of transient clusters between which they constantly exchange. A dynamic cluster model nearly quantitatively explains the increase in viscosity and the decrease in protein diffusivity with protein volume fraction, which both exceed the predictions from widely used colloid models. The Stokes-Einstein relations for translational and rotational diffusion remain valid, but the effective hydrodynamic radius grows linearly with protein volume fraction. This increase follows the observed increase in cluster size and explains the more dramatic slowdown of protein rotation compared with translation. Baxter's sticky-sphere model of colloidal suspensions captures the concentration dependence of cluster size, viscosity, and rotational and translational diffusion. The consistency between simulations and experiments for a diverse set of soluble globular proteins indicates that the cluster model applies broadly to concentrated protein solutions, with equilibrium dissociation constants for nonspecific protein-protein binding in the Kd ≈ 10-mM regime.
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Affiliation(s)
- Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Marc Siggel
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Max Linke
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany;
- Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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30
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Ferreira J, Castro F, Rocha F, Kuhn S. Protein crystallization in a droplet-based microfluidic device: Hydrodynamic analysis and study of the phase behaviour. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2018.06.066] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Li Y, Koopal LK, Xiong J, Wang M, Yang C, Tan W. Influence of humic acid on transport, deposition and activity of lysozyme in quartz sand. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:298-306. [PMID: 29990937 DOI: 10.1016/j.envpol.2018.06.096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/24/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
Interaction with natural organic matter (NOM) is hypothesized to impact the fate and bioavailability of enzymes and some hazardous proteins in terrestrial and aquatic environments. By using saturated column transport experiments the transport and deposition of the model enzyme lysozyme (LSZ), in the absence and presence of purified Aldrich humic acid (PAHA), was investigated at a series of mass ratios PAHA/LSZ at pH 5 and 8 and two ionic strength values (0.5 mM and 50 mM KCl solution). PAHA decreased LSZ transport under all conditions. The shapes of breakthrough curves (BTCs) and retention profiles (RPs) during cotransport of both colloids evolved from symmetrical to blocking with time and from flat to hyper-exponential with depth, respectively, in response to increases in mass ratio PAHA/LSZ. The results indicated that the "size-selective retention" and concurrent homo- and hetero-aggregation induced straining, which resulted in preferential retention of relatively large PAHA-LSZ aggregates in the column and elution of relatively small ones. Due to differences in aggregate size, in general, the enzyme activity of LSZ in the effluent was larger and that of the retained LSZ was smaller than that of the influent. Therefore, protein transport process could partially increase the enzyme activity and bring potential environmental hazards.
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Affiliation(s)
- Yan Li
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Luuk K Koopal
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China; Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Juan Xiong
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mingxia Wang
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Chenfeng Yang
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wenfeng Tan
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China.
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Wawer J, Szociński M, Olszewski M, Piątek R, Naczk M, Krakowiak J. Influence of the ionic strength on the amyloid fibrillogenesis of hen egg white lysozyme. Int J Biol Macromol 2018; 121:63-70. [PMID: 30290259 DOI: 10.1016/j.ijbiomac.2018.09.165] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/17/2018] [Accepted: 09/25/2018] [Indexed: 10/28/2022]
Abstract
The study investigates the role of the electrostatic interactions in the fibrillation of the hen egg white lysozyme (HEWL). In order to achieve this aim the influence of the cations Na+, Mg2+ and Al3+ on the amyloid fibril formation and amorphous aggregation was tested. The amyloids are formed in the solution without added salt but the Thioflavin T fluorescence gives the false-negative result. In these conditions, the HEWL fibrils are long and curvy. If the ionic strength of the solution is sufficiently high, the formed amyloids are shorter and fragmented. Our study shows that the addition of the aluminium salt promotes protein fibrillation. The amorphous aggregation dominates in the high concentration of electrolyte. The in vitro amyloid fibril formation seems to be regulated by universal mechanisms. The theories implemented in the polymer science or for colloidal solutions give the qualitative description of the aggregation phenomena. However, the specific interactions and the additional effects (e.g. fibril fragmentation) modulate the amyloidogenesis.
