1
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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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2
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Baranov DS, Kashnik AS, Atnyukova AN, Dzuba SA. Spin-Labeled Diclofenac: Synthesis and Interaction with Lipid Membranes. Molecules 2023; 28:5991. [PMID: 37630243 PMCID: PMC10458756 DOI: 10.3390/molecules28165991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Diclofenac is a non-steroidal anti-inflammatory drug (NSAID) from the group of phenylacetic acid derivatives, which has analgesic, anti-inflammatory and antipyretic properties. The interaction of non-steroidal anti-inflammatory drugs with cell membranes can affect their physicochemical properties, which, in turn, can cause a number of side effects in the use of these drugs. Electron paramagnetic resonance (EPR) spectroscopy could be used to study the interaction of diclofenac with a membrane, if its spin-labeled analogs existed. This paper describes the synthesis of spin-labeled diclofenac (diclofenac-SL), which consists of a simple sequence of transformations such as iodination, esterification, Sonogashira cross-coupling, oxidation and saponification. EPR spectra showed that diclofenac-SL binds to a lipid membrane composed of palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). 2H electron spin echo spectroscopy (ESEEM) was used to determine the position of the diclofenac-SL relative to the membrane surface. It was established that its average depth of immersion corresponds to the 5th position of the carbon atom in the lipid chain.
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Affiliation(s)
- Denis S. Baranov
- Voevodsky Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.S.B.); (A.S.K.)
| | - Anna S. Kashnik
- Voevodsky Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.S.B.); (A.S.K.)
| | | | - Sergei A. Dzuba
- Voevodsky Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.S.B.); (A.S.K.)
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3
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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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4
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Syryamina VN, Yulikov M, Nyström L. The Cu(ii) - dietary fibre interactions at molecular level unveiled via EPR spectroscopy. RSC Adv 2022; 12:19901-19916. [PMID: 35865208 PMCID: PMC9261904 DOI: 10.1039/d2ra01164f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/01/2022] [Indexed: 11/21/2022] Open
Abstract
While dietary fibres have a reputation of a healthy food component, the interaction between nutrients and neutral fibers is non-covalent, and its characterization is challenging for most analytical techniques. Here, on the example of barley β-glucan (BBG) and paramagnetic Cu(ii) ions we demonstrate the performance of different Electron Paramagnetic Resonance (EPR) methods in the fibre studies. EPR techniques were tested on two spin probe systems with different affinity in the interaction with dietary fibres – Cu(OAc)2 salt, which weakly dissociates under physiological conditions and CuSO4 salt, which easily dissociates, so that in the latter case Cu(ii) can be considered as a ‘free’ ion, only chelated by water molecules. The Cu(ii)-BBG interaction was determined by pulse EPR relaxation measurements, but this interaction appears not strong enough for continuous wave EPR detection. The capability of the fibres for Cu(ii) absorption was successfully analyzed by comparison of the results from the pulse dipolar spectroscopy with numerical simulations. The local distribution of sugar hydrogen atoms around the Cu(ii) ion has been determined by electron spin echo envelope modulation (ESEEM) and electron-nuclei double resonance (ENDOR) techniques. Binding of paramagnetic Cu(ii) ions to barley beta-glucane dietary fibers and the local surrounding of bound ions have been studied by pulse EPR techniques.![]()
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Affiliation(s)
- Victoria N Syryamina
- ETH Zürich, Institute of Food, Nutrition and Health, Laboratory of Food Biochemistry Schmelzbergstrasse 9 8092 Zürich Switzerland .,Voevodsky Institute of Chemical Kinetics and Combustion of the Siberian Branch of the Russian Academy of Sciences 630090 Novosibirsk Russia
| | - Maxim Yulikov
- ETH Zürich, Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Laura Nyström
- ETH Zürich, Institute of Food, Nutrition and Health, Laboratory of Food Biochemistry Schmelzbergstrasse 9 8092 Zürich Switzerland
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5
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Synthesis of Spin-Labeled Ibuprofen and Its Interaction with Lipid Membranes. Molecules 2022; 27:molecules27134127. [PMID: 35807376 PMCID: PMC9268589 DOI: 10.3390/molecules27134127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Ibuprofen is a non-steroidal anti-inflammatory drug possessing analgesic and antipyretic activity. Electron paramagnetic resonance (EPR) spectroscopy could be applied to study its interaction with biological membranes and proteins if its spin-labeled analogs were synthesized. Here, a simple sequence of ibuprofen transformations—nitration, esterification, reduction, Sandmeyer reaction, Sonogashira cross-coupling, oxidation and saponification—was developed to attain this goal. The synthesis resulted in spin-labeled ibuprofen (ibuprofen-SL) in which the spin label TEMPOL is attached to the benzene ring. EPR spectra confirmed interaction of ibuprofen-SL with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Using 2H electron spin echo envelope modulation (ESEEM) spectroscopy, ibuprofen-SL was found to be embedded into the hydrophobic bilayer interior.
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6
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Aloi E, Bartucci R. Influence of hydration on segmental chain librations and dynamical transition in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183805. [PMID: 34662568 DOI: 10.1016/j.bbamem.2021.183805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/29/2021] [Accepted: 10/10/2021] [Indexed: 12/23/2022]
Abstract
Continuous wave electron paramagnetic resonance spectroscopy of chain-labeled phospholipids is used to investigate the effects of hydration on the librational oscillations and the dynamical transition of phospholipid membranes in the low-temperature range 120-270 K. Bilayers of dipalmitoylphostatidiycholine (DPPC) spin-labeled at the first acyl chain segments and at the methyl ends and prepared at full, low, and very low hydration are considered. The segmental mean-square angular amplitudes of librations, 〈α2〉, are larger in the bilayer interior than at the polar/apolar interface and larger in the fully and low hydrated than in the very low hydrated membranes. For chain segments at the beginning of the hydrocarbon region, 〈α2〉-values are markedly restricted and temperature independent in DPPC with the lowest water content, whereas they increase with temperature in the low and fully hydrated bilayers, particularly at the highest temperatures. For chain segments at the chain termini, the librational amplitudes increase progressively, first slowly and then more rapidly with temperature in bilayers at any level of hydration. From the temperature dependence of the mean-square librational amplitude, the dynamical transition is detected around 240 K at the polar/apolar interface in fully and low hydrated DPPC and at around 225 K at the inner hydrocarbon region for bilayers at any hydration condition. At the dynamical transition the bilayers cross low energy barriers of activation energy in the range 10-20 kJ/mol. The results highlight biophysical properties of DPPC bilayers at low-temperature and provide evidence of the effects of the hydration on the dynamical transition in bilayers.
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Affiliation(s)
- Erika Aloi
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria, 87036 Rende, (CS), Italy
| | - Rosa Bartucci
- Department of Chemistry and Chemical Technologies, Molecular Biophysics Laboratory, University of Calabria, 87036 Rende, (CS), Italy.
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7
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Evidence for an Ordering Transition near 120 K in an Intrinsically Disordered Protein, Casein. Molecules 2021; 26:molecules26195971. [PMID: 34641515 PMCID: PMC8512290 DOI: 10.3390/molecules26195971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/25/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are proteins that possess large unstructured regions. Their importance is increasingly recognized in biology but their characterization remains a challenging task. We employed field swept Electron Spin Echoes in pulsed EPR to investigate low-temperature stochastic molecular librations in a spin-labeled IDP, casein (the main protein of milk). For comparison, a spin-labeled globular protein, hen egg white lysozyme, is also investigated. For casein these motions were found to start at 100 K while for lysozyme only above 130 K, which was ascribed to a denser and more ordered molecular packing in lysozyme. However, above 120 K, the motions in casein were found to depend on temperature much slower than those in lysozyme. This abrupt change in casein was assigned to an ordering transition in which peptide residues rearrange making the molecular packing more rigid and/or more cohesive. The found features of molecular motions in these two proteins turned out to be very similar to those known for gel-phase lipid bilayers composed of conformationally ordered and conformationally disordered lipids. This analogy with a simpler molecular system may appear helpful for elucidation properties of molecular packing in IDPs.
