1
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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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2
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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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3
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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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4
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Biondi B, Syryamina VN, Rocchio G, Barbon A, Formaggio F, Toniolo C, Raap J, Dzuba SA. Is Cys(MTSL) the Best α-Amino Acid Residue to Electron Spin Labeling of Synthetically Accessible Peptide Molecules with Nitroxides? ACS OMEGA 2022; 7:5154-5165. [PMID: 35187331 PMCID: PMC8851612 DOI: 10.1021/acsomega.1c06227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Electron paramagnetic resonance spectroscopy, particularly its pulse technique double electron-electron resonance (DEER) (also termed PELDOR), is rapidly becoming an extremely useful tool for the experimental determination of side chain-to-side chain distances between free radicals in molecules fundamental for life, such as polypeptides. Among appropriate probes, the most popular are undoubtedly nitroxide electron spin labels. In this context, suitable biosynthetically derived, helical regions of proteins, along with synthetic peptides with amphiphilic properties and antibacterial activities, are the most extensively investigated compounds. A strict requirement for a precise distance measurement has been identified in a minimal dynamic flexibility of the two nitroxide-bearing α-amino acid side chains. To this end, in this study, we have experimentally compared in detail the side-chain mobility properties of the two currently most widely utilized residues, namely, Cys(MTSL) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, two double-labeled, chemically synthesized 20-mer peptide molecules have been adopted as appropriate templates for our investigation on the determination of the model intramolecular separations. These double-Cys(MTSL) and double-TOAC compounds are both analogues of the almost completely rigid backbone peptide ruler which we have envisaged and 3D structurally analyzed as our original, unlabeled compound. Here, we have clearly found that the TOAC side-chain labels are largely more 3D structurally restricted than the MTSL labels. From this result, we conclude that the TOAC residue offers more precise information than the Cys(MTSL) residue on the side chain-to-side chain distance distribution in synthetically accessible peptide molecules.
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Affiliation(s)
- Barbara Biondi
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Victoria N. Syryamina
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
| | - Gabriele Rocchio
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Antonio Barbon
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Jan Raap
- Leiden
Institute of Chemistry, Gorlaeus Laboratories,
Leiden University, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
- Department
of Physics, Novosibirsk State University, 630090 Novosibirsk, Russian Federation
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5
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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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6
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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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7
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Salnikov ES, De Zotti M, Bobone S, Mazzuca C, Raya J, Siano AS, Peggion C, Toniolo C, Stella L, Bechinger B. Trichogin GA IV Alignment and Oligomerization in Phospholipid Bilayers. Chembiochem 2019; 20:2141-2150. [PMID: 31125169 DOI: 10.1002/cbic.201900263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Indexed: 12/21/2022]
Abstract
Trichogin GA IV is a short peptaibol with antimicrobial activity. This uncharged, but amphipathic, sequence is aligned at the membrane interface and undergoes a transition to an aggregated state that inserts more deeply into the membrane, an assembly that predominates at a peptide-to-lipid ratio (P/L) of 1:20. In this work, the natural trichogin sequence was prepared and reconstituted into oriented lipid bilayers. The 15 N NMR chemical shift is indicative of a well-defined alignment of the peptide parallel to the membrane surface at P/Ls of 1:120 and 1:20. When the P/L is increased to 1:8, an additional peptide topology is observed that is indicative of a heterogeneous orientation, with helix alignments ranging from around the magic angle to perfectly in-plane. The topological preference of the trichogin helix for an orientation parallel to the membrane surface was confirmed by attenuated total reflection FTIR spectroscopy. Furthermore, 19 F CODEX experiments were performed on a trichogin sequence with 19 F-Phe at position 10. The CODEX decay is in agreement with a tetrameric complex, in which the 19 F sites are about 9-9.5 Å apart. Thus, a model emerges in which the monomeric peptide aligns along the membrane surface. When the peptide concentration increases, first dimeric and then tetrameric assemblies form, made up from helices oriented predominantly parallel to the membrane surface. The formation of these aggregates correlates with the release of vesicle contents including relatively large molecules.