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Affiliation(s)
- Jarosław Wawer
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland.
| | - Michał Szociński
- Department of Electrochemistry, Corrosion and Materials Engineering, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland
| | - Marcin Olszewski
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland
| | - Rafał Piątek
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland
| | - Mateusz Naczk
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland
| | - Joanna Krakowiak
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland
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33
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Golubev VA. 1H NMR study of self-diffusion and molecular association of caffeine, theophylline and theobromine in the binary solvent methanol‑d4–carbon tetrachloride. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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34
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Greenland KN, Carvajal MFCA, Preston JM, Ekblad S, Dean WL, Chiang JY, Koder RL, Wittebort RJ. Order, Disorder, and Temperature-Driven Compaction in a Designed Elastin Protein. J Phys Chem B 2018; 122:2725-2736. [PMID: 29461832 DOI: 10.1021/acs.jpcb.7b11596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Artificial minielastin constructs have been designed that replicate the structure and function of natural elastins in a simpler context, allowing the NMR observation of structure and dynamics of elastin-like proteins with complete residue-specific resolution. We find that the alanine-rich cross-linking domains of elastin have a partially helical structure, but only when capped by proline-rich hydrophobic domains. We also find that the hydrophobic domains, composed of prominent 6-residue repeats VPGVGG and APGVGV found in natural elastins, appear random coil by both NMR chemical shift analysis and circular dichroism. However, these elastin hydrophobic domains exhibit structural bias for a dynamically disordered conformation that is neither helical nor β sheet with a degree of nonrandom structural bias which is dependent on residue type and position in the sequence. Another nonrandom-coil aspect of hydrophobic domain structure lies in the fact that, in contrast to other intrinsically disordered proteins, these hydrophobic domains retain a relatively condensed conformation whether attached to cross-linking domains or not. Importantly, these domains and the proteins containing them constrict with increasing temperature by up to 30% in volume without becoming more ordered. This property is often observed in nonbiological polymers and suggests that temperature-driven constriction is a new type of protein structural change that is linked to elastin's biological functions of coacervation-driven assembly and elastic recoil.
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Affiliation(s)
- Kelly N Greenland
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | | | - Jonathan M Preston
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | - Siri Ekblad
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | - William L Dean
- Department of Biochemistry and Molecular Genetics and the James Brown Cancer Center , University of Louisville School of Medicine , Louisville , Kentucky 40292 , United States
| | - Jeff Y Chiang
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | - Ronald L Koder
- Department of Physics , The City College of New York , New York , New York 10031 , United States.,Graduate Programs of Physics, Chemistry and Biochemistry , The Graduate Center of CUNY , New York , New York 10016 , United States
| | - Richard J Wittebort
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
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35
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Golubev VA, Kumeev RS, Gurina DL, Nikiforov MY, Alper GA, Durov VA. Self-diffusion of caffeine and methanol in ternary mixtures caffeine–methanol–carbon tetrachloride at temperatures of 298 and 313 K. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.06.102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Huang R, Brady JP, Sekhar A, Yuwen T, Kay LE. An enhanced sensitivity methyl 1H triple-quantum pulse scheme for measuring diffusion constants of macromolecules. JOURNAL OF BIOMOLECULAR NMR 2017; 68:249-255. [PMID: 28717997 DOI: 10.1007/s10858-017-0122-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
We present a pulse scheme that exploits methyl 1H triple-quantum (TQ) coherences for the measurement of diffusion rates of slowly diffusing molecules in solution. It is based on the well-known stimulated echo experiment, with encoding and decoding of TQ coherences. The size of quantifiable diffusion coefficients is thus lowered by an order of magnitude with respect to single-quantum (SQ) approaches. Notably, the sensitivity of the scheme is high, approximately ¾ that of the corresponding single quantum experiment, neglecting relaxation losses, and on the order of a factor of 4 more sensitive than a previously published sequence for AX3 spin systems (Zheng et al. in JMR 198:271-274, 2009) for molecules that are only 13C labeled at the methyl carbon position. Diffusion coefficients measured from TQ- and SQ-based experiments recorded on a range of protein samples are in excellent agreement. We present an application of this technique to the study of phase-separated proteins where protein concentrations in the condensed phase can exceed 400 mg/mL, diffusion coefficients can be as low as ~10-9 cm2s-1 and traditional SQ experiments fail.
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Affiliation(s)
- Rui Huang
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jacob P Brady
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Ashok Sekhar
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Tairan Yuwen
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- The Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada.