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8
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Isaev N, Steinhoff HJ. Protein and solutes freeze-concentration in water/glycerol mixtures revealed by pulse EPR. Eur J Pharm Biopharm 2021; 169:44-51. [PMID: 34534655 DOI: 10.1016/j.ejpb.2021.08.017] [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: 03/18/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022]
Abstract
Lyophilization can extend protein drugs stability and shelf life, but it also can lead to protein degradation in some cases. The development of safe freeze-drying approaches for sensitive proteins requires a better understanding of lyophilization on the molecular level. The evaluation of the freezing process and its impact on the protein environment in the nm scale is challenging because feasible experimental methods are scarce. In the present work we apply pulse EPR as a tool to study the local concentrations of the solute in the 20 nm range and of the solvent in the 1 nm range for a spin labeled 27 kDa monomeric green fluorescent protein, mEGFP, and the 172 Da TEMPOL spin probe, frozen in different water/glycerol-d5 mixtures. For average glycerol volume fractions, φgly-d5avg, ≥ 0.4 we observed transparent glassy media; the local concentration and the 1 nm solvent shell of TEMPOL and the protein correspond to those of a uniform vitrified glass. At φgly-d5avg ≤ 0.3 we observed partial ice crystallization, which led to ice exclusion of glycerol and TEMPOL with freeze-concentration up to the glycerol maximal-freeze local volume fraction, φgly-d5loc, of 0.64. The protein concentration and its shell behavior was similar except for the lowest φgly-d5avg (0.1), which showed a 4.7-fold freeze-concentration factor compared to sevenfold for TEMPOL, and also a smaller φgly-d5loc. We explain this behavior with an increased probability for proteins to get stuck in the ice phase during fast freezing at higher freeze-concentration and the related large-scale mass transfer.
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Affiliation(s)
- Nikolay Isaev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Novosibirsk, Russia.
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9
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Hoffmann M, Haselberger D, Hofmann T, Müller L, Janson K, Meister A, Das M, Vargas C, Keller S, Kastritis PL, Schmidt C, Hinderberger D. Nanoscale Model System for the Human Myelin Sheath. Biomacromolecules 2021; 22:3901-3912. [PMID: 34324309 DOI: 10.1021/acs.biomac.1c00714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Neurodegenerative disorders are among the most common diseases in modern society. However, the molecular bases of diseases such as multiple sclerosis or Charcot-Marie-Tooth disease remain far from being fully understood. Research in this field is limited by the complex nature of native myelin and by difficulties in obtaining good in vitro model systems of myelin. Here, we introduce an easy-to-use model system of the myelin sheath that can be used to study myelin proteins in a native-like yet well-controlled environment. To this end, we present myelin-mimicking nanodiscs prepared through one of the amphiphilic copolymers styrene/maleic acid (SMA), diisobutylene/maleic acid (DIBMA), and styrene/maleimide sulfobetaine (SMA-SB). These nanodiscs were tested for their lipid composition using chromatographic (HPLC) and mass spectrometric (MS) methods and, utilizing spin probes within the nanodisc, their comparability with liposomes was studied. In addition, their binding behavior with bovine myelin basic protein (MBP) was scrutinized to ensure that the nanodiscs represent a suitable model system of myelin. Our results suggest that both SMA and SMA-SB are able to solubilize the myelin-like (cytoplasmic) liposomes without preferences for specific lipid headgroups or fatty acyl chains. In nanodiscs of both SMA and SMA-SB (called SMA(-SB)-lipid particles, short SMALPs or SMA-SBLPs, respectively), the polymers restrict the lipids' motion in the hydrophobic center of the bilayer. The headgroups of the lipids, however, are sterically less hindered in nanodiscs when compared with liposomes. Myelin-like SMALPs are able to bind bovine MBP, which can stack the lipid bilayers like in native myelin, showing the usability of these simple, well-controlled systems in further studies of protein-lipid interactions of native myelin.
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Affiliation(s)
- Matthias Hoffmann
- Interdisciplinary Research Center HALOmem, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany.,Institute of Chemistry, Martin Luther University (MLU) Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - David Haselberger
- Interdisciplinary Research Center HALOmem, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany.,Institute of Chemistry, Martin Luther University (MLU) Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Tommy Hofmann
- Interdisciplinary Research Center HALOmem, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany
| | - Lisa Müller
- Institute of Pharmacy, Martin Luther University (MLU) Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Kevin Janson
- Interdisciplinary Research Center HALOmem, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany
| | - Manabendra Das
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, 67663 Kaiserslautern, Germany
| | - Carolyn Vargas
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, 67663 Kaiserslautern, Germany.,Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstraße 50/III, 8010 Graz, Austria.,Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria.,BioTechMed-Graz, 8010 Graz, Austria
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, 67663 Kaiserslautern, Germany.,Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstraße 50/III, 8010 Graz, Austria.,Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria.,BioTechMed-Graz, 8010 Graz, Austria
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany
| | - Dariush Hinderberger
- Interdisciplinary Research Center HALOmem, Martin Luther University (MLU) Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany.,Institute of Chemistry, Martin Luther University (MLU) Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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10
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Hoffmann M, Eisermann J, Schöffmann FA, Das M, Vargas C, Keller S, Hinderberger D. Influence of different polymer belts on lipid properties in nanodiscs characterized by CW EPR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183681. [PMID: 34186033 DOI: 10.1016/j.bbamem.2021.183681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/31/2021] [Accepted: 06/14/2021] [Indexed: 12/21/2022]
Abstract
With this study we aim at comparing the well-known lipid membrane model system of liposomes and polymer-encapsulated nanodiscs regarding their lipid properties. Using differential scanning calorimetry (DSC) and continuous-wave electron paramagnetic resonance (CW EPR) spectroscopy, we characterize the temperature-dependent lipid behavior within 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes and nanodiscs made from such liposomes by application of various polymers based on styrene-co-maleic acid (SMA), diisobutylene-alt-maleic acid (DIBMA), and styrene-co-maleic amide sulfobetaine (SMA-SB), a new SMA-derived copolymer containing sulfobetaine side chains. By incorporating a spin label doxyl moiety into the lipid bilayer in position 16 or 5 we were able to study the micropolarity as well as rotational restrictions onto the lipids in the apolar bilayer center and the chain region adjacent to the carbonyl groups, respectively. Our results suggest that all polymers broaden the main melting transition of DMPC, change the water accessibility within the lipid bilayer, and exhibit additional constraints onto the lipids. Independent of the used polymer, the rotational mobility of both spin-labeled lipids decreased with DIBMA exerting less restraints probably due to its aliphatic side chains. Our findings imply that the choice of the solubilizing polymer has to be considered an important step to form lipid nanodiscs which should be included into research of lipid membranes and membrane proteins in the future.
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Affiliation(s)
- Matthias Hoffmann
- Institute of Chemistry, Physical Chemistry - Complex Self-Organizing Systems, Martin Luther University (MLU) Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Jana Eisermann
- Institute of Chemistry, Physical Chemistry - Complex Self-Organizing Systems, Martin Luther University (MLU) Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; Department of Chemistry - Molecular Sciences Research Hub, Imperial College London, 82 Wood Ln, W12 0BZ London, United Kingdom
| | - Florian Arndt Schöffmann
- Institute of Chemistry, Physical Chemistry - Complex Self-Organizing Systems, Martin Luther University (MLU) Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Manabendra Das
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Carolyn Vargas
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany; Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany; Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Dariush Hinderberger
- Institute of Chemistry, Physical Chemistry - Complex Self-Organizing Systems, Martin Luther University (MLU) Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany.
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11
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Geometry and water accessibility of the inhibitor binding site of Na +-pump: Pulse- and CW-EPR study. Biophys J 2021; 120:2679-2690. [PMID: 34087213 PMCID: PMC8390900 DOI: 10.1016/j.bpj.2021.05.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 11/22/2022] Open
Abstract
Spin labels based on cinobufagin, a specific inhibitor of the Na,K-ATPase, have proved valuable tools to characterize the binding site of cardiotonic steroids (CTSs), which also constitutes the extracellular cation pathway. Because existing literature suggests variations in the physiological responses caused by binding of different CTSs, we extended the original set of spin-labeled inhibitors to the more potent bufalin derivatives. Positioning of the spin labels within the Na,K-ATPase site was defined and visualized by molecular docking. Although the original cinobufagin labels exhibited lower affinity, continuous-wave electron paramagnetic resonance spectra of spin-labeled bufalins and cinobufagins revealed a high degree of pairwise similarity, implying that these two types of CTS bind in the same way. Further analysis of the spectral lineshapes of bound spin labels was performed with emphasis on their structure (PROXYL vs. TEMPO), as well as length and rigidity of the linkers. For comparable structures, the dynamic flexibility increased in parallel with linker length, with the longest linker placing the spin label at the entrance to the binding site. Temperature-related changes in spectral lineshapes indicate that six-membered nitroxide rings undergo boat-chair transitions, showing that the binding-site cross section can accommodate the accompanying changes in methyl-group orientation. D2O-electron spin echo envelope modulation in pulse-electron paramagnetic resonance measurements revealed high water accessibilities and similar polarity profiles for all bound spin labels, implying that the vestibule leading to steroid-binding site and cation-binding sites is relatively wide and water-filled.