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Affiliation(s)
- Evgeniy S Salnikov
- Institut de Chimie, University of Strasbourg, CNRS, UMR 7177, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Marta De Zotti
- ICB, Padova Unit, CNR', Department of Chemistry, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Claudia Mazzuca
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Jesus Raya
- Institut de Chimie, University of Strasbourg, CNRS, UMR 7177, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Alvaro S Siano
- Departamento de Química Organica, Facultad de Bioquímica y Ciencias Biologicas, Universidad Nacional del Litoral, Ciudad Universitaria UNL, Ruta Nacional N° 168, Km 472, Santa Fe, 3000, Argentina
| | - Cristina Peggion
- ICB, Padova Unit, CNR', Department of Chemistry, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Claudio Toniolo
- ICB, Padova Unit, CNR', Department of Chemistry, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Burkhard Bechinger
- Institut de Chimie, University of Strasbourg, CNRS, UMR 7177, 4, rue Blaise Pascal, 67070, Strasbourg, France
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8
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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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9
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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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10
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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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11
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Bortolus M, Dalzini A, Maniero AL, Panighel G, Siano A, Toniolo C, De Zotti M, Formaggio F. Insights into peptide-membrane interactions of newly synthesized, nitroxide-containing analogs of the peptaibiotic trichogin GAIV using EPR. Biopolymers 2017; 108. [DOI: 10.1002/bip.22913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/21/2016] [Accepted: 06/29/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Marco Bortolus
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | - Annalisa Dalzini
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | | | - Giacomo Panighel
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | - Alvaro Siano
- Department of Chemistry; University of Padova; Padova 35131 Italy
- Departamento de Química Orgánica; Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL); 3000 Santa Fe Argentina
| | - Claudio Toniolo
- Department of Chemistry; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
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12
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Schmidt T, Ghirlando R, Baber J, Clore GM. Quantitative Resolution of Monomer-Dimer Populations by Inversion Modulated DEER EPR Spectroscopy. Chemphyschem 2016; 17:2987-2991. [PMID: 27442455 PMCID: PMC5590656 DOI: 10.1002/cphc.201600726] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Indexed: 12/13/2022]
Abstract
A simple method, based on inversion modulated double electron-electron resonance electron paramagnetic resonance (DEER EPR) spectroscopy, is presented for determining populations of monomer and dimer in proteins (as well as any other biological macromolecules). The method is based on analysis of modulation depth versus electron double resonance (ELDOR) pulse flip angle. High accuracy is achieved by complete deuteration, extensive sampling of a large number of ELDOR pulse flip angle values, and combined analysis of differently labeled spin samples. We demonstrate the method using two different proteins: an obligate monomer exemplified by the small immunoglobulin binding B domain of protein A, and the p66 subunit of HIV-1 reverse transcriptase which exists as an equilibrium mixture of monomer and dimer species whose relative populations are affected by glycerol content. This information is crucial for quantitative analysis of distance distributions involving proteins that may exist as mixtures of monomer, dimer and high order multimers under the conditions of the DEER EPR experiment.
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Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Rodolfo Ghirlando
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - James Baber
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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13
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Milov AD, Tsvetkov YD, Raap J, De Zotti M, Formaggio F, Toniolo C. Review conformation, self-aggregation, and membrane interaction of peptaibols as studied by pulsed electron double resonance spectroscopy. Biopolymers 2016; 106:6-24. [DOI: 10.1002/bip.22713] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/29/2015] [Accepted: 08/09/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Alexander D. Milov
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk 630090 Russian Federation
| | - Yuri D. Tsvetkov
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk 630090 Russian Federation
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University; 2300 RA Leiden The Netherlands
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | | | - Claudio Toniolo
- Department of Chemistry; University of Padova; Padova 35131 Italy
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14
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Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy is a well-established method that has recently grown in popularity as an experimental technique, with multiple applications in protein and peptide science. The growth is driven by development of labeling strategies, as well as by considerable technical advances in the field, that are paralleled by an increased availability of EPR instrumentation. While the method requires an introduction of a paramagnetic probe at a well-defined position in a peptide sequence, it has been shown to be minimally destructive to the peptide structure and energetics of the peptide-membrane interactions. In this chapter, we describe basic approaches for using SDSL EPR spectroscopy to study interactions between small peptides and biological membranes or membrane mimetic systems. We focus on experimental approaches to quantify peptide-membrane binding, topology of bound peptides, and characterize peptide aggregation. Sample preparation protocols including spin-labeling methods and preparation of membrane mimetic systems are also described.
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Affiliation(s)
- Tatyana I Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA.
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
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15
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Manukovsky N, Frydman V, Goldfarb D. Gd3+ Spin Labels Report the Conformation and Solvent Accessibility of Solution and Vesicle-Bound Melittin. J Phys Chem B 2015; 119:13732-41. [DOI: 10.1021/acs.jpcb.5b03523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Nurit Manukovsky
- Departments of †Chemical Physics and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Veronica Frydman
- Departments of †Chemical Physics and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Daniella Goldfarb
- Departments of †Chemical Physics and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
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16
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Kinde MN, Chen Q, Lawless MJ, Mowrey DD, Xu J, Saxena S, Xu Y, Tang P. Conformational Changes Underlying Desensitization of the Pentameric Ligand-Gated Ion Channel ELIC. Structure 2015; 23:995-1004. [PMID: 25960405 DOI: 10.1016/j.str.2015.03.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/24/2015] [Accepted: 03/30/2015] [Indexed: 11/18/2022]
Abstract
Structural rearrangements underlying functional transitions of pentameric ligand-gated ion channels (pLGICs) are not fully understood. Using (19)F nuclear magnetic resonance and electron spin resonance spectroscopy, we found that ELIC, a pLGIC from Erwinia chrysanthemi, expanded the extracellular end and contracted the intracellular end of its pore during transition from the resting to an apparent desensitized state. Importantly, the contraction at the intracellular end of the pore likely forms a gate to restrict ion transport in the desensitized state. This gate differs from the hydrophobic gate present in the resting state. Conformational changes of the TM2-TM3 loop were limited to the N-terminal end. The TM4 helices and the TM3-TM4 loop appeared relatively insensitive to agonist-mediated structural rearrangement. These results indicate that conformational changes accompanying functional transitions are not uniform among different ELIC regions. This work also revealed the co-existence of multiple conformations for a given state and suggested asymmetric conformational arrangements in a homomeric pLGIC.
