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Syryamina VN, Wu X, Boulos S, Nyström L, Yulikov M. Pulse EPR spectroscopy and molecular modeling reveal the origins of the local heterogeneity of dietary fibers. Carbohydr Polym 2023; 319:121167. [PMID: 37567691 DOI: 10.1016/j.carbpol.2023.121167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 08/13/2023]
Abstract
Optimizing human diet by including dietary fibers would be more efficient when the fibers' chain interactions with other molecules are understood in depth. Thereby, it is important to develop methods for characterizing the fiber chain to be able to monitor its structural alterations upon intermolecular interactions. Here, we demonstrate the utility of the electron paramagnetic resonance (EPR) spectroscopy, complemented by simulations in probing the atomistic details of the chain conformations for spin-labeled fibers. Barley β-glucan, a native polysaccharide with linear chain, was utilized as a test fiber system to demonstrate the technique's capabilities. Pulse dipolar EPR data show good agreement with results of the fiber chain modeling, revealing sinuous chain conformations and providing polymer shape descriptors: the gyration tensor, spin-spin distance distribution function, and information about proton density near the spin probe. Results from EPR measurements point to the fiber aggregation in aqueous solution, which agrees with the results of the dynamic light scattering. We propose that the combination of pulse EPR measurements with modeling can be a perfect experimental tool for in-depth structural investigation of dietary fibers and their interaction under such conditions, and that the presented methodology can be extended to other weakly ordered or disordered macromolecules.
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Affiliation(s)
- Victoria N Syryamina
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland; Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation.
| | - Xiaowen Wu
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland.
| | - Samy Boulos
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland.
| | - Laura Nyström
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland.
| | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg, 2, 8093 Zürich, Switzerland.
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Uvarov MN, Kulik LV, Dzuba SA. Assembly of galvinoxyl doped in polymer-fullerene photovoltaic blends. Phys Chem Chem Phys 2023; 25:26219-26224. [PMID: 37740340 DOI: 10.1039/d3cp02513f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Galvinoxyl (Gx) is a stable free radical used as a dopant in active layers of organic solar cells. Here, the nanoscale arrangement of Gx molecules in a composite of the PCDTBT polymer and modified C60 fullerene, PCBM, was studied using a two-pulse electron spin echo (ESE) technique. The results show that the Gx molecules assemble into clusters, which can be described by the model of 8 molecules on the surface of a sphere with a radius of 2.0 nm. Such a structure can arise due to the octahedral packing of 6 PCBM molecules surrounded by 8 Gx molecules. ESE decays also indicate that these clusters repel each other, forming a quasi-regular nanostructure in the matrix. The Gx concentration of 2 wt% at which clusters appear correlates with the literature data on the Gx-induced enhancement of photocurrent, which provides structural insight into the possible molecular mechanism of this enhancement.
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Affiliation(s)
- Mikhail N Uvarov
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation.
| | - Leonid V Kulik
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation.
| | - Sergei A Dzuba
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation.
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russian Federation
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Wu X, Boulos S, Syryamina V, Nyström L, Yulikov M. Interaction of barley β-glucan with food dye molecules - An insight from pulse dipolar EPR spectroscopy. Carbohydr Polym 2023; 309:120698. [PMID: 36906364 DOI: 10.1016/j.carbpol.2023.120698] [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: 11/23/2022] [Revised: 01/25/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
The interactions between dietary fibers (DFs) and small molecules are of great interest to food chemistry and nutrition science. However, the corresponding interaction mechanisms and structural rearrangements of DFs at the molecular level are still opaque due to the usually weak binding and the lack of appropriate techniques to determine details of conformational distributions in such weakly organized systems. By combining our previously established methodology on stochastic spin-labelling of DFs with the appropriately revised set of pulse electron paramagnetic resonance techniques, we present here a toolkit to determine the interactions between DFs and small molecules, using barley β-glucan as an example for neutral DF and a selection of food dye molecules as examples for small molecules. The proposed here methodology allowed us to observe subtle conformational changes of β-glucan by detecting multiple details of the local environment of the spin labels. Substantial variations of binding propensities were detected for different food dyes.