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12
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Nian B, Xu YJ, Liu Y. Molecular dynamics simulation for mechanism revelation of the safety and nutrition of lipids and derivatives in food: State of the art. Food Res Int 2021; 145:110399. [PMID: 34112402 DOI: 10.1016/j.foodres.2021.110399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/26/2021] [Accepted: 05/06/2021] [Indexed: 11/29/2022]
Abstract
Molecular dynamics (MD) simulation has proved to be a powerful tool in the study of proteins, nucleic acids, lipids, and carbohydrates et al. in fields of health, nutrition, and food science. In particular, MD simulation has been employed in the investigation of various lipid systems such as triglycerides, phospholipid membranes, etc. Due to the continuous updating of computing resources and the development of new MD simulation methods and force field parameters, the simulation's time and size scale of lipids system has increased by several orders of magnitude. However, MD simulation cannot be used for systems invovle chemical reactions. These greatly limit its further application in the field of lipid research. This paper reviews the progress and development of MD simulation, especially for the application of MD simulation in different lipid systems. In this paper, MD simulation and its general workflow was briefly introduced firstly. Subsequently, the application of MD simulation in various lipid systems was reviewed in-depth. Finally, the limitation and future prospects of MD simulation in lipid research were also discussed. This review provided new insights into the investigation of MD simulation, and a novel thought for lipid study. We believe that MD simulation will exhibit more and more great advantages in the investigation of lipids in the future due to the development of novlel methods.
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Affiliation(s)
- Binbin Nian
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
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13
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Syryamina VN, Sannikova NE, De Zotti M, Gobbo M, Formaggio F, Dzuba SA. Tylopeptin B peptide antibiotic in lipid membranes at low concentrations: Self-assembling, mutual repulsion and localization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183585. [PMID: 33640429 DOI: 10.1016/j.bbamem.2021.183585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/27/2021] [Accepted: 02/08/2021] [Indexed: 02/08/2023]
Abstract
The medium-length peptide Tylopeptin B possesses activity against Gram-positive bacteria. It binds to bacterial membranes altering their mechanical properties and increasing their permeability. This action is commonly related with peptide self-assembling, resulting in the formation of membrane channels. Here, pulsed double electron-electron resonance (DEER) data for spin-labeled Tylopeptin B in palmitoyl-oleoyl-glycero-phosphocholine (POPC) model membrane reveal that peptide self-assembling starts at concentration as low as 0.1 mol%; above 0.2 mol% it attains a saturation-like dependence with a mean number of peptides in the cluster <n> = 3.3. Using the electron spin echo envelope modulation (ESEEM) technique, Tylopeptin B molecules are found to possess a planar orientation in the membrane. In the peptide concentration range between 0.1 and 0.2 mol%, DEER data show that the peptide clusters have tendency of mutual repulsion, with a circle of inaccessibility of radius around 20 nm. It may be proposed that within this radius the peptides destabilize the membrane, providing so the peptide antimicrobial activity. Exploiting spin-labeled stearic acids as a model for free fatty acids (FFA), we found that at concentrations of 0.1-0.2 mol% the peptide promotes formation of lipid-mediated FFA clusters; further increase in peptide concentration results in dissipation of these clusters.
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Affiliation(s)
- Victoria N Syryamina
- Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation.
| | | | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Marina Gobbo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation.
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14
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H. Haeri H, Jerschabek V, Sadeghi A, Hinderberger D. Copper–Calcium Poly(Acrylic Acid) Composite Hydrogels as Studied by Electron Paramagnetic Resonance (EPR) Spectroscopy. MACROMOL CHEM PHYS 2020. [DOI: 10.1002/macp.202000262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Haleh H. Haeri
- Institut für Chemie Martin‐Luther‐Universität Halle‐Wittenberg Von‐Danckelmann‐Platz 4 Halle (Saale) 06120 Germany
| | - Vanessa Jerschabek
- Institut für Chemie Martin‐Luther‐Universität Halle‐Wittenberg Von‐Danckelmann‐Platz 4 Halle (Saale) 06120 Germany
| | - Arash Sadeghi
- Institut für Chemie Martin‐Luther‐Universität Halle‐Wittenberg Von‐Danckelmann‐Platz 4 Halle (Saale) 06120 Germany
| | - Dariush Hinderberger
- Institut für Chemie Martin‐Luther‐Universität Halle‐Wittenberg Von‐Danckelmann‐Platz 4 Halle (Saale) 06120 Germany
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15
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Muzio MD, Millan-Solsona R, Borrell JH, Fumagalli L, Gomila G. Cholesterol Effect on the Specific Capacitance of Submicrometric DOPC Bilayer Patches Measured by in-Liquid Scanning Dielectric Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12963-12972. [PMID: 33084346 DOI: 10.1021/acs.langmuir.0c02251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The specific capacitance of biological membranes is a key physical parameter in bioelectricity that also provides valuable physicochemical information on composition, phase, or hydration properties. Cholesterol is known to modulate the physicochemical properties of biomembranes, but its effect on the specific capacitance has not been fully established yet. Here we use the high spatial resolution capabilities of in-liquid scanning dielectric microscopy in force detection mode to directly demonstrate that DOPC bilayer patches at 50% cholesterol concentration show a strong reduction of their specific capacitance with respect to pure DOPC bilayer patches. The reduction observed (∼35%) cannot be explained by the small increase in bilayer thickness (∼16%). We suggest that the reduction of the specific capacitance might be due to the dehydration of the polar head groups caused by the insertion of cholesterol molecules in the bilayer. The results reported confirm the potential of in-liquid SDM to study the electrical and physicochemical properties of lipid bilayers at very small scales (down to ∼200 nm here), with implications in fields such as biophysics, bioelectricity, biochemistry, and biosensing.
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Affiliation(s)
- Martina Di Muzio
- Nanoscale Bioelectrical Characterization, Institut de Bioenginyeria de Catalunya, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Ruben Millan-Solsona
- Nanoscale Bioelectrical Characterization, Institut de Bioenginyeria de Catalunya, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | | | | | - Gabriel Gomila
- Nanoscale Bioelectrical Characterization, Institut de Bioenginyeria de Catalunya, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
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16
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Aloi E, Bartucci R. Cryogenically frozen PEGylated liposomes and micelles: Water penetration and polarity profiles. Biophys Chem 2020; 266:106463. [PMID: 32911450 DOI: 10.1016/j.bpc.2020.106463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/23/2020] [Accepted: 08/23/2020] [Indexed: 11/24/2022]
Abstract
Poly(ethylene glycol) (PEG)-grafted lipid dispersions are widely investigated in fundamental and biotechnological research for their successful use in drug-delivery. Here, we consider mixtures of the bilayer-forming lipid dipalmitoylphosphatidylcholine (DPPC) with the micelle-forming lipid PEG:2000-phosphatidilethanolamine (PEG:2000-DPPE) fully hydrated in D2O and measured at 77 K. Electron Spin Echo Envelope Modulation and continuous wave Electron Paramagnetic Resonance of chain-labelled lipids are employed to detect the extent of solvent permeation and the environmental polarity, respectively, across the hydrocarbon regions of the lipid assemblies. Sigmoidal water penetration and polarity profiles are described in sterically stabilized liposomes (SSL) formed at submicellar content of PEG:2000-DPPE incorporated in DPPC. Compared to DPPC bilayers, SSL show increased hydrophobicity at both the polar/apolar interface and the chain termini, and a broader transition that is shifted toward the interface. Solvent exposure and polarity decrease on going down the chain in PEG:2000-DPPE micelles. However, compared to SSL, polymer-lipid micelles show higher solvent permeation at any chain segment and the chain termini are accessible to water. In any sample, heterogeneity is found in H-bond formation between the spin-label nitroxide groups and the solvent molecules. The results at cryogenic temperature add new insights into the biophysico-chemical characterization of PEGylated lipid dispersions.