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Affiliation(s)
- Monica N Kinde
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Qiang Chen
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - David D Mowrey
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Jiawei Xu
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Yan Xu
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Pei Tang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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17
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De Zotti M, Bobone S, Bortolotti A, Longo E, Biondi B, Peggion C, Formaggio F, Toniolo C, Dalla Bona A, Kaptein B, Stella L. 4-Cyano-α-methyl-l-phenylalanine as a Spectroscopic Marker for the Investigation of PeptaibioticMembrane Interactions. Chem Biodivers 2015; 12:513-27. [DOI: 10.1002/cbdv.201400404] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 11/10/2022]
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18
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Iftemi S, De Zotti M, Formaggio F, Toniolo C, Stella L, Luchian T. Electrophysiology investigation of Trichogin GA IV activity in planar lipid membranes reveals ion channels of well-defined size. Chem Biodivers 2015; 11:1069-77. [PMID: 25044592 DOI: 10.1002/cbdv.201300334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Indexed: 11/07/2022]
Abstract
Trichogin GA IV, an antimicrobial peptaibol, exerts its function by augmenting membrane permeability, but the molecular aspects of its pore-forming mechanism are still debated. Several lines of evidence indicate a 'barrel-stave' channel structure, similar to that of alamethicin, but the length of a trichogin helix is too short to span a normal bilayer. Herein, we present electrophysiology measurements in planar bilayers, showing that trichogin does form channels of a well-defined size (R=4.2⋅10(9) Ω; corresponding at least to a trimeric aggregate) that span the membrane and allow ion diffusion, but do not exhibit voltage-dependent rectification, unlike those of alamethicin.
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Affiliation(s)
- Sorana Iftemi
- Department of Physics, Laboratory of Molecular Biophysics and Medical Physics, Alexandru I. Cuza University, 11, Blvd. Carol I, RO-700506 Iasi (phone: +40-232-201191)
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19
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Smetanin M, Sek S, Maran F, Lipkowski J. Molecular resolution visualization of a pore formed by trichogin, an antimicrobial peptide, in a phospholipid matrix. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3130-6. [DOI: 10.1016/j.bbamem.2014.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 08/05/2014] [Accepted: 08/07/2014] [Indexed: 11/16/2022]
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20
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Bortolus M, Dalzini A, Toniolo C, Hahm KS, Maniero AL. Interaction of hydrophobic and amphipathic antimicrobial peptides with lipid bicelles. J Pept Sci 2014; 20:517-25. [PMID: 24863176 DOI: 10.1002/psc.2645] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/10/2014] [Indexed: 02/03/2023]
Abstract
Bicelles are model membrane systems that can be macroscopically oriented in a magnetic field at physiological temperature. The macroscopic orientation of bicelles allows to detect, by means of magnetic resonance spectroscopies, small changes in the order of the bilayer caused by solutes interacting with the membrane. These changes would be hardly detectable in isotropic systems such as vesicles or micelles. The aim of this work is to show that bicelles represent a convenient tool to investigate the behavior of antimicrobial peptides (AMPs) interacting with membranes, using electron paramagnetic resonance (EPR) spectroscopy. We performed the EPR experiments on spin-labeled bicelles using various AMPs of different length, charge, and amphipathicity: alamethicin, trichogin GA IV, magainin 2, HP(2-20), and HPA3. We evaluated the changes in the order parameter of the spin-labeled lipids as a function of the peptide-to-lipid ratio. We show that bicelles labeled at position 5 of the lipid chains are very sensitive to the perturbation induced by the AMPs even at low peptide concentrations. Our study indicates that peptides that are known to disrupt the membrane by different mechanisms (i.e., alamethicin vs magainin 2) show very distinct trends of the order parameter as a function of peptide concentration. Therefore, spin-labeled bicelles proved to be a good system to evaluate the membrane disruption mechanism of new AMPs.