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37
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Challenges in Predicting Protein-Protein Interactions from Measurements of Molecular Diffusivity. Biophys J 2017; 111:1831-1842. [PMID: 27806265 DOI: 10.1016/j.bpj.2016.09.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/26/2016] [Accepted: 09/14/2016] [Indexed: 01/11/2023] Open
Abstract
Dynamic light scattering can be used to measure the diffusivity of a protein within a formulation. The dependence of molecular diffusivity on protein concentration (traditionally expressed in terms of the interaction parameter kD) is often used to infer whether protein-protein interactions are repulsive or attractive, resulting in solutions that are colloidally stable or unstable, respectively. However, a number of factors unrelated to intermolecular forces can also impact protein diffusion, complicating this interpretation. Here, we investigate the influence of multicomponent diffusion in a ternary protein-salt-water system on protein diffusion and kD in the context of Nernst-Planck theory. This analysis demonstrates that large changes in protein diffusivity with protein concentration can result even for hard-sphere systems in the absence of protein-protein interactions. In addition, we show that dynamic light scattering measurements of diffusivity made at low ionic strength cannot be reliably used to detect protein conformational changes. We recommend comparing experimentally determined kD values to theoretically predicted excluded-volume contributions, which will allow a more accurate assessment of protein-protein interactions.
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38
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Zubkov M, Dennis GR, Stait-Gardner T, Torres AM, Willis SA, Zheng G, Price WS. Physical characterization using diffusion NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:414-424. [PMID: 27657736 DOI: 10.1002/mrc.4530] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/16/2016] [Accepted: 09/19/2016] [Indexed: 06/06/2023]
Abstract
NMR diffusion measurements (or dNMR) provide a powerful tool for analysis of solution organization and microgeometry of the environment by probing random molecular motion. Being a very versatile method, dNMR can be applied to a large variety of samples and systems. Here, a brief introduction into dNMR and a summary of recent advances in the field are presented. The research topics include restricted diffusion, anisotropic diffusion, polymer dynamics, solution structuring and dNMR method development. The dNMR studied systems include plants, cells (cell models), liquid crystals, polymer solutions, ionic liquids, supercooled solutions, untreated water, amino acid solutions and more. It is demonstrated how a variety of dNMR methods can be applied to a system to extract the data on particular structures present among, formed by or surrounding the diffusing particles. It is also demonstrated how dNMR methods can be developed to allow probing larger geometries, low sample concentrations and faster processes. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Mikhail Zubkov
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Gary R Dennis
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Tim Stait-Gardner
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Allan M Torres
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Scott A Willis
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Gang Zheng
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - William S Price
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, Australia
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39
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Melnikova DL, Skirda VD, Nesmelova IV. Effect of Intrinsic Disorder and Self-Association on the Translational Diffusion of Proteins: The Case of α-Casein. J Phys Chem B 2017; 121:2980-2988. [PMID: 28346777 DOI: 10.1021/acs.jpcb.7b00772] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Translational diffusion is the major mode of macromolecular transport in leaving organisms, and therefore it is vital to many biological and biotechnological processes. Although translational diffusion of proteins has received considerable theoretical and experimental scrutiny, much of that attention has been directed toward the description of globular proteins. The translational diffusion of intrinsically disordered proteins (IDPs), however, is much less studied. Here, we use a pulsed-gradient nuclear magnetic resonance technique (PFG NMR) to investigate the translational diffusion of a disordered protein in a wide range of concentrations using α-casein that belongs to the class of natively disordered proteins as an example.
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Affiliation(s)
- Daria L Melnikova
- Department of Physics, Kazan Federal University , Kazan 420011, Russia
| | - Vladimir D Skirda
- Department of Physics, Kazan Federal University , Kazan 420011, Russia
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40
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41
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Ellery AJ, Baker RE, Simpson MJ. An analytical method for disentangling the roles of adhesion and crowding for random walk models on a crowded lattice. Phys Biol 2016; 13:05LT02. [PMID: 27597573 DOI: 10.1088/1478-3975/13/5/05lt02] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Migration of cells and molecules in vivo is affected by interactions with obstacles. These interactions can include crowding effects, as well as adhesion/repulsion between the motile cell/molecule and the obstacles. Here we present an analytical framework that can be used to separately quantify the roles of crowding and adhesion/repulsion using a lattice-based random walk model. Our method leads to an exact calculation of the long time Fickian diffusivity, and avoids the need for computationally expensive stochastic simulations.