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Affiliation(s)
- Erika Aloi
- Molecular Biophysics Laboratory, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Rosa Bartucci
- Molecular Biophysics Laboratory, Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Rende, Italy.
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17
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Sannikova N, Timofeev I, Bagryanskaya E, Bowman M, Fedin M, Krumkacheva O. Electron Spin Relaxation of Photoexcited Porphyrin in Water-Glycerol Glass. Molecules 2020; 25:E2677. [PMID: 32527023 PMCID: PMC7321249 DOI: 10.3390/molecules25112677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 02/07/2023] Open
Abstract
Recently, the photoexcited triplet state of porphyrin was proposed as a promising spin-label for pulsed dipolar electron paramagnetic resonance (EPR). Herein, we report the factors that determine the electron spin echo dephasing of the photoexcited porphyrin in a water-glycerol matrix. The electron spin relaxation of a water-soluble porphyrin was measured by Q-band EPR, and the temperature dependence and the effect of solvent deuteration on the relaxation times were studied. The phase memory relaxation rate (1/Tm) is noticeably affected by solvent nuclei and is substantially faster in protonated solvents than in deuterated solvents. The Tm is as large as 13-17 μs in deuterated solvent, potentially expanding the range of distances available for measurement by dipole spectroscopy with photoexcited porphyrin. The 1/Tm depends linearly on the degree of solvent deuteration and can be used to probe the environment of a porphyrin in or near a biopolymer, including the solvent accessibility of porphyrins used in photodynamic therapy. We characterized the noncovalent binding of porphyrin to human serum albumin (HSA) from 1/Tm and electron spin echo envelope modulation (ESEEM) and found that porphyrin is quite exposed to solvent on the surface of HSA. The 1/Tm and ESEEM are equally effective and provide complementary methods to determine the solvent accessibility of a porphyrin bound to protein or to determine the location of the porphyrin.
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Affiliation(s)
- Natalya Sannikova
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia; (N.S.); (I.T.)
| | - Ivan Timofeev
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia; (N.S.); (I.T.)
| | - Elena Bagryanskaya
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia
| | - Michael Bowman
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - Matvey Fedin
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia; (N.S.); (I.T.)
| | - Olesya Krumkacheva
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia; (N.S.); (I.T.)
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18
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Monroe J, Barry M, DeStefano A, Aydogan Gokturk P, Jiao S, Robinson-Brown D, Webber T, Crumlin EJ, Han S, Shell MS. Water Structure and Properties at Hydrophilic and Hydrophobic Surfaces. Annu Rev Chem Biomol Eng 2020; 11:523-557. [PMID: 32169001 DOI: 10.1146/annurev-chembioeng-120919-114657] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The properties of water on both molecular and macroscopic surfaces critically influence a wide range of physical behaviors, with applications spanning from membrane science to catalysis to protein engineering. Yet, our current understanding of water interfacing molecular and material surfaces is incomplete, in part because measurement of water structure and molecular-scale properties challenges even the most advanced experimental characterization techniques and computational approaches. This review highlights progress in the ongoing development of tools working to answer fundamental questions on the principles that govern the interactions between water and surfaces. One outstanding and critical question is what universal molecular signatures capture the hydrophobicity of different surfaces in an operationally meaningful way, since traditional macroscopic hydrophobicity measures like contact angles fail to capture even basic properties of molecular or extended surfaces with any heterogeneity at the nanometer length scale. Resolving this grand challenge will require close interactions between state-of-the-art experiments, simulations, and theory, spanning research groups and using agreed-upon model systems, to synthesize an integrated knowledge of solvation water structure, dynamics, and thermodynamics.
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Affiliation(s)
- Jacob Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Mikayla Barry
- Department of Materials, University of California, Santa Barbara, California 93106, USA
| | - Audra DeStefano
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Pinar Aydogan Gokturk
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Dennis Robinson-Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Thomas Webber
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Ethan J Crumlin
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; .,Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
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19
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Fichou Y, Oberholtzer ZR, Ngo H, Cheng CY, Keller TJ, Eschmann NA, Han S. Tau-Cofactor Complexes as Building Blocks of Tau Fibrils. Front Neurosci 2019; 13:1339. [PMID: 31920504 PMCID: PMC6923735 DOI: 10.3389/fnins.2019.01339] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/27/2019] [Indexed: 12/30/2022] Open
Abstract
The aggregation of the human tau protein into neurofibrillary tangles is directly diagnostic of many neurodegenerative conditions termed tauopathies. The species, factors and events that are responsible for the initiation and propagation of tau aggregation are not clearly established, even in a simplified and artificial in vitro system. This motivates the mechanistic study of in vitro aggregation of recombinant tau from soluble to fibrillar forms, for which polyanionic cofactors are the most commonly used external inducer. In this study, we performed biophysical characterizations to unravel the mechanisms by which cofactors induce fibrillization. We first reinforce the idea that cofactors are the limiting factor to generate ThT-active tau fibrils, and establish that they act as templating reactant that trigger tau conformational rearrangement. We show that heparin has superior potency for recruiting monomeric tau into aggregation-competent species compared to any constituent intermediate or aggregate "seeds." We show that tau and cofactors form intermediate complexes whose evolution toward ThT-active fibrils is tightly regulated by tau-cofactor interactions. Remarkably, it is possible to find mild cofactors that complex with tau without forming ThT-active species, except when an external catalyst (e.g., a seed) is provided to overcome the energy barrier. In a cellular context, we propose the idea that tau could associate with cofactors to form a metastable complex that remains "inert" and reversible, until encountering a relevant seed that can trigger an irreversible transition to β-sheet containing species.
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Affiliation(s)
- Yann Fichou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Zachary R. Oberholtzer
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Hoang Ngo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Chi-Yuan Cheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Timothy J. Keller
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Neil A. Eschmann
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
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20
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Aloi E, Bartucci R. Interdigitated lamellar phases in the frozen state: Spin-label CW- and FT-EPR. Biophys Chem 2019; 253:106229. [DOI: 10.1016/j.bpc.2019.106229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/24/2022]
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21
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Aloi E, Bartucci R. Solvent accessibility in interdigitated and micellar phases formed by DPPC/Lyso-PPC mixtures: D2O-ESEEM of chain labeled lipids. Chem Phys Lipids 2019; 221:39-45. [DOI: 10.1016/j.chemphyslip.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/27/2019] [Accepted: 03/11/2019] [Indexed: 11/16/2022]
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22
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Jeong D, Han S, Lim YB, Kim SH. Investigation of the Hydration State of Self-Assembled Peptide Nanostructures with Advanced Electron Paramagnetic Resonance Spectroscopy. ACS OMEGA 2019; 4:114-120. [PMID: 31459317 PMCID: PMC6648812 DOI: 10.1021/acsomega.8b02450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/07/2018] [Indexed: 06/10/2023]
Abstract
Probing the intermolecular interactions and local environments of self-assembled peptide nanostructures (SPNs) is crucial for a better understanding of the underlying molecular details of self-assembling phenomena. In particular, investigation of the hydration state is important to understand the nanoscale structural and functional characteristics of SPNs. In this report, we examined the local hydration environments of SPNs in detail to understand the driving force of the discrete geometric structural self-assembling phenomena for peptide nanostructures. Advanced electron paramagnetic resonance spectroscopy was used to probe the hydrogen bond formation and geometry as well as the hydrophobicity of the local environments at various spin-labeled sites in SPNs. The experimental results supplement the sparse experimental data regarding local structures of SPNs, such as the hydrogen bonding and the hydrophobicity of the local environment, providing important information on the formation of SPNs, which have immense potential for bioactive materials.