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Affiliation(s)
- Marco Bortolus
- Department of Chemistry, University of Padova, via Marzolo 1, Padova, 35131, Italy
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21
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Becucci L, Guidelli R. Mercury-supported biomimetic membranes for the investigation of antimicrobial peptides. Pharmaceuticals (Basel) 2014; 7:136-68. [PMID: 24463343 PMCID: PMC3942690 DOI: 10.3390/ph7020136] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/17/2014] [Indexed: 11/16/2022] Open
Abstract
Tethered bilayer lipid membranes (tBLMs) consist of a lipid bilayer interposed between an aqueous solution and a hydrophilic "spacer" anchored to a gold or mercury electrode. There is great potential for application of these biomimetic membranes for the elucidation of structure-function relationships of membrane peptides and proteins. A drawback in the use of mercury-supported tBLMs with respect to gold-supported ones is represented by the difficulty in applying surface sensitive, spectroscopic and scanning probe microscopic techniques to gather information on the architecture of these biomimetic membranes. Nonetheless, mercury-supported tBLMs are definitely superior to gold-supported biomimetic membranes for the investigation of the function of membrane peptides and proteins, thanks to a fluidity and lipid lateral mobility comparable with those of bilayer lipid membranes interposed between two aqueous phases (BLMs), but with a much higher robustness and resistance to electric fields. The different features of mercury-supported tBLMs reconstituted with functionally active membrane proteins and peptides of bacteriological or pharmacological interest may be disclosed by a judicious choice of the most appropriate electrochemical techniques. We will describe the way in which electrochemical impedance spectroscopy, potential-step chronocoulometry, cyclic voltammetry and phase-sensitive AC voltammetry are conveniently employed to investigate the structure of mercury-supported tBLMs and the mode of interaction of antimicrobial peptides reconstituted into them.
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Affiliation(s)
- Lucia Becucci
- Department of Chemistry "Ugo Schiff", Florence University, Via della Lastruccia 3, Sesto Fiorentino (Firenze) 50019, Italy.
| | - Rolando Guidelli
- Retired professor from Florence University, Firenze 50121, Italy.
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22
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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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23
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Tsvetkov YD. Nitroxyls and PELDOR: Nitroxyl radicals in pulsed electron-electron double resonance spectroscopy. J STRUCT CHEM+ 2013. [DOI: 10.1134/s0022476613070044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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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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25
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Peggion C, Biondi B, Battistella C, De Zotti M, Oancea S, Formaggio F, Toniolo C. Spectroscopically Labeled Peptaibiotics. Synthesis and Properties of Selected Trichogin GA IV Analogs Bearing a Side-Chain-Monofluorinated Aromatic Amino Acid for19F-NMR Analysis. Chem Biodivers 2013; 10:904-19. [DOI: 10.1002/cbdv.201200389] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 11/08/2022]
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26
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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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27
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Lueders P, Jäger H, Hemminga MA, Jeschke G, Yulikov M. Distance Measurements on Orthogonally Spin-Labeled Membrane Spanning WALP23 Polypeptides. J Phys Chem B 2013; 117:2061-8. [DOI: 10.1021/jp311287t] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Petra Lueders
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Heidrun Jäger
- Laboratory
of Biophysics, Wageningen University, Wageningen,
The Netherlands
| | - Marcus A. Hemminga
- Laboratory
of Biophysics, Wageningen University, Wageningen,
The Netherlands
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
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28
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Peggion C, Biondi B, De Zotti M, Oancea S, Formaggio F, Toniolo C. Spectroscopically labeled peptaibiotic analogs: the 4-nitrophenylalanine infrared absorption probe inserted at different positions into trichogin GA IV. J Pept Sci 2012; 19:246-56. [DOI: 10.1002/psc.2475] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 11/22/2012] [Accepted: 11/23/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Cristina Peggion
- ICB, Padova Unit, CNR, Department of Chemistry; University of Padova; via Marzolo 1 35131 Padova Italy
| | - Barbara Biondi
- ICB, Padova Unit, CNR, Department of Chemistry; University of Padova; via Marzolo 1 35131 Padova Italy
| | - Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry; University of Padova; via Marzolo 1 35131 Padova Italy
| | - Simona Oancea
- Department of Biochemistry and Toxicology; University ‘Lucian Blaga’; 550012 Sibiu Romania