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Affiliation(s)
- Adam J Ellery
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
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42
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Kheddo P, Cliff MJ, Uddin S, van der Walle CF, Golovanov AP. Characterizing monoclonal antibody formulations in arginine glutamate solutions using 1H NMR spectroscopy. MAbs 2016; 8:1245-1258. [PMID: 27589351 PMCID: PMC5058632 DOI: 10.1080/19420862.2016.1214786] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Assessing how excipients affect the self-association of monoclonal antibodies (mAbs) requires informative and direct in situ measurements for highly concentrated solutions, without sample dilution or perturbation. This study explores the application of solution nuclear magnetic resonance (NMR) spectroscopy for characterization of typical mAb behavior in formulations containing arginine glutamate. The data show that the analysis of signal intensities in 1D 1H NMR spectra, when compensated for changes in buffer viscosity, is invaluable for identifying conditions where protein-protein interactions are minimized. NMR-derived molecular translational diffusion rates for concentrated solutions are less useful than transverse relaxation rates as parameters defining optimal formulation. Furthermore, NMR reports on the solution viscosity and mAb aggregation during accelerated stability study assessment, generating data consistent with that acquired by size-exclusion chromatography. The methodology developed here offers NMR spectroscopy as a new tool providing complementary information useful to formulation development of mAbs and other large therapeutic proteins.
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Affiliation(s)
- Priscilla Kheddo
- a Manchester Institute of Biotechnology, University of Manchester , Manchester , UK.,b School of Chemistry, University of Manchester , Manchester , UK
| | - Matthew J Cliff
- a Manchester Institute of Biotechnology, University of Manchester , Manchester , UK
| | - Shahid Uddin
- c Formulation Sciences, MedImmune Ltd , Granta Park, Cambridge , UK
| | | | - Alexander P Golovanov
- a Manchester Institute of Biotechnology, University of Manchester , Manchester , UK.,b School of Chemistry, University of Manchester , Manchester , UK
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43
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Singh S, Demco DE, Rahimi K, Fechete R, Rodriguez-Cabello JC, Möller M. Aggregation behaviour of biohybrid microgels from elastin-like recombinamers. SOFT MATTER 2016; 12:6240-6252. [PMID: 27378252 DOI: 10.1039/c6sm00954a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Investigation of the aggregation behavior of biohybrid microgels, which can potentially be used as drug carriers, is an important topic, because aggregation not only causes loss of activity, but also toxicity and immunogenicity. To study this effect we synthesized microgels from elastin-like recombinamers (ELRs) using the miniemulsion technique. The existence of aggregation for such biohybrid microgels at different concentrations and temperatures was studied by different methods which include dynamic light scattering (DLS), (1)H high-resolution magic angle sample spinning (HRMAS) NMR spectroscopy, relaxometry and diffusometry. A hysteresis effect was detected in the process of aggregation by DLS as a function of temperature that strongly depends on ELR microgel concentration. The aggregation process was further quantitatively analyzed by the concentration dependence of the (1)H amino-acid residue chemical shifts and microgel diffusivity measured by NMR methods using the population balance kinetic aggregation model.
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Affiliation(s)
- Smriti Singh
- DWI-Leibniz-Institute for Interactive Materials, e.V., RWTH-Aachen University, Forckenbeckstraße 50, D-52074 Aachen, Germany.
| | - Dan Eugen Demco
- DWI-Leibniz-Institute for Interactive Materials, e.V., RWTH-Aachen University, Forckenbeckstraße 50, D-52074 Aachen, Germany. and Technical University of Cluj-Napoca, Department of Physics and Chemistry, 25 G. Baritiu Str., RO-400027, Cluj-Napoca, Romania
| | - Khosrow Rahimi
- DWI-Leibniz-Institute for Interactive Materials, e.V., RWTH-Aachen University, Forckenbeckstraße 50, D-52074 Aachen, Germany.
| | - Radu Fechete
- Technical University of Cluj-Napoca, Department of Physics and Chemistry, 25 G. Baritiu Str., RO-400027, Cluj-Napoca, Romania
| | | | - Martin Möller
- DWI-Leibniz-Institute for Interactive Materials, e.V., RWTH-Aachen University, Forckenbeckstraße 50, D-52074 Aachen, Germany.