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Affiliation(s)
- Donghyuk Jeong
- Western
Seoul Center, Korea Basic Science Institute
(KBSI), Seoul 03759, Republic of Korea
| | - Sanghun Han
- Department
of Materials Science & Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Yong-beom Lim
- Department
of Materials Science & Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Sun Hee Kim
- Western
Seoul Center, Korea Basic Science Institute
(KBSI), Seoul 03759, Republic of Korea
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23
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Wegner J, Valora G, Halbmair K, Kehl A, Worbs B, Bennati M, Diederichsen U. Semi-Rigid Nitroxide Spin Label for Long-Range EPR Distance Measurements of Lipid Bilayer Embedded β-Peptides. Chemistry 2019; 25:2203-2207. [DOI: 10.1002/chem.201805880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Janine Wegner
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
| | - Gabriele Valora
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
- Dipartimento di Scienze Chimiche; University of Catania; Italy
| | - Karin Halbmair
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Annemarie Kehl
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Brigitte Worbs
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
| | - Marina Bennati
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Ulf Diederichsen
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Tammannstrasse 2 37077 Göttingen Germany
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24
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Afanasyeva EF, Syryamina VN, De Zotti M, Formaggio F, Toniolo C, Dzuba SA. Peptide antibiotic trichogin in model membranes: Self-association and capture of fatty acids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:524-531. [PMID: 30550880 DOI: 10.1016/j.bbamem.2018.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 10/27/2022]
Abstract
The antimicrobial action of peptides in bacterial membranes is commonly related to their mode of self-assembling which results in pore formation. To optimize peptide antibiotic use for therapeutic purposes, a study on the concentration dependence of self-assembling process is thus desirable. In this work, we investigate this dependence for peptaibol trichogin GA IV (Tric) in the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) model membrane in the range of peptide concentrations between 0.5 and 3.3 mol%. Pulsed double electron-electron resonance (PELDOR) applied on spin-labeled peptide analogs highlights the onset of peptide dimerization above a critical peptide concentration value, namely ~ 2 mol%. Electron spin echo (ESE) envelope modulation (ESEEM) for D2O-hydrated bilayers shows that dimerization is accompanied by peptide re-orientation towards a trans-membrane disposition. For spin-labeled stearic acids (5-DSA) in POPC bilayers, the study of ESE decays and ESEEM in the presence of a deuterated peptide analog indicates that above the critical peptide concentration the 5-DSA molecules are attracted by peptide molecules, forming nanoclusters. As the 5-DSA molecules represent a model for the behavior of fatty acids participating in bacterial membrane homeostasis, such capturing action by Tric may represent an additional mechanism of its antibiotic activity.
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Affiliation(s)
- Ekaterina F Afanasyeva
- Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Victoria N Syryamina
- Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation.
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25
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Ether-linked lipids: Spin-label EPR and spin echoes. Chem Phys Lipids 2018; 212:130-137. [DOI: 10.1016/j.chemphyslip.2018.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 11/22/2022]
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26
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Syryamina VN, De Zotti M, Toniolo C, Formaggio F, Dzuba SA. Alamethicin self-assembling in lipid membranes: concentration dependence from pulsed EPR of spin labels. Phys Chem Chem Phys 2018; 20:3592-3601. [DOI: 10.1039/c7cp07298h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antimicrobial action of the peptide antibiotic alamethicin (Alm) is commonly related to peptide self-assembling resulting in the formation of voltage-dependent channels in bacterial membranes, which induces ion permeation.
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Affiliation(s)
- Victoria N. Syryamina
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
| | - Marta De Zotti
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Claudio Toniolo
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Fernando Formaggio
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
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27
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Segawa TF, Doppelbauer M, Garbuio L, Doll A, Polyhach YO, Jeschke G. Water accessibility in a membrane-inserting peptide comparing Overhauser DNP and pulse EPR methods. J Chem Phys 2017; 144:194201. [PMID: 27208942 DOI: 10.1063/1.4948988] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Water accessibility is a key parameter for the understanding of the structure of biomolecules, especially membrane proteins. Several experimental techniques based on the combination of electron paramagnetic resonance (EPR) spectroscopy with site-directed spin labeling are currently available. Among those, we compare relaxation time measurements and electron spin echo envelope modulation (ESEEM) experiments using pulse EPR with Overhauser dynamic nuclear polarization (DNP) at X-band frequency and a magnetic field of 0.33 T. Overhauser DNP transfers the electron spin polarization to nuclear spins via cross-relaxation. The change in the intensity of the (1)H NMR spectrum of H2O at a Larmor frequency of 14 MHz under a continuous-wave microwave irradiation of the nitroxide spin label contains information on the water accessibility of the labeled site. As a model system for a membrane protein, we use the hydrophobic α-helical peptide WALP23 in unilamellar liposomes of DOPC. Water accessibility measurements with all techniques are conducted for eight peptides with different spin label positions and low radical concentrations (10-20 μM). Consistently in all experiments, the water accessibility appears to be very low, even for labels positioned near the end of the helix. The best profile is obtained by Overhauser DNP, which is the only technique that succeeds in discriminating neighboring positions in WALP23. Since the concentration of the spin-labeled peptides varied, we normalized the DNP parameter ϵ, being the relative change of the NMR intensity, by the electron spin concentration, which was determined from a continuous-wave EPR spectrum.
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Affiliation(s)
- Takuya F Segawa
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Maximilian Doppelbauer
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Luca Garbuio
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Andrin Doll
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Yevhen O Polyhach
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
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28
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Syryamina VN, Dzuba SA. Dynamical Transitions at Low Temperatures in the Nearest Hydration Shell of Phospholipid Bilayers. J Phys Chem B 2017; 121:1026-1032. [DOI: 10.1021/acs.jpcb.6b10133] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. N. Syryamina
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
- Physics
Department, Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - S. A. Dzuba
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
- Physics
Department, Novosibirsk State University, Novosibirsk 630090, Russian Federation
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29
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Basso LGM, Vicente EF, Crusca E, Cilli EM, Costa-Filho AJ. SARS-CoV fusion peptides induce membrane surface ordering and curvature. Sci Rep 2016; 6:37131. [PMID: 27892522 PMCID: PMC5125003 DOI: 10.1038/srep37131] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 10/24/2016] [Indexed: 12/23/2022] Open
Abstract
Viral membrane fusion is an orchestrated process triggered by membrane-anchored viral fusion glycoproteins. The S2 subunit of the spike glycoprotein from severe acute respiratory syndrome (SARS) coronavirus (CoV) contains internal domains called fusion peptides (FP) that play essential roles in virus entry. Although membrane fusion has been broadly studied, there are still major gaps in the molecular details of lipid rearrangements in the bilayer during fusion peptide-membrane interactions. Here we employed differential scanning calorimetry (DSC) and electron spin resonance (ESR) to gather information on the membrane fusion mechanism promoted by two putative SARS FPs. DSC data showed the peptides strongly perturb the structural integrity of anionic vesicles and support the hypothesis that the peptides generate opposing curvature stresses on phosphatidylethanolamine membranes. ESR showed that both FPs increase lipid packing and head group ordering as well as reduce the intramembrane water content for anionic membranes. Therefore, bending moment in the bilayer could be generated, promoting negative curvature. The significance of the ordering effect, membrane dehydration, changes in the curvature properties and the possible role of negatively charged phospholipids in helping to overcome the high kinetic barrier involved in the different stages of the SARS-CoV-mediated membrane fusion are discussed.