| | - Fernando Formaggio
- ICB, Padova Unit, CNR, Department of Chemistry; University of Padova; via Marzolo 1 35131 Padova Italy
| | - Claudio Toniolo
- ICB, Padova Unit, CNR, Department of Chemistry; University of Padova; via Marzolo 1 35131 Padova Italy
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29
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Bobone S, Gerelli Y, De Zotti M, Bocchinfuso G, Farrotti A, Orioni B, Sebastiani F, Latter E, Penfold J, Senesi R, Formaggio F, Palleschi A, Toniolo C, Fragneto G, Stella L. Membrane thickness and the mechanism of action of the short peptaibol trichogin GA IV. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:1013-24. [PMID: 23220179 DOI: 10.1016/j.bbamem.2012.11.033] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/20/2012] [Accepted: 11/27/2012] [Indexed: 12/21/2022]
Abstract
Trichogin GA IV (GAIV) is an antimicrobial peptide of the peptaibol family, like the extensively studied alamethicin (Alm). GAIV acts by perturbing membrane permeability. Previous data have shown that pore formation is related to GAIV aggregation and insertion in the hydrophobic core of the membrane. This behavior is similar to that of Alm and in agreement with a barrel-stave mechanism, in which transmembrane oriented peptides aggregate to form a channel. However, while the 19-amino acid long Alm has a length comparable to the membrane thickness, GAIV comprises only 10 amino acids, and its helix is about half the normal bilayer thickness. Here, we report the results of neutron reflectivity measurements, showing that GAIV inserts in the hydrophobic region of the membrane, causing a significant thinning of the bilayer. Molecular dynamics simulations of GAIV/membrane systems were also performed. For these studies we developed a novel approach for constructing the initial configuration, by embedding the short peptide in the hydrophobic core of the bilayer. These calculations indicated that in the transmembrane orientation GAIV interacts strongly with the polar phospholipid headgroups, drawing them towards its N- and C-termini, inducing membrane thinning and becoming able to span the bilayer. Finally, vesicle leakage experiments demonstrated that GAIV activity is significantly higher with thinner membranes, becoming similar to that of Alm when the bilayer thickness is comparable to its size. Overall, these data indicate that a barrel-stave mechanism of pore formation might be possible for GAIV and for similarly short peptaibols despite their relatively small size.
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Affiliation(s)
- S Bobone
- Department of Chemical Sciences and Technologies, University of Rome, Rome, Italy
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30
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Becucci L, Maran F, Guidelli R. Probing membrane permeabilization by the antibiotic lipopeptaibol trichogin GA IV in a tethered bilayer lipid membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1656-62. [DOI: 10.1016/j.bbamem.2012.03.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/16/2012] [Accepted: 03/30/2012] [Indexed: 10/28/2022]
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31
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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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32
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The spin label amino acid TOAC and its uses in studies of peptides: chemical, physicochemical, spectroscopic, and conformational aspects. Biophys Rev 2012; 4:45-66. [PMID: 22347893 PMCID: PMC3271205 DOI: 10.1007/s12551-011-0064-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 12/20/2011] [Indexed: 01/21/2023] Open
Abstract
We review work on the paramagnetic amino acid 2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid, TOAC, and its applications in studies of peptides and peptide synthesis. TOAC was the first spin label probe incorporated in peptides by means of a peptide bond. In view of the rigid character of this cyclic molecule and its attachment to the peptide backbone via a peptide bond, TOAC incorporation has been very useful to analyze backbone dynamics and peptide secondary structure. Many of these studies were performed making use of EPR spectroscopy, but other physical techniques, such as X-ray crystallography, CD, fluorescence, NMR, and FT-IR, have been employed. The use of double-labeled synthetic peptides has allowed the investigation of their secondary structure. A large number of studies have focused on the interaction of peptides, both synthetic and biologically active, with membranes. In the latter case, work has been reported on ligands and fragments of GPCR, host defense peptides, phospholamban, and β-amyloid. EPR studies of macroscopically aligned samples have provided information on the orientation of peptides in membranes. More recent studies have focused on peptide–protein and peptide–nucleic acid interactions. Moreover, TOAC has been shown to be a valuable probe for paramagnetic relaxation enhancement NMR studies of the interaction of labeled peptides with proteins. The growth of the number of TOAC-related publications suggests that this unnatural amino acid will find increasing applications in the future.
