1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Golysheva EA, Boyle AL, Biondi B, Ruzza P, Kros A, Raap J, Toniolo C, Formaggio F, Dzuba SA. Probing the E/K Peptide Coiled-Coil Assembly by Double Electron-Electron Resonance and Circular Dichroism. Biochemistry 2020; 60:19-30. [PMID: 33320519 DOI: 10.1021/acs.biochem.0c00773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Double electron-electron resonance (DEER, also known as PELDOR) and circular dichroism (CD) spectroscopies were explored for the purpose of studying the specificity of the conformation of peptides induced by their assembly into a self-recognizing system. The E and K peptides are known to form a coiled-coil heterodimer. Two paramagnetic TOAC α-amino acid residues were incorporated into each of the peptides (denoted as K** and E**), and a three-dimensional structural investigation in the presence or absence of their unlabeled counterparts E and K was performed. The TOAC spin-labels, replacing two Ala residues in each compound, are covalently and quasi-rigidly connected to the peptide backbone. They are known not to disturb the native structure, so that any conformational change can easily be monitored and assigned. DEER spectroscopy enables the measurement of the intramolecular electron spin-spin distance distribution between the two TOAC labels, within a length range of 1.5-8 nm. This method allows the individual conformational changes for the K**, K**/E, E**, and E**/K molecules to be investigated in glassy frozen solutions. Our data reveal that the conformations of the E** and K** peptides are strongly influenced by the presence of their counterparts. The results are discussed with those from CD spectroscopy and with reference to the already reported nuclear magnetic resonance data. We conclude that the combined DEER/TOAC approach allows us to obtain accurate and reliable information about the conformation of the peptides before and after their assembly into coiled-coil heterodimers. Applications of this induced fit method to other two-component, but more complex, systems, like a receptor and antagonists, a receptor and a hormone, and an enzyme and a ligand, are discussed.
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Affiliation(s)
- Elena A Golysheva
- Novosibirsk State University, Novosibirsk 630090, Russian Federation.,V. V. Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk 630090, Russian Federation
| | - Aimee L Boyle
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Paolo Ruzza
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Alexander Kros
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Department of Chemistry, 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
| | - Sergei A Dzuba
- Novosibirsk State University, Novosibirsk 630090, Russian Federation.,V. V. Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk 630090, Russian Federation
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Salnikov ES, Raya J, De Zotti M, Zaitseva E, Peggion C, Ballano G, Toniolo C, Raap J, Bechinger B. Alamethicin Supramolecular Organization in Lipid Membranes from 19F Solid-State NMR. Biophys J 2017; 111:2450-2459. [PMID: 27926846 DOI: 10.1016/j.bpj.2016.09.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/10/2016] [Accepted: 09/29/2016] [Indexed: 11/24/2022] Open
Abstract
Alamethicins (ALMs) are antimicrobial peptides of fungal origin. Their sequences are rich in hydrophobic amino acids and strongly interact with lipid membranes, where they cause a well-defined increase in conductivity. Therefore, the peptides are thought to form transmembrane helical bundles in which the more hydrophilic residues line a water-filled pore. Whereas the peptide has been well characterized in terms of secondary structure, membrane topology, and interactions, much fewer data are available regarding the quaternary arrangement of the helices within lipid bilayers. A new, to our knowledge, fluorine-labeled ALM derivative was prepared and characterized when reconstituted into phospholipid bilayers. As a part of these studies, C19F3-labeled compounds were characterized and calibrated for the first time, to our knowledge, for 19F solid-state NMR distance and oligomerization measurements by centerband-only detection of exchange (CODEX) experiments, which opens up a large range of potential labeling schemes. The 19F-19F CODEX solid-state NMR experiments performed with ALM in POPC lipid bilayers and at peptide/lipid ratios of 1:13 are in excellent agreement with molecular-dynamics calculations of dynamic pentameric assemblies. When the peptide/lipid ratio was lowered to 1:30, ALM was found in the dimeric form, indicating that the supramolecular organization is tuned by equilibria that can be shifted by changes in environmental conditions.
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Affiliation(s)
- Evgeniy S Salnikov
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France
| | - Jesus Raya
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France
| | - Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Ekaterina Zaitseva
- Department of Membrane Physiology and Technology, Institute of Physiology, University of Freiburg, Freiburg, Germany
| | - Cristina Peggion
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Gema Ballano
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Claudio Toniolo
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, Leiden, the Netherlands
| | - Burkhard Bechinger
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France.