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Affiliation(s)
- Luis G M Basso
- Grupo de Biofísica Molecular Sérgio Mascarenhas, Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Centro, São Carlos, SP, Brazil.,Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo. Av. Bandeirantes, 3900, 14040-901, Ribeirão Preto, SP, Brazil
| | - Eduardo F Vicente
- Faculdade de Ciências e Engenharia, UNESP - Univ Estadual Paulista, Campus de Tupã. Rua Domingos da Costa Lopes, 780, 17602-496, Tupã, SP, Brazil
| | - Edson Crusca
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP - Univ Estadual Paulista. Rua Prof. Franscisco Degni, 55, 14800-900, Araraquara, SP, Brazil
| | - Eduardo M Cilli
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP - Univ Estadual Paulista. Rua Prof. Franscisco Degni, 55, 14800-900, Araraquara, SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo. Av. Bandeirantes, 3900, 14040-901, Ribeirão Preto, SP, Brazil
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30
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Goslar J, Hoffmann SK, Lijewski S. Dynamics of 4-oxo-TEMPO-d16-(15)N nitroxide-propylene glycol system studied by ESR and ESE in liquid and glassy state in temperature range 10-295K. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 269:162-175. [PMID: 27323281 DOI: 10.1016/j.jmr.2016.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
ESR spectra and electron spin relaxation of nitroxide radical in 4-oxo-TEMPO-d16-(15)N in propylene glycol were studied at X-band in the temperature range 10-295K. The spin-lattice relaxation in the liquid viscous state determined from the resonance line shape is governed by three mechanisms occurring during isotropic molecular reorientations. In the glassy state below 200K the spin-lattice relaxation, phase relaxation and electron spin echo envelope modulations (ESEEM) were studied by pulse spin echo technique using 2-pulse and 3-pulse induced signals. Electron spin-lattice relaxation is governed by a single non-phonon relaxation process produced by localized oscillators of energy 76cm(-1). Electron spin dephasing is dominated by a molecular motion producing a resonance-type peak in the temperature dependence of the dephasing rate around 120K. The origin of the peak is discussed and a simple method for the peak shape analysis is proposed, which gives the activation energy of a thermally activated motion Ea=7.8kJ/mol and correlation time τ0=10(-8)s. The spin echo amplitude is strongly modulated and FT spectrum contains a doublet of lines centered around the (2)D nuclei Zeeman frequency. The splitting into the doublet is discussed as due to a weak hyperfine coupling of nitroxide unpaired electron with deuterium of reorienting CD3 groups.
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Affiliation(s)
- Janina Goslar
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179 Poznan, Poland
| | - Stanislaw K Hoffmann
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179 Poznan, Poland.
| | - Stefan Lijewski
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179 Poznan, Poland
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31
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Kaminker I, Shimon D, Hovav Y, Feintuch A, Vega S. Heteronuclear DNP of protons and deuterons with TEMPOL. Phys Chem Chem Phys 2016; 18:11017-41. [DOI: 10.1039/c5cp06689a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic nuclear polarization (DNP) experiments on samples with several types of magnetic nuclei sometimes exhibit “cross-talk” between the nuclei, such as different nuclei having DNP spectra with similar shapes and enhancements.
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Affiliation(s)
| | - D. Shimon
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Y. Hovav
- Weizmann Institute of Science
- Rehovot
- Israel
| | | | - S. Vega
- Weizmann Institute of Science
- Rehovot
- Israel
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32
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Konov KB, Leonov DV, Isaev NP, Fedotov KY, Voronkova VK, Dzuba SA. Membrane–Sugar Interactions Probed by Pulsed Electron Paramagnetic Resonance of Spin Labels. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b06864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Konstantin B. Konov
- Zavoisky
Physical-Technical Institute, Russian Academy of Sciences, Kazan 420029, Russia
| | - Dmitry V. Leonov
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Nikolay P. Isaev
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Kirill Yu. Fedotov
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Violeta K. Voronkova
- Zavoisky
Physical-Technical Institute, Russian Academy of Sciences, Kazan 420029, Russia
| | - Sergei A. Dzuba
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
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33
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Bartucci R, Guzzi R, Esmann M, Marsh D. Water penetration profile at the protein-lipid interface in Na,K-ATPase membranes. Biophys J 2015; 107:1375-82. [PMID: 25229145 DOI: 10.1016/j.bpj.2014.07.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/05/2014] [Accepted: 07/30/2014] [Indexed: 11/28/2022] Open
Abstract
The affinity of ionized fatty acids for the Na,K-ATPase is used to determine the transmembrane profile of water penetration at the protein-lipid interface. The standardized intensity of the electron spin echo envelope modulation (ESEEM) from (2)H-hyperfine interaction with D2O is determined for stearic acid, n-SASL, spin-labeled systematically at the C-n atoms throughout the chain. In both native Na,K-ATPase membranes from shark salt gland and bilayers of the extracted membrane lipids, the D2O-ESEEM intensities of fully charged n-SASL decrease progressively with position down the fatty acid chain toward the terminal methyl group. Whereas the D2O intensities decrease sharply at the n = 9 position in the lipid bilayers, a much broader transition region in the range n = 6 to 10 is found with Na,K-ATPase membranes. Correction for the bilayer population in the membranes yields the intrinsic D2O-intensity profile at the protein-lipid interface. For positions at either end of the chains, the D2O concentrations at the protein interface are greater than in the lipid bilayer, and the positional profile is much broader. This reveals the higher polarity, and consequently higher intramembrane water concentration, at the protein-lipid interface. In particular, there is a significant water concentration adjacent to the protein at the membrane midplane, unlike the situation in the bilayer regions of this cholesterol-rich membrane. Experiments with protonated fatty acid and phosphatidylcholine spin labels, both of which have a considerably lower affinity for the Na,K-ATPase, confirm these results.
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Affiliation(s)
- Rosa Bartucci
- Department of Physics, Molecular Biophysics Laboratory and CNISM Unit, University of Calabria, Ponte P. Bucci, Cubo 31C, 87036 Rende (CS), Italy
| | - Rita Guzzi
- Department of Physics, Molecular Biophysics Laboratory and CNISM Unit, University of Calabria, Ponte P. Bucci, Cubo 31C, 87036 Rende (CS), Italy
| | - Mikael Esmann
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Derek Marsh
- Max-Planck-Institut für biophysikalische Chemie, 37070 Göttingen, Germany.
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Stirpe A, Pantusa M, Guzzi R, Bartucci R, Sportelli L. Chain interdigitation in DPPC bilayers induced by HgCl2: Evidences from continuous wave and pulsed EPR. Chem Phys Lipids 2014; 183:176-83. [DOI: 10.1016/j.chemphyslip.2014.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 01/07/2023]
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35
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Franck JM, Sokolovski M, Kessler N, Matalon E, Gordon-Grossman M, Han SI, Goldfarb D, Horovitz A. Probing water density and dynamics in the chaperonin GroEL cavity. J Am Chem Soc 2014; 136:9396-403. [PMID: 24888581 PMCID: PMC4091268 DOI: 10.1021/ja503501x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
ATP-dependent binding of the chaperonin
GroEL to its cofactor GroES
forms a cavity in which encapsulated substrate proteins can fold in
isolation from bulk solution. It has been suggested that folding in
the cavity may differ from that in bulk solution owing to steric confinement,
interactions with the cavity walls, and differences between the properties
of cavity-confined and bulk water. However, experimental data regarding
the cavity-confined water are lacking. Here, we report measurements
of water density and diffusion dynamics in the vicinity of a spin
label attached to a cysteine in the Tyr71 → Cys GroES mutant
obtained using two magnetic resonance techniques: electron-spin echo
envelope modulation and Overhauser dynamic nuclear polarization. Residue
71 in GroES is fully exposed to bulk water in free GroES and to confined
water within the cavity of the GroEL–GroES complex. Our data
show that water density and translational dynamics in the vicinity
of the label do not change upon complex formation, thus indicating
that bulk water-exposed and cavity-confined GroES surface water share
similar properties. Interestingly, the diffusion dynamics of water
near the GroES surface are found to be unusually fast relative to
other protein surfaces studied. The implications of these findings
for chaperonin-assisted folding mechanisms are discussed.
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Affiliation(s)
- John M Franck
- Department of Chemistry and Biochemistry, University of California Santa Barbara, California 93106, United States
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36
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Dzuba SA. Structural studies of biological membranes using ESEEM spectroscopy of spin labels and deuterium substitution. J STRUCT CHEM+ 2013. [DOI: 10.1134/s0022476613070019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Matalon E, Faingold O, Eisenstein M, Shai Y, Goldfarb D. The topology, in model membranes, of the core peptide derived from the T-cell receptor transmembrane domain. Chembiochem 2013; 14:1867-75. [PMID: 23881822 DOI: 10.1002/cbic.201300191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Indexed: 01/16/2023]
Abstract
The T-cell receptor-CD3 complex (TCR-CD3) serves a critical role in protecting organisms from infectious agents. The TCR is a heterodimer composed of α- and β-chains, which are responsible for antigen recognition. Within the transmembrane domain of the α-subunit, a region has been identified to be crucial for the assembly and function of the TCR. This region, termed core peptide (CP), consists of nine amino acids (GLRILLLKV), two of which are charged (lysine and arginine) and are crucial for the interaction with CD3. Earlier studies have shown that a synthetic peptide corresponding to the CP sequence can suppress the immune response in animal models of T-cell-mediated inflammation, by disrupting proper assembly of the TCR. As a step towards the understanding of the source of the CP activity, we focused on CP in egg phosphatidylcholine/cholesterol (9:1, mol/mol) model membranes and determined its secondary structure, oligomerization state, and orientation with respect to the membrane. To achieve this goal, 15-residue segments of TCRα, containing the CP, were synthesized and spin-labeled at different locations with a nitroxide derivative. Electron spin-echo envelope modulation spectroscopy was used to probe the position and orientation of the peptides within the membrane, and double electron-electron resonance measurements were used to probe its conformation and oligomerization state. We found that the peptide is predominantly helical in a membrane environment and tends to form oligomers (mostly dimers) that are parallel to the membrane plane.