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33
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De Zotti M, Biondi B, Peggion C, Formaggio F, Park Y, Hahm KS, Toniolo C. Trichogin GA IV: a versatile template for the synthesis of novel peptaibiotics. Org Biomol Chem 2011; 10:1285-99. [PMID: 22179201 DOI: 10.1039/c1ob06178j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trichogin GA IV, isolated from the fungus Trichoderma longibrachiatum, is the prototype of lipopeptaibols, the sub-class of short-length peptaibiotics exhibiting membrane-modifying properties. This peptaibol is predominantly folded in a mixed 3(10)-/α- helical conformation with a clear, albeit modest, amphiphilic character, which is likely to be responsible for its capability to perturb bacterial membranes and to induce cell death. In previous papers, we reported on the interesting biological properties of trichogin GA IV, namely its good activity against Gram positive bacteria, in particular methicillin-resistant S. aureus strains, its stability towards proteolytic degradation, and its low hemolytic activity. Aiming at broadening the antimicrobial activity spectrum by increasing the peptide helical amphiphilicity, in this work we synthesized, by solution and solid-phase methodologies, purified and fully characterized a set of trichogin GA IV analogs in which the four Gly residues at positions 2, 5, 6, 9, lying in the poorly hydrophilic face of the helical structure, are substituted by one (position 2, 5, 6 or 9), two (positions 5 and 6), three (positions 2, 5, and 9), and four (positions 2, 5, 6, and 9) Lys residues. The conformational preferences of the Lys-containing analogs were assessed by FT-IR absorption, CD and 2D-NMR techniques in aqueous, organic, and membrane-mimetic environments. Interestingly, it turns out that the presence of charged residues induces a transition of the helical conformation adopted by the peptaibols (from 3(10)- to α-helix) as a function of pH in a reversible process. The role played in the analogs by the markedly increased amphiphilicity was further tested by fluorescence leakage experiments in model membranes, protease resistance, antibacterial and antifungal activities, cytotoxicity, and hemolysis. Taken together, our biological results provide evidence that some of the least substituted among these analogs are good candidates for the development of new membrane-active antimicrobial agents.
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Affiliation(s)
- Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131, Padova, Italy
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34
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Gordon-Grossman M, Zimmermann H, Wolf SG, Shai Y, Goldfarb D. Investigation of Model Membrane Disruption Mechanism by Melittin using Pulse Electron Paramagnetic Resonance Spectroscopy and Cryogenic Transmission Electron Microscopy. J Phys Chem B 2011; 116:179-88. [DOI: 10.1021/jp207159z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Chu S, Maltsev S, Emwas AH, Lorigan GA. Solid-state NMR paramagnetic relaxation enhancement immersion depth studies in phospholipid bilayers. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 207:89-94. [PMID: 20851650 PMCID: PMC2978330 DOI: 10.1016/j.jmr.2010.08.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 08/11/2010] [Accepted: 08/18/2010] [Indexed: 05/20/2023]
Abstract
A new approach for determining the membrane immersion depth of a spin-labeled probe has been developed using paramagnetic relaxation enhancement (PRE) in solid-state NMR spectroscopy. A DOXYL spin label was placed at different sites of 1-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholine (PSPC) phospholipid bilayers as paramagnetic moieties and the resulting enhancements of the longitudinal relaxation (T₁) times of ³¹P nuclei on the surface of the bilayers were measured by a standard inversion recovery pulse sequence. The ³¹P NMR spin-lattice relaxation times decrease steadily as the DOXYL spin label moves closer to the surface as well as the concentration of the spin-labeled lipids increase. The enhanced relaxation vs. the position and concentration of spin-labels indicate that PRE induced by the DOXYL spin label are significant to determine longer distances over the whole range of the membrane depths. When these data were combined with estimated correlation times τ(c), the r⁻⁶-weighted, time-averaged distances between the spin-labels and the ³¹P nuclei on the membrane surface were estimated. The application of using this solid-state NMR PRE approach coupled with site-directed spin labeling (SDSL) may be a powerful method for measuring membrane protein immersion depth.
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Affiliation(s)
- Shidong Chu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA 45056
| | - Sergey Maltsev
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA 45056
| | - A-H Emwas
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA 45056
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA 45056
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36
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Syryamina VN, Isaev NP, Peggion C, Formaggio F, Toniolo C, Raap J, Dzuba SA. Small-Amplitude Backbone Motions of the Spin-Labeled Lipopeptide Trichogin GA IV in a Lipid Membrane As Revealed by Electron Spin Echo. J Phys Chem B 2010; 114:12277-83. [DOI: 10.1021/jp106769q] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Victoria N. Syryamina
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands
| | - Nikolay P. Isaev
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands
| | - Cristina Peggion
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands
| | - Fernando Formaggio
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands
| | - Claudio Toniolo
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands
| | - Jan Raap
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands
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Gordon-Grossman M, Gofman Y, Zimmermann H, Frydman V, Shai Y, Ben-Tal N, Goldfarb D. A Combined Pulse EPR and Monte Carlo Simulation Study Provides Molecular Insight on Peptide−Membrane Interactions. J Phys Chem B 2009; 113:12687-95. [DOI: 10.1021/jp905129b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michal Gordon-Grossman
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Yana Gofman
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Herbert Zimmermann
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Veronica Frydman
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Yechiel Shai
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Nir Ben-Tal
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Daniella Goldfarb
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
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38
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Milov AD, Samoilova RI, Tsvetkov YD, De Zotti M, Formaggio F, Toniolo C, Handgraaf JW, Raap J. Structure of self-aggregated alamethicin in ePC membranes detected by pulsed electron-electron double resonance and electron spin echo envelope modulation spectroscopies. Biophys J 2009; 96:3197-209. [PMID: 19383464 DOI: 10.1016/j.bpj.2009.01.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 01/14/2009] [Accepted: 01/15/2009] [Indexed: 11/17/2022] Open
Abstract
PELDOR spectroscopy was exploited to study the self-assembled super-structure of the [Glu(OMe)(7,18,19)]alamethicin molecules in vesicular membranes at peptide to lipid molar ratios in the range of 1:70-1:200. The peptide molecules were site-specifically labeled with TOAC electron spins. From the magnetic dipole-dipole interaction between the nitroxides of the monolabeled constituents and the PELDOR decay patterns measured at 77 K, intermolecular-distance distribution functions were obtained and the number of aggregated molecules (n approximately 4) was estimated. The distance distribution functions exhibit a similar maximum at 2.3 nm. In contrast to Alm16, for Alm1 and Alm8 additional maxima were recorded at 3.2 and approximately 5.2 nm. From ESEEM experiments and based on the membrane polarity profiles, the penetration depths of the different spin-labeled positions into the membrane were qualitatively estimated. It was found that the water accessibility of the spin-labels follows the order TOAC-1 > TOAC-8 approximately TOAC-16. The geometric data obtained are discussed in terms of a penknife molecular model. At least two peptide chains are aligned parallel and eight ester groups of the polar Glu(OMe)(18,19) residues are suggested to stabilize the self-aggregate superstructure.