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5
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Rabe M, Aisenbrey C, Pluhackova K, de Wert V, Boyle AL, Bruggeman DF, Kirsch SA, Böckmann RA, Kros A, Raap J, Bechinger B. A Coiled-Coil Peptide Shaping Lipid Bilayers upon Fusion. Biophys J 2016; 111:2162-2175. [PMID: 27851940 PMCID: PMC5113151 DOI: 10.1016/j.bpj.2016.10.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/08/2016] [Accepted: 10/06/2016] [Indexed: 12/19/2022] Open
Abstract
A system based on two designed peptides, namely the cationic peptide K, (KIAALKE)3, and its complementary anionic counterpart called peptide E, (EIAALEK)3, has been used as a minimal model for membrane fusion, inspired by SNARE proteins. Although the fact that docking of separate vesicle populations via the formation of a dimeric E/K coiled-coil complex can be rationalized, the reasons for the peptides promoting fusion of vesicles cannot be fully explained. Therefore it is of significant interest to determine how the peptides aid in overcoming energetic barriers during lipid rearrangements leading to fusion. In this study, investigations of the peptides' interactions with neutral PC/PE/cholesterol membranes by fluorescence spectroscopy show that tryptophan-labeled K∗ binds to the membrane (KK∗ ∼6.2 103 M-1), whereas E∗ remains fully water-solvated. 15N-NMR spectroscopy, depth-dependent fluorescence quenching, CD-spectroscopy experiments, and MD simulations indicate a helix orientation of K∗ parallel to the membrane surface. Solid-state 31P-NMR of oriented lipid membranes was used to study the impact of peptide incorporation on lipid headgroup alignment. The membrane-immersed K∗ is found to locally alter the bilayer curvature, accompanied by a change of headgroup orientation relative to the membrane normal and of the lipid composition in the vicinity of the bound peptide. The NMR results were supported by molecular dynamics simulations, which showed that K reorganizes the membrane composition in its vicinity, induces positive membrane curvature, and enhances the lipid tail protrusion probability. These effects are known to be fusion relevant. The combined results support the hypothesis for a twofold role of K in the mechanism of membrane fusion: 1) to bring opposing membranes into close proximity via coiled-coil formation and 2) to destabilize both membranes thereby promoting fusion.
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Affiliation(s)
- Martin Rabe
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands.
| | | | - Kristyna Pluhackova
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Vincent de Wert
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands
| | - Aimee L Boyle
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands
| | - Didjay F Bruggeman
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands
| | - Sonja A Kirsch
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Alexander Kros
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands
| | - Jan Raap
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS UMR7177, Institut de Chimie, Strasbourg, France.
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Zheng T, Bulacu M, Daudey G, Versluis F, Voskuhl J, Martelli G, Raap J, Sevink GJA, Kros A, Boyle AL. A non-zipper-like tetrameric coiled coil promotes membrane fusion. RSC Adv 2016. [DOI: 10.1039/c5ra26175a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A parallel heterodimeric coiled coil can be mutated to an antiparallel tetrameric species by reversing the sequences of one of the peptides. This tetramer is capable of facilitating fast, efficient, membrane fusion of liposomes.
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Affiliation(s)
- Tingting Zheng
- Supramolecular and Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | | | - Geert Daudey
- Supramolecular and Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Frank Versluis
- Supramolecular and Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Jens Voskuhl
- Supramolecular and Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Giuliana Martelli
- Supramolecular and Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Jan Raap
- Supramolecular and Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - G. J. Agur Sevink
- Solid State NMR
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Alexander Kros
- Supramolecular and Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Aimee L. Boyle
- Supramolecular and Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
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8
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Steendam RRE, Kulka MW, Meekes H, van Enckevort WJP, Raap J, Vlieg E, Rutjes FPJT. One-Pot Synthesis, Crystallization and Deracemization of Isoindolinones from Achiral Reactants. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Zheng T, Boyle A, Robson Marsden H, Valdink D, Martelli G, Raap J, Kros A. Probing coiled-coil assembly by paramagnetic NMR spectroscopy. Org Biomol Chem 2015; 13:1159-68. [DOI: 10.1039/c4ob02125h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Here a new method to determine the orientation of coiled-coil peptide motifs is described.