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44
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Hopkins JB, Thorne RE. Quantifying radiation damage in biomolecular small-angle X-ray scattering. J Appl Crystallogr 2016; 49:880-890. [PMID: 27275138 PMCID: PMC4886981 DOI: 10.1107/s1600576716005136] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/25/2016] [Indexed: 11/10/2022] Open
Abstract
Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations of the technique, such as minimum required sample volume, and of experimental design, such as sample flow cells, are necessary because the biological samples are sensitive to damage from the X-rays. Radiation damage typically manifests as aggregation of the sample, which makes the collected data unreliable. However, there has been little systematic investigation of the most effective methods to reduce damage rates, and results from previous damage studies are not easily compared with results from other beamlines. Here a methodology is provided for quantifying radiation damage in SAXS to provide consistent results between different experiments, experimenters and beamlines. These methods are demonstrated on radiation damage data collected from lysozyme, glucose isomerase and xylanase, and it is found that no single metric is sufficient to describe radiation damage in SAXS for all samples. The radius of gyration, molecular weight and integrated SAXS profile intensity constitute a minimal set of parameters that capture all types of observed behavior. Radiation sensitivities derived from these parameters show a large protein dependence, varying by up to six orders of magnitude between the different proteins tested. This work should enable consistent reporting of radiation damage effects, allowing more systematic studies of the most effective minimization strategies.
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Affiliation(s)
| | - Robert E. Thorne
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
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45
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46
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Joshi PN, Purushottam L, Das NK, Mukherjee S, Rai V. Protein self-assembly induces promiscuous nucleophilic biocatalysis in Morita–Baylis–Hillman (MBH) reaction. RSC Adv 2016. [DOI: 10.1039/c5ra23949d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Self-assembled states of proteins render efficient promiscuous nucleophilic biocatalysis in MBH reaction in a green process.
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Affiliation(s)
- Pralhad N. Joshi
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER) Bhopal
- Bhopal
- India
| | - Landa Purushottam
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER) Bhopal
- Bhopal
- India
| | - Nirmal K. Das
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER) Bhopal
- Bhopal
- India
| | - Saptarshi Mukherjee
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER) Bhopal
- Bhopal
- India
| | - Vishal Rai
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER) Bhopal
- Bhopal
- India
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47
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Sutisna B, Polymeropoulos G, Mygiakis E, Musteata V, Peinemann KV, Smilgies DM, Hadjichristidis N, Nunes SP. Artificial membranes with selective nanochannels for protein transport. Polym Chem 2016. [DOI: 10.1039/c6py01401a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Membranes based on poly(styrene-b-4-hydroxystyrene-b-styrene) were prepared with nanochannels for preferential transport of proteins with molecular weight 14.3 kg mol−1 and rejection of neutral polyethylene glycol molecules with molecular size of 10 kg mol−1.
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Affiliation(s)
- B. Sutisna
- King Abdullah University of Science and Technology (KAUST)
- Physical Science and Engineering Division (PSE)
- Thuwal
- Saudi Arabia
| | - G. Polymeropoulos
- King Abdullah University of Science and Technology (KAUST)
- KAUST Catalysis Center (KCC)
- Physical Science and Engineering Division (PSE)
- Thuwal
- Saudi Arabia
| | - E. Mygiakis
- King Abdullah University of Science and Technology (KAUST)
- KAUST Catalysis Center (KCC)
- Physical Science and Engineering Division (PSE)
- Thuwal
- Saudi Arabia
| | - V. Musteata
- King Abdullah University of Science and Technology (KAUST)
- Biological and Environmental Science and Engineering Division (BESE)
- Thuwal
- Saudi Arabia
| | - K.-V. Peinemann
- King Abdullah University of Science and Technology (KAUST)
- Advanced Membranes and Porous Materials Center (AMPMC)
- Physical Science and Engineering Division (PSE)
- Thuwal
- Saudi Arabia
| | - D.-M. Smilgies
- Cornell High Energy Synchrotron Source
- Wilson Laboratory
- Cornell University
- Ithaca
- USA
| | - N. Hadjichristidis
- King Abdullah University of Science and Technology (KAUST)
- KAUST Catalysis Center (KCC)
- Physical Science and Engineering Division (PSE)
- Thuwal
- Saudi Arabia
| | - S. P. Nunes
- King Abdullah University of Science and Technology (KAUST)
- Biological and Environmental Science and Engineering Division (BESE)
- Thuwal
- Saudi Arabia
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48
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Pulsed-field gradient 1H NMR study of diffusion and self-aggregation of long-chain imidazolium-based ionic liquids. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.05.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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49
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Invernizzi C, Dalvit C, Stoeckli-Evans H, Neier R. Synthesis and NMR Spectroscopic Study of the Self-Aggregation of 2-Substituted Benzene-1,3,5-tricarboxamides. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500506] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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50
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Zubkov M, Stait-Gardner T, Price WS, Stilbs P. Steady state effects in a two-pulse diffusion-weighted sequence. J Chem Phys 2015; 142:154201. [DOI: 10.1063/1.4918279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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