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Kumar P, van Son M, Zheng T, Valdink D, Raap J, Kros A, Huber M. Coiled-coil formation of the membrane-fusion K/E peptides viewed by electron paramagnetic resonance. PLoS One 2018; 13:e0191197. [PMID: 29351320 PMCID: PMC5774749 DOI: 10.1371/journal.pone.0191197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/29/2017] [Indexed: 11/18/2022] Open
Abstract
The interaction of the complementary K (Ac-(KIAALKE)3-GW-NH2) and E (Ac-(EIAALEK)3-GY-NH2) peptides, components of the zipper of an artificial membrane fusion system (Robson Marsden H. et al. Angew Chemie Int Ed. 2009) is investigated by electron paramagnetic resonance (EPR). By frozen solution continuous-wave EPR and double electron-electron resonance (DEER), the distance between spin labels attached to the K- and to the E-peptide is measured. Three constructs of spin-labelled K- and E-peptides are used in five combinations for low temperature investigations. The K/E heterodimers are found to be parallel, in agreement with previous studies. Also, K homodimers in parallel orientation were observed, a finding that was not reported before. Comparison to room-temperature, solution EPR shows that the latter method is less specific to detect this peptide-peptide interaction. Combining frozen solution cw-EPR for short distances (1.8 nm to 2.0 nm) and DEER for longer distances thus proves versatile to detect the zipper interaction in membrane fusion. As the methodology can be applied to membrane samples, the approach presented suggests itself for in-situ studies of the complete membrane fusion process, opening up new avenues for the study of membrane fusion.
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Affiliation(s)
- Pravin Kumar
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands
| | - Martin van Son
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands
| | - Tingting Zheng
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Dayenne Valdink
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Jan Raap
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Alexander Kros
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands
- * E-mail:
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Biondi B, Peggion C, De Zotti M, Pignaffo C, Dalzini A, Bortolus M, Oancea S, Hilma G, Bortolotti A, Stella L, Pedersen JZ, Syryamina VN, Tsvetkov YD, Dzuba SA, Toniolo C, Formaggio F. Conformational properties, membrane interaction, and antibacterial activity of the peptaibiotic chalciporin A: Multitechnique spectroscopic and biophysical investigations on the natural compound and labeled analogs. Biopolymers 2017; 110. [PMID: 29127716 DOI: 10.1002/bip.23083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/06/2017] [Accepted: 10/15/2017] [Indexed: 02/28/2024]
Abstract
In this work, an extensive set of spectroscopic and biophysical techniques (including FT-IR absorption, CD, 2D-NMR, fluorescence, and CW/PELDOR EPR) was used to study the conformational preferences, membrane interaction, and bioactivity properties of the naturally occurring synthetic 14-mer peptaibiotic chalciporin A, characterized by a relatively low (≈20%), uncommon proportion of the strongly helicogenic Aib residue. In addition to the unlabeled peptide, we gained in-depth information from the study of two labeled analogs, characterized by one or two residues of the helicogenic, nitroxyl radical-containing TOAC. All three compounds were prepared using the SPPS methodology, which was carefully modified in the course of the syntheses of TOAC-labeled analogs in view of the poorly reactive α-amino function of this very bulky residue and the specific requirements of its free-radical side chain. Despite its potentially high flexibility, our results point to a predominant, partly amphiphilic, α-helical conformation for this peptaibiotic. Therefore, not surprisingly, we found an effective membrane affinity and a remarkable penetration propensity. However, chalciporin A exhibits a selectivity in its antibacterial activity not in agreement with that typical of the other members of this peptide class.
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Affiliation(s)
- Barbara Biondi
- Institute of Biomolecular, Chemistry, Padova Unit, CNR, Padova, 35131, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Chiara Pignaffo
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Annalisa Dalzini
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Simona Oancea
- Department of Agricultural Sciences and Food Engineering, "Lucian Blaga" University of Sibiu, Sibiu, 550012, Romania
| | - Geta Hilma
- Department of Medicine, "Lucian Blaga" University of Sibiu, Sibiu, 550012, Romania
| | - Annalisa Bortolotti
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Lorenzo Stella
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Jens Z Pedersen
- Department of Biology, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Victoria N Syryamina
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090, Russian Federation
| | - Yuri D Tsvetkov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090, Russian Federation
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090, Russian Federation
| | - Claudio Toniolo
- Institute of Biomolecular, Chemistry, Padova Unit, CNR, Padova, 35131, Italy
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Fernando Formaggio
- Institute of Biomolecular, Chemistry, Padova Unit, CNR, Padova, 35131, Italy
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
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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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Möbius K, Lubitz W, Savitsky A. High-field EPR on membrane proteins - crossing the gap to NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 75:1-49. [PMID: 24160760 DOI: 10.1016/j.pnmrs.2013.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 06/02/2023]
Abstract
In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented.
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Affiliation(s)
- Klaus Möbius
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany; Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany.
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Milov AD, Tsvetkov YD, De Zotti M, Prinzivalli C, Biondi B, Formaggio F, Toniolo C, Gobbo M. Aggregation modes of the spin mono-labeled tylopeptin B and heptaibin peptaibiotics in frozen solutions of weak polarity as studied by PELDOR spectroscopy. J STRUCT CHEM+ 2013. [DOI: 10.1134/s0022476613070056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Yang Z, Kise D, Saxena S. An Approach towards the Measurement of Nanometer Range Distances Based on Cu2+ Ions and ESR. J Phys Chem B 2010; 114:6165-74. [DOI: 10.1021/jp911637s] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhongyu Yang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Drew Kise
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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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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Milov AD, Samoilova RI, Tsvetkov YD, De Zotti M, Toniolo C, Raap J. PELDOR Conformational Analysis of bis-Labeled Alamethicin Aggregated in Phospholipid Vesicles. J Phys Chem B 2008; 112:13469-72. [DOI: 10.1021/jp8046714] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander D. Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Rimma I. Samoilova
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Yuri D. Tsvetkov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Marta De Zotti
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Claudio Toniolo
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jan Raap
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
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Peggion C, Jost M, Baldini C, Formaggio F, Toniolo C. Total syntheses in solution of TOAC-labelled alamethicin F50/5 analogues. Chem Biodivers 2007; 4:1183-99. [PMID: 17589860 DOI: 10.1002/cbdv.200790104] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Total syntheses in solution of a set of four selected analogues of the 19-mer component F50/5 of alamethicin, the most extensively studied among the channel-former peptaibol antibiotics, are planned and reported. All analogues bear three Glu(OMe) residues, replacing the Gln residues at positions 7, 18, and 19 of the naturally occurring compound. Three analogues are mono-labelled with the free-radical-containing amino acid residue TOAC at the strategic positions 1, 8, or 16. The fourth analogue is bis-labelled with the same EPR-active residue at both positions 1 and 16. In the native sequence, all of the positions where TOAC replacements have been introduced are characterized by residues of Aib, the prototype of the class of helicogenic C(alpha)-tetrasubstituted alpha-amino acids. All of the TOAC analogues synthesized exhibit significant membrane-modifying properties.
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Affiliation(s)
- Cristina Peggion
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
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