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Affiliation(s)
- TingTing Zheng
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Aimee Boyle
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Hana Robson Marsden
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Dayenne Valdink
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Giuliana Martelli
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Jan Raap
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Alexander Kros
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
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10
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Steendam RRE, Brouwer MCT, Huijs EME, Kulka MW, Meekes H, van Enckevort WJP, Raap J, Rutjes FPJT, Vlieg E. Enantiopure isoindolinones through Viedma ripening. Chemistry 2014; 20:13527-30. [PMID: 25168197 DOI: 10.1002/chem.201404320] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Indexed: 11/08/2022]
Abstract
Here we demonstrate that deracemization of isoindolinones using Viedma ripening is possible starting from a racemic mixture of conglomerate crystals. Crystals of the enantiopure isoindolinones lose their chiral identity upon dissolution even without the need for a catalyst. This enabled complete deracemization of the reported isoindolinones without a catalyst.
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Affiliation(s)
- René R E Steendam
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (The Netherlands)
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11
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van Son M, Zheng T, Kumar P, Valdink D, Raap J, Kros A, Huber M. Towards Artificial Membrane Fusion: Ek-Peptides, the Coilied-Coil Zipper. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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12
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 11/08/2022]
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cappon JJ, Witters KD, Baart J, Verdegem PJE, Hoek AC, Luiten RJH, Raap J, Lugtenburg J. Synthesis of L-histidine specifically labelled with stable isotopes. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19941130603] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ogrel A, Vasilenko IA, Lugtenburg J, Raap J. Enzymatic synthesis of specifically 2
H-labelled L-glutamic acids and 2
H-, 15
N-, 13
C-labelled L-glutamines on a preparative scale. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19941130706] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Cappon JJ, Baart J, van der Walk GAM, Raap J, Lugtenburg J. Chemo-enzymatic synthesis of specifically stable-isotope labelledL-glutamic acid and 2-oxoglutaric acid. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19911100505] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Raap J, van der Wielen CM, Lugtenburg J. Enantioselective syntheses of isotopically labelled α-amino acids. Preparation of (ϵ-13C)-L-α-aminoadipic acid and five isotopomers of L-lysine with 13C, 15N and 2H in the δ- and ϵ-positions. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19901090404] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Serdijn J, Hoes C, Raap J, Kerling KET. Studies on polypeptides XXXIII: Semisynthetic Ribonuclease analogues. The role of histidine-119. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19800991107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Visser S, Raap J, Kerling KET, Havinga E. Studies on polypeptides. Part IX: Combination of solid-phase and classical methods of peptide synthesis in the preparation of 1-13[13-Leucine] bovine pancreatic ribonuclease. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19700890813] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hoes C, Raap J, Bloemhoff W, Kerling KET. Studies on polypeptides XXXII: Solid-phase synthesis of RNase S-peptide 1-14 analogues; replacement of histidine-12 by β-(2-pyridyl)-L
-alanine and β-(4-pyridyl)-L
-alanine. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19800990308] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Cappon JJ, van der Walle GAM, Verdegem PJE, Raap J, Lugtenburg J. Synthesis of specifically stable-isotope-labeled l-proline via L-glutamic acid. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19921111204] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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van den Berg EMM, Baldew AU, de Goede ATJW, Raap J, Lugtenburg J. Synthesis of three isotopomers of L-tryptophan via a combination of organic synthesis and biotechnology. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19881070206] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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van Batenburg O, Raap J, Kerling K, Havinga E. Studies on polypeptides XVIII Solid-phase synthesis of RNase S-peptide analogues with high S-protein activating ability; replacement of histidine-12 by L-homohistidine. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19760951108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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26
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Salnikov E, Bertani P, Raap J, Bechinger B. Analysis of the amide (15)N chemical shift tensor of the C(alpha) tetrasubstituted constituent of membrane-active peptaibols, the alpha-aminoisobutyric acid residue, compared to those of di- and tri-substituted proteinogenic amino acid residues. J Biomol NMR 2009; 45:373-387. [PMID: 19823773 DOI: 10.1007/s10858-009-9380-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 09/11/2009] [Indexed: 05/28/2023]
Abstract
In protein NMR spectroscopy the chemical shift provides important information for the assignment of residues and a first structural evaluation of dihedral angles. Furthermore, angular restraints are obtained from oriented samples by solution and solid-state NMR spectroscopic approaches. Whereas the anisotropy of chemical shifts, quadrupolar couplings and dipolar interactions have been used to determine the structure, dynamics and topology of oriented membrane polypeptides using solid-state NMR spectroscopy similar concepts have been introduced to solution NMR through the measurements of residual dipolar couplings. The analysis of (15)N chemical shift spectra depends on the accuracy of the chemical shift tensors. When investigating alamethicin and other peptaibols, i.e. polypeptides rich in alpha-aminoisobutyric acid (Aib), the (15)N chemical shift tensor of this C(alpha)-tetrasubstituted amino acid exhibits pronounced differences when compared to glycine, alanine and other proteinogenic residues. Here we present an experimental investigation on the (15)N amide Aib tensor of N-acetyl-Aib-OH and for the Aib residues within peptaibols. Furthermore, a statistical analysis of the tensors published for di- (glycine) and tri-substituted residues has been performed, where for the first time the published data sets are compiled using a common reference. The size of the isotropic chemical shift and main tensor elements follows the order di- < tri- < tetra-substituted amino acids. A (15)N chemical shift-(1)H-(15)N dipolar coupling correlation NMR spectrum of alamethicin is used to evaluate the consequences of variations in the main tensor elements for the structural analysis of this membrane peptide.