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Affiliation(s)
- Erez Matalon
- Department of Chemical Physics, Weizmann Institute of Science, 234 Hertzl St, Rehovot, 7632700 (Israel)
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38
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Lai YC, Chen YF, Chiang YW. ESR study of interfacial hydration layers of polypeptides in water-filled nanochannels and in vitrified bulk solvents. PLoS One 2013; 8:e68264. [PMID: 23840841 PMCID: PMC3695931 DOI: 10.1371/journal.pone.0068264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/03/2013] [Indexed: 01/04/2023] Open
Abstract
There is considerable evidence for the essential role of surface water in protein function and structure. However, it is unclear to what extent the hydration water and protein are coupled and interact with each other. Here, we show by ESR experiments (cw, DEER, ESEEM, and ESE techniques) with spin-labeling and nanoconfinement techniques that the vitrified hydration layers can be evidently recognized in the ESR spectra, providing nanoscale understanding for the biological interfacial water. Two peptides of different secondary structures and lengths are studied in vitrified bulk solvents and in water-filled nanochannels of different pore diameter (6.1∼7.6 nm). The existence of surface hydration and bulk shells are demonstrated. Water in the immediate vicinity of the nitroxide label (within the van der Waals contacts, ∼0.35 nm) at the water-peptide interface is verified to be non-crystalline at 50 K, and the water accessibility changes little with the nanochannel dimension. Nevertheless, this water accessibility for the nanochannel cases is only half the value for the bulk solvent, even though the peptide structures remain largely the same as those immersed in the bulk solvents. On the other hand, the hydration density in the range of ∼2 nm from the nitroxide spin increases substantially with decreasing pore size, as the density for the largest pore size (7.6 nm) is comparable to that for the bulk solvent. The results demonstrate that while the peptides are confined but structurally unaltered in the nanochannels, their surrounding water exhibits density heterogeneity along the peptide surface normal. The causes and implications, especially those involving the interactions between the first hydration water and peptides, of these observations are discussed. Spin-label ESR techniques are proven useful for studying the structure and influences of interfacial hydration.
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Affiliation(s)
- Yei-Chen Lai
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Fan Chen
- Department of Chemical and Materials Engineering, National Central University, Jhongli, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail:
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39
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Pogozheva ID, Tristram-Nagle S, Mosberg HI, Lomize AL. Structural adaptations of proteins to different biological membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2592-608. [PMID: 23811361 DOI: 10.1016/j.bbamem.2013.06.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/04/2013] [Accepted: 06/19/2013] [Indexed: 02/06/2023]
Abstract
To gain insight into adaptations of proteins to their membranes, intrinsic hydrophobic thicknesses, distributions of different chemical groups and profiles of hydrogen-bonding capacities (α and β) and the dipolarity/polarizability parameter (π*) were calculated for lipid-facing surfaces of 460 integral α-helical, β-barrel and peripheral proteins from eight types of biomembranes. For comparison, polarity profiles were also calculated for ten artificial lipid bilayers that have been previously studied by neutron and X-ray scattering. Estimated hydrophobic thicknesses are 30-31Å for proteins from endoplasmic reticulum, thylakoid, and various bacterial plasma membranes, but differ for proteins from outer bacterial, inner mitochondrial and eukaryotic plasma membranes (23.9, 28.6 and 33.5Å, respectively). Protein and lipid polarity parameters abruptly change in the lipid carbonyl zone that matches the calculated hydrophobic boundaries. Maxima of positively charged protein groups correspond to the location of lipid phosphates at 20-22Å distances from the membrane center. Locations of Tyr atoms coincide with hydrophobic boundaries, while distributions maxima of Trp rings are shifted by 3-4Å toward the membrane center. Distributions of Trp atoms indicate the presence of two 5-8Å-wide midpolar regions with intermediate π* values within the hydrocarbon core, whose size and symmetry depend on the lipid composition of membrane leaflets. Midpolar regions are especially asymmetric in outer bacterial membranes and cell membranes of mesophilic but not hyperthermophilic archaebacteria, indicating the larger width of the central nonpolar region in the later case. In artificial lipid bilayers, midpolar regions are observed up to the level of acyl chain double bonds.
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Affiliation(s)
- Irina D Pogozheva
- College of Pharmacy, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA.
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40
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Krumkacheva OA, Fedin MV, Polovyanenko DN, Jicsinszky L, Marque SRA, Bagryanskaya EG. Structural Equilibrium in New Nitroxide-Capped Cyclodextrins: CW and Pulse EPR Study. J Phys Chem B 2013; 117:8223-31. [DOI: 10.1021/jp404173j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Olesya A. Krumkacheva
- International Tomography Center SB RAS, Institutskaya 3a, Novosibirsk 630090,
Russia
- Novosibirsk State University, Pirogova strasse 2, Novosibirsk 630090,
Russia
| | - Matvey V. Fedin
- International Tomography Center SB RAS, Institutskaya 3a, Novosibirsk 630090,
Russia
| | - Dmitry N. Polovyanenko
- N. N.Voroztsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva
9, Novosibirsk 630090, Russia
| | | | - Sylvain R. A. Marque
- Aix-Marseille Université, CNRS-ICR UMR 7273, case 521, Avenue
Escadrille Normandie-Niemen,
13397 Marseille cedex 20, France
| | - Elena G. Bagryanskaya
- International Tomography Center SB RAS, Institutskaya 3a, Novosibirsk 630090,
Russia
- N. N.Voroztsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva
9, Novosibirsk 630090, Russia
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41
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42
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Manukovsky N, Sanders E, Matalon E, Wolf SG, Goldfarb D. Membrane curvature and cholesterol effects on lipids packing and spin-labelled lipids conformational distributions. Mol Phys 2013. [DOI: 10.1080/00268976.2013.800601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Dzuba SA, Raap J. Spin-Echo Electron Paramagnetic Resonance (EPR) Spectroscopy of a Pore-Forming (Lipo)Peptaibol in Model and Bacterial Membranes. Chem Biodivers 2013; 10:864-75. [DOI: 10.1002/cbdv.201200387] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 11/08/2022]
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Konov K, Isaev N, Dzuba S. Glycerol penetration profile in phospholipid bilayers measured by ESEEM of spin-labelled lipids. Mol Phys 2013. [DOI: 10.1080/00268976.2013.796416] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Matalon E, Kaminker I, Zimmermann H, Eisenstein M, Shai Y, Goldfarb D. Topology of the trans-membrane peptide WALP23 in model membranes under negative mismatch conditions. J Phys Chem B 2013; 117:2280-93. [PMID: 23311473 DOI: 10.1021/jp310056h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The organization and orientation of membrane-inserted helices is important for better understanding the mode of action of membrane-active peptides and of protein-membrane interactions. Here we report on the application of ESEEM (electron spin-echo envelope modulation) and DEER (double electron-electron resonance) techniques to probe the orientation and oligomeric state of an α-helical trans-membrane model peptide, WALP23, under conditions of negative mismatch between the hydrophobic cores of the model membrane and the peptide. Using ESEEM, we measured weak dipolar interactions between spin-labeled WALP23 and (2)H nuclei of either the solvent (D2O) or of lipids specifically deuterated at the choline group. The ESEEM data obtained from the deuterated lipids were fitted using a model that provided the spin label average distance from a layer of (2)H nuclei in the hydrophilic region of the membrane and the density of the (2)H nuclei in the layer. DEER was used to probe oligomerization through the dipolar interaction between two spin-labels on different peptides. We observed that the center of WALP23 does not coincide with the bilayer midplane and its N-terminus is more buried than the C-terminus. In addition, the ESEEM data fitting yielded a (2)H layer density that was much lower than expected. The DEER experiments revealed the presence of oligomers, the presence of which was attributable to the negative mismatch and the electrostatic dipole of the peptide. A discussion of a possible arrangement of the individual helices in the oligomers that is consistent with the ESEEM and DEER data is presented.