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Affiliation(s)
- Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation
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39
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Different mechanisms of action of antimicrobial peptides: insights from fluorescence spectroscopy experiments and molecular dynamics simulations. J Pept Sci 2009; 15:550-8. [DOI: 10.1002/psc.1144] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Bartucci R, Guzzi R, Sportelli L, Marsh D. Intramembrane water associated with TOAC spin-labeled alamethicin: electron spin-echo envelope modulation by D2O. Biophys J 2009; 96:997-1007. [PMID: 19186137 DOI: 10.1016/j.bpj.2008.10.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 10/21/2008] [Indexed: 11/30/2022] Open
Abstract
Alamethicin is a 20-residue, hydrophobic, helical peptide, which forms voltage-sensitive ion channels in lipid membranes. The helicogenic, nitroxyl amino acid TOAC was substituted isosterically for Aib at residue positions 1, 8, or 16 in a F50/5 alamethicin analog to enable EPR studies. Electron spin-echo envelope modulation (ESEEM) spectroscopy was used to investigate the water exposure of TOAC-alamethicin introduced into membranes of saturated or unsaturated diacyl phosphatidylcholines that were dispersed in D2O. Echo-detected EPR spectra were used to assess the degree of assembly of the peptide in the membrane, via the instantaneous diffusion from intermolecular spin-spin interactions. The profile of residue exposure to water differs between membranes of saturated and unsaturated lipids. In monounsaturated dioleoyl phosphatidylcholine, D2O-ESEEM intensities decrease from TOAC(1) to TOAC(8) and TOAC(16) but not uniformly. This is consistent with a transmembrane orientation for the protoassembled state, in which TOAC(16) is located in the bilayer leaflet opposite to that of TOAC(1) and TOAC(8). Relative to the monomer in fluid bilayers, assembled alamethicin is disposed asymmetrically about the bilayer midplane. In saturated dimyristoyl phosphatidylcholine, the D2O-ESEEM intensity is greatest for TOAC(8), indicating a more superficial location for alamethicin, which correlates with the difference in orientation between gel- and fluid-phase membranes found by conventional EPR of TOAC-alamethicin in aligned phosphatidylcholine bilayers. Increasing alamethicin/lipid ratio in saturated phosphatidylcholine shifts the profile of water exposure toward that with unsaturated lipid, consistent with proposals of a critical concentration for switching between the two different membrane-associated states.