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Affiliation(s)
- Xiaowen Wu
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland.
| | - Samy Boulos
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland.
| | - Victoria Syryamina
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland; Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia.
| | - Laura Nyström
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland.
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland.
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Syryamina VN, Afanasyeva EF, Dzuba SA, Formaggio F, De Zotti M. Peptide-membrane binding is not enough to explain bioactivity: A case study. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183978. [PMID: 35659865 DOI: 10.1016/j.bbamem.2022.183978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/11/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Membrane-active peptides are a promising class of antimicrobial and anticancer therapeutics. For this reason, their molecular mechanisms of action are currently actively investigated. By exploiting Electron Paramagnetic Resonance, we study the membrane interaction of two spin-labeled analogs of the antimicrobial and cytotoxic peptide trichogin GA IV (Tri), with opposite bioactivity: Tri(Api8), able to selectively kill cancer cells, and Tri(Leu4), which is completely nontoxic. In our attempt to determine the molecular basis of their different biological activity, we investigate peptide impact on the lateral organization of lipid membranes, peptide localization and oligomerization, in the zwitter-ionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) model membrane We show that, despite their divergent bioactivity, both peptide analogs (i) are membrane-bound, (ii) display a weak tendency to oligomerization, and (iii) do not induce significant lipid rearrangement. Conversely, literature data show that the parent peptide trichogin, which is cytotoxic without any selectivity, is strongly prone to dimerization and affects the reorganization of POPC membranes. Its dimers are involved in the rotation around the peptide helix, as observed at cryogenic temperatures in the millisecond timescale. Since this latter behavior is not observed for the inactive Tri(Leu4), we propose that for short-length peptides as trichogin oligomerization and molecular motions are crucial for bioactivity, and membrane binding alone is not enough to predict or explain it. We envisage that small changes in the peptide sequence that affect only their ability to oligomerize, or their molecular motions inside the membrane, can tune the peptide activity on membranes of different compositions.
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Affiliation(s)
- Victoria N Syryamina
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation.
| | - Ekaterina F Afanasyeva
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation
| | - Sergei A Dzuba
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation; Department of Physics, Novosibirsk State University,630090 Novosibirsk, Russian Federation
| | - Fernando Formaggio
- ICB-CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Marta De Zotti
- ICB-CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy.
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Smorygina AS, Golysheva EA, Dzuba SA. Clustering of Stearic Acids in Model Phospholipid Membranes Revealed by Double Electron-Electron Resonance. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:13909-13916. [PMID: 34787421 DOI: 10.1021/acs.langmuir.1c02460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Free fatty acids play various important roles in biological membranes. Double electron-electron resonance spectroscopy (DEER, also known as PELDOR) of spin-labeled biomolecules is capable of studying magnetic dipole-dipole (d-d) interactions between spin labels at the nanoscale range of distances. Here, DEER is applied to study intermolecular d-d interactions between doxyl-spin-labeled stearic acids (DSA) in gel-phase phospholipid bilayers composed either of an equimolecular mixture of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1,2-dioleoyl-sn-glycero-3-phosphocholine or of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. DEER data obtained for different DSA concentrations showed that DSA molecules at their concentration in the bilayer χ larger than 0.5 mol % are assembled into lateral lipid-mediated clusters, with a characteristic intermolecular distance of 2 nm. Some evidences were obtained indicating that clusters may consist of "subclusters", alternatively appearing in two opposite leaflets. Conventional electron paramagnetic resonance (EPR) spectra for the gel-phase bilayers showed that for χ larger than 2 mol % the molecules in the clusters stick together, forming oligomers. Room-temperature EPR spectra for the liquid-crystalline phase were found to change noticeably for χ larger than 0.5 mol %, which may indicate the clustering in a liquid-crystalline phase similar to that observed by DEER in the gel phase.
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Affiliation(s)
- Anna S Smorygina
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena A Golysheva
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russia
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