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Affiliation(s)
- Erez Matalon
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel 76100
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Lipid peroxidation and water penetration in lipid bilayers: a W-band EPR study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:510-7. [PMID: 23036933 DOI: 10.1016/j.bbamem.2012.09.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 11/20/2022]
Abstract
Lipid peroxidation plays a key role in the alteration of cell membrane's properties. Here we used as model systems multilamellar vesicles (MLVs) made of the first two products in the oxidative cascade of linoleoyl lecithin, namely 1-palmitoyl-2-(13-hydroperoxy-9,11-octadecanedienoyl)-lecithin (HpPLPC) and 1-palmitoyl-2-(13-hydroxy-9,11-octadecanedienoyl)-lecithin (OHPLPC), exhibiting a hydroperoxide or a hydroxy group at position 13, respectively. The two oxidized lipids were used either pure or in a 1:1 molar ratio mixture with untreated 1-palmitoyl-2-linoleoyl-lecithin (PLPC). The model membranes were doped with spin-labeled lipids to study bilayer alterations by electron paramagnetic resonance (EPR) spectroscopy. Two different spin-labeled lipids were used, bearing the doxyl ring at position (n) 5 or 16: γ-palmitoyl-β-(n-doxylstearoyl)-lecithin (n-DSPPC) and n-doxylstearic acid (n-DSA). Small changes in the acyl chain order in the sub-polar region and at the methyl-terminal induced by lipid peroxidation were detected by X-band EPR. Concomitantly, the polarity and proticity of the membrane bilayer in those regions were investigated at W band in frozen samples. Analysis of the g(xx) and A(zz) parameters revealed that OHPLPC, but mostly HpPLPC, induced a measurable increase in polarity and H-bonding propensity in the central region of the bilayer. Molecular dynamics simulation performed on 16-DSA in the PLPC-HpPLPC bilayer revealed that water molecules are statistically favored with respect to the hydroperoxide groups to interact with the nitroxide at the methyl-terminal, confirming that the H-bonds experimentally observed are due to increased water penetration in the bilayer. The EPR and MD data on model membranes demonstrate that cell membrane damage by oxidative stress cause alteration of water penetration in the bilayer.
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Guzzi R, Rizzuti B, Bartucci R. Dynamics and binding affinity of spin-labeled stearic acids in β-lactoglobulin: evidences from EPR spectroscopy and molecular dynamics simulation. J Phys Chem B 2012; 116:11608-15. [PMID: 22950964 DOI: 10.1021/jp3074392] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
β-Lactoglobulin (β-LG) is a member of the lipocalin protein family involved in the transport of fatty acids and other small hydrophobic molecules. The main binding site is at a central cavity, referred to as "calyx", formed by the protein β-barrel sandwich. Continuous-wave and pulsed Fourier transform electron spin resonance (cw- and FT-EPR) spectroscopy and molecular dynamics (MD) simulation were combined to investigate the interaction of fatty acids with bovine β-LG. Stearic acid bearing the nitroxide label at different positions, n, along the acyl chain (n-SASL, n = 5, 7, 10, 12, 16) were used. The EPR data show that the protein affinity for SASL decreases on going from n = 5 to 16. This behavior is due to the accommodation of the SASL in the protein calyx, which is hampered by steric hindrance of the doxyl ring for n ≥ 10, as evidenced by MD data. Conformation and dynamics of 5-SASL are similar to those of the unlabeled stearate molecule. 5-SASL in the protein binding site undergoes librational motion of small amplitude on the nanosecond time scale at cryogenic temperature and rotational dynamics with correlation time of 4.2 ns at physiological temperature. The results highlight the dynamical features of fatty acids/β-LG interaction.
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Affiliation(s)
- Rita Guzzi
- Department of Physics, University of Calabria, Ponte P. Bucci 31C, 87036 Rende (CS), Italy.
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Syryamina VN, De Zotti M, Peggion C, Formaggio F, Toniolo C, Raap J, Dzuba SA. A Molecular View on the Role of Cholesterol upon Membrane Insertion, Aggregation, and Water Accessibility of the Antibiotic Lipopeptide Trichogin GA IV As Revealed by EPR. J Phys Chem B 2012; 116:5653-60. [DOI: 10.1021/jp301660a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Victoria N. Syryamina
- Institute
of Chemical Kinetics
and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Marta De Zotti
- ICB, Padova Unit, CNR, Department
of Chemistry, University of Padova, 35131
Padova, Italy
| | - Cristina Peggion
- ICB, Padova Unit, CNR, Department
of Chemistry, University of Padova, 35131
Padova, Italy
| | - Fernando Formaggio
- ICB, Padova Unit, CNR, Department
of Chemistry, University of Padova, 35131
Padova, Italy
| | - Claudio Toniolo
- ICB, Padova Unit, CNR, Department
of Chemistry, University of Padova, 35131
Padova, Italy
| | - Jan Raap
- Leiden Institute
of Chemistry,
Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Institute
of Chemical Kinetics
and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
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Ghimire H, Hustedt EJ, Sahu ID, Inbaraj JJ, McCarrick R, Mayo DJ, Benedikt MR, Lee RT, Grosser SM, Lorigan GA. Distance measurements on a dual-labeled TOAC AChR M2δ peptide in mechanically aligned DMPC bilayers via dipolar broadening CW-EPR spectroscopy. J Phys Chem B 2012; 116:3866-73. [PMID: 22379959 DOI: 10.1021/jp212272d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A membrane alignment technique has been used to measure the distance between two TOAC nitroxide spin labels on the membrane-spanning M2δ, peptide of the nicotinic acetylcholine receptor (AChR), via CW-EPR spectroscopy. The TOAC-labeled M2δ peptides were mechanically aligned using DMPC lipids on a planar quartz support, and CW-EPR spectra were recorded at specific orientations. Global analysis in combination with rigorous spectral simulation was used to simultaneously analyze data from two different sample orientations for both single- and double-labeled peptides. We measured an internitroxide distance of 14.6 Å from a dual TOAC-labeled AChR M2δ peptide at positions 7 and 13 that closely matches with the 14.5 Å distance obtained from a model of the labeled AChR M2δ peptide. In addition, the angles determining the relative orientation of the two nitroxides have been determined, and the results compare favorably with molecular modeling. The global analysis of the data from the aligned samples gives much more precise estimates of the parameters defining the geometry of the two labels than can be obtained from a randomly dispersed sample.
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Affiliation(s)
- Harishchandra Ghimire
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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Dzikovski B, Tipikin D, Freed J. Conformational distributions and hydrogen bonding in gel and frozen lipid bilayers: a high frequency spin-label ESR study. J Phys Chem B 2012; 116:6694-706. [PMID: 22324811 DOI: 10.1021/jp211879s] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The ESR parameters of PC spin labels in frozen membranes do not simply represent the membrane polarity or water penetration profile. Instead, they show a distribution between hydrogen-bonded (HB) and non-hydrogen-bonded (non-HB) states, which is affected by a number of factors in the membrane composition. Similar to the exclusion of solutes from crystallizing solvents, the pure bulk gel phase excludes nitroxides, forcing acyl chains to take bent conformations. In these conformations, the nitroxide is hydrogen-bonded. Furthermore, upon gradual cooling in the supercooled gel, PC labels undergo slow lateral aggregation, resulting in a broad background signal. However, if the sample is instantly frozen, this background is replaced by the HB component. In membranes with cholesterol, the observed HB/non-HB ratio can best be described by a partition-like equilibrium between nitroxides located in defects of lipid structure within the hydrophobic core and those close to the membrane surface.
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Affiliation(s)
- Boris Dzikovski
- National Biomedical Center for Advanced ESR Technology, Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
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