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Affiliation(s)
- R Bartucci
- Dipartimento di Fisica and Unità di Recerca Consorzio Nazionale Interuniversitario per le Scienze fisiche della Materia, Università della Calabria, Arcavacata di Rende, Italy
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41
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Salnikov ES, Zotti MD, Formaggio F, Li X, Toniolo C, OʼNeil JDJ, Raap J, Dzuba SA, Bechinger B. Alamethicin Topology in Phospholipid Membranes by Oriented Solid-state NMR and EPR Spectroscopies: a Comparison. J Phys Chem B 2009; 113:3034-42. [DOI: 10.1021/jp8101805] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evgeniy S. Salnikov
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Marta De Zotti
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Fernando Formaggio
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Xing Li
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Claudio Toniolo
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Joe D. J. OʼNeil
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jan Raap
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Burkhard Bechinger
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
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Volkov A, Dockter C, Bund T, Paulsen H, Jeschke G. Pulsed EPR determination of water accessibility to spin-labeled amino acid residues in LHCIIb. Biophys J 2009; 96:1124-41. [PMID: 19186148 PMCID: PMC2716639 DOI: 10.1016/j.bpj.2008.09.047] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 09/22/2008] [Indexed: 11/24/2022] Open
Abstract
Membrane proteins reside in a structured environment in which some of their residues are accessible to water, some are in contact with alkyl chains of lipid molecules, and some are buried in the protein. Water accessibility of residues may change during folding or function-related structural dynamics. Several techniques based on the combination of pulsed electron paramagnetic resonance (EPR) with site-directed spin labeling can be used to quantify such water accessibility. Accessibility parameters for different residues in major plant light-harvesting complex IIb are determined by electron spin echo envelope modulation spectroscopy in the presence of deuterated water, deuterium contrast in transversal relaxation rates, analysis of longitudinal relaxation rates, and line shape analysis of electron-spin-echo-detected EPR spectra as well as by the conventional techniques of measuring the maximum hyperfine splitting and progressive saturation in continuous-wave EPR. Systematic comparison of these parameters allows for a more detailed characterization of the environment of the spin-labeled residues. These techniques are applicable independently of protein size and require approximately 10-20 nmol of singly spin-labeled protein per sample. For a residue close to the N-terminus, in a domain unresolved in the existing x-ray structures of light-harvesting complex IIb, all methods indicate high water accessibility.
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Affiliation(s)
- A. Volkov
- Max-Planck Institute for Polymer Research, Mainz, Germany
| | - C. Dockter
- Institute of General Botany, Johannes Gutenberg University, Mainz, Germany
| | - T. Bund
- Institute of General Botany, Johannes Gutenberg University, Mainz, Germany
| | - H. Paulsen
- Institute of General Botany, Johannes Gutenberg University, Mainz, Germany
| | - G. Jeschke
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich, Switzerland
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Schiemann O, Prisner TF. Long-range distance determinations in biomacromolecules by EPR spectroscopy. Q Rev Biophys 2007; 40:1-53. [PMID: 17565764 DOI: 10.1017/s003358350700460x] [Citation(s) in RCA: 423] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy provides a variety of tools to study structures and structural changes of large biomolecules or complexes thereof. In order to unravel secondary structure elements, domain arrangements or complex formation, continuous wave and pulsed EPR methods capable of measuring the magnetic dipole coupling between two unpaired electrons can be used to obtain long-range distance constraints on the nanometer scale. Such methods yield reliably and precisely distances of up to 80 A, can be applied to biomolecules in aqueous buffer solutions or membranes, and are not size limited. They can be applied either at cryogenic or physiological temperatures and down to amounts of a few nanomoles. Spin centers may be metal ions, metal clusters, cofactor radicals, amino acid radicals, or spin labels. In this review, we discuss the advantages and limitations of the different EPR spectroscopic methods, briefly describe their theoretical background, and summarize important biological applications. The main focus of this article will be on pulsed EPR methods like pulsed electron-electron double resonance (PELDOR) and their applications to spin-labeled biosystems.
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Affiliation(s)
- Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, J. W. Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany.
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44
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De Simone F, Guzzi R, Sportelli L, Marsh D, Bartucci R. Electron spin-echo studies of spin-labelled lipid membranes and free fatty acids interacting with human serum albumin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:1541-9. [PMID: 17397796 DOI: 10.1016/j.bbamem.2007.02.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 01/29/2007] [Accepted: 02/12/2007] [Indexed: 11/23/2022]
Abstract
Human serum albumin (HSA) is an abundant plasma protein that transports fatty acids and also binds a wide variety of hydrophobic pharmacores. Echo-detected (ED) EPR spectra and D(2)O-electron spin echo envelope modulation (ESEEM) Fourier-transform spectra of spin-labelled free fatty acids and phospholipids were used jointly to investigate the binding of stearic acid to HSA and the adsorption of the protein on dipalmitoyl phosphatidylcholine (DPPC) membranes. In membranes, torsional librations are detected in the ED-spectra, the intensity of which depends on chain position at low temperature. Water penetration into the membrane is seen in the D(2)O-ESEEM spectra, the intensity of which decreases greatly at the middle of the membrane. Both the chain librational motion and the water penetration are only little affected by adsorption of serum albumin at the DPPC membrane surface. In contrast, both the librational motion and the accessibility of the chains to water are very different in the hydrophobic fatty acid binding sites of HSA from those in membranes. Indeed, the librational motion of bound fatty acids is suppressed at low temperature, and is similar for the different chain positions, at all temperatures. Correspondingly, all segments of the bound chains are accessible to water, to rather similar extents.
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Affiliation(s)
- Francesco De Simone
- Dipartimento di Fisica, Laboratorio di Biofisica Molecolare and UdR CNISM, Università della Calabria, I-87036 Arcavacata di Rende, CS, Italy
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