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Affiliation(s)
- Evgeniy Salnikov
- Institut de Chimie, Université de Strasbourg/CNRS, UMR7177, Strasbourg, France
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Milov AD, Samoilova RI, Tsvetkov YD, Formaggio F, Toniolo C, Raap J. Self-Aggregation of Spin-Labeled Alamethicin in ePC Vesicles Studied by Pulsed Electron−Electron Double Resonance. J Am Chem Soc 2007; 129:9260-1. [PMID: 17616195 DOI: 10.1021/ja072851d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation
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Abstract
Catalytic reactions performed with enzymes localized in lipid vesicles or in whole cells represent a new, promising approach in biocatalysis. The delivery of different substrates into these micro- or nano-'reactors' requires a sufficient permeability of lipid membranes. To increase the permeability of lipid bilayers, one may use different membrane-active peptides, including peptaibols. In the present study, the trypsin-catalyzed hydrolysis of N(alpha)-benzoyl-L-arginine-para-nitroanilide (BAPA; 1) was studied in a phospholipid vesicular system made of phosphatidylcholine (POC), in the presence of the peptaibols alamethicin (ALM) or zervamicin IIB (ZER). Two different manners of compartmentalization of substrate and enzyme (enzyme- vs. substrate-containing vesicles) were used. The kinetics parameters of the reaction in homogeneous solution and in the vesicular systems were determined. The rate of the extra- or intravesicular enzymatic reaction was found to be controlled by substrate diffusion through the lipid bilayer. In comparison with untreated vesicular systems, an up to seven-fold increase in reaction rate was observed in the presence of either ALM or ZER.
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Milov AD, Tsvetkov YD, Gorbunova EY, Mustaeva LG, Ovchinnikova TV, Handgraaf JW, Raap J. Solvent effects on the secondary structure of the membrane-active zervamicin determined by PELDOR spectroscopy. Chem Biodivers 2007; 4:1243-55. [PMID: 17589863 DOI: 10.1002/cbdv.200790107] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Zervamicin is a voltage-gated ion-channel-forming peptide. Channels are generally considered to be formed by first insertion of amphipathic molecules into the phospholipid bilayer, followed by self-assembly of a variable number of transmembrane helices. We have studied the length of the peptide structure to address the question whether this peptide is long enough to span the phospholipid bilayer. The pulsed electron-electron double resonance (PELDOR) spectroscopic technique was used to determine the length of the helical molecule in membrane-mimicking solvents. This was achieved from the distance-related dipole-dipole interaction between spin labels, which were located at both ends of the linear peptide chain. The data were obtained by using samples of frozen glassy solutions of MeOH, MeOH/toluene, and MeOH/CHCl(3). Contributions of inter- and intramolecular interactions of spin labels were separated to analyze the intramolecular interaction and the distance distribution function between the labels. It is shown that the main maximum of the distribution functions is located at a distance of ca. 3.3 nm, and this distance appears to be only slightly dependent on the solvent composition. The distribution function was observed to narrow after addition of either CHCl(3) or toluene to MeOH. This effect is rationalized in terms of a decreased mobility of the terminal amino acid residues. By molecular-dynamics simulations, it was shown that the conformation, corresponding with the predominant distance found by PELDOR, agrees well with the mixed alpha/3(10)-helical that was previously determined by NMR. However, in the case toluene was added to the MeOH solution to further increase the hydrophobicity of the environment of the membrane-active peptide, the distribution function gives rise to a minor fraction (7-8%) with a distance of 4.2 nm. This distance corresponds most likely to the more extended 2(7)-helix structure.
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Affiliation(s)
- Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, Russian Federation
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Weidema AF, Kropacheva TN, Raap J, Ypey DL. Membrane permeabilization of a mammalian neuroendocrine cell type (PC12) by the channel-forming peptides zervamicin, alamethicin, and gramicidin. Chem Biodivers 2007; 4:1347-59. [PMID: 17589868 DOI: 10.1002/cbdv.200790115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Zervamicin IIB (ZER) is a 16-mer peptaibol that produces voltage-dependent conductances in artificial membranes, a property considered responsible for its antimicrobial activity to mainly Gram-positive microorganisms. In addition, ZER appears to inhibit the locomotor activity of the mouse (see elsewhere in this Issue), probably by affecting the brain. To examine whether the electrophysiological properties of the neuronal cells of the central neural system might be possibly influenced by the pore forming ZER, the present study was undertaken as a first attempt to unravel the molecular mechanism of this biological activity. To this end, membrane permeabilization of the neuron-like rat pheochromocytoma cell (PC12) by the channel-forming ZER was studied with the whole-cell patch-clamp technique, and compared with the permeabilizations of the well-known voltage-gated peptaibol alamethicin F50/5 (ALA) and the cation channel-forming peptide-antibiotic gramicidin D (GRAM). While 1 muM GRAM addition to PC12 cells kept at a membrane potential V(m)=0 mV causes an undelayed gradual increase of a leak conductance with a negative reversal potential of ca. -24 mV, ZER and ALA are ineffective at that concentration and potential. However, if ZER and ALA are added in 5-10 microM concentrations while V(m) is kept at -60 mV, they cause a sudden and strong permeabilization of the PC12 cell membrane after a delay of 1-2 min, usually leading to disintegrating morphology changes of the patched cell but not of the surrounding cells of the culture at that time scale. The zero reversal potential of the established conductance is consistent with the known aselectivity of the channels formed. This sudden permeabilization does not occur within 10-20 min at V(m)=0 mV, in accordance with the known voltage dependency of ZER and ALA channel formation in artificial lipid membranes. The permeabilizing action of these peptaibols on the culture as a whole is further supported by K(+)-release measurements from a PC12 suspension with a K(+)-selective electrode. Further analysis suggested that the permeabilizing action is associated with extra- or intracellular calcium effects, because barium inhibited the permeabilizing effects of ZER and ALA. We conclude, for the membrane of the mammalian neuron-like PC12 cell, that the permeabilizing effects of the peptides ZER and ALA are different from those of GRAM, consistent with earlier studies of these peptides in other (artificial) membrane systems. They are increased by cis-positive membrane potentials in the physiological range and may include calcium entry into the PC12 cell.
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Affiliation(s)
- Adam F Weidema
- Department of Neurophysiology, Leiden University Medical Center, NL-Leiden, The Netherlands
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Milov AD, Samoilova MI, Tsvetkov YD, Jost M, Peggion C, Formaggio F, Crisma M, Toniolo C, Handgraaf JW, Raap J. Supramolecular Structure of Self-Assembling Alamethicin Analog Studied by ESR and PELDOR. Chem Biodivers 2007; 4:1275-98. [PMID: 17589866 DOI: 10.1002/cbdv.200790110] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Three analogs of alamethicin F50/5, labelled with the TOAC (='2,2,6,6-tetramethylpiperidin-1-oxyl-4-amino-4-carboxylic acid') spin label at positions 1 (Alm1), 8 (Alm8), and 16 (Alm16), resp., were studied by Electron-Spin-Resonance (ESR) and Pulsed Electron-Electron Double-Resonance (PELDOR) techniques in solvents of different polarity to investigate the self-assembly of amphipathic helical peptides in membrane-mimicking environments. In polar solvents, alamethicin forms homogeneous solutions. In the weakly polar chloroform/toluene 1 : 1 mixture, however, this peptide forms aggregates that are detectable at 293 K by ESR in liquid solution, as well as by PELDOR in frozen, glassy solution at 77 K. In liquid solution, free alamethicin molecules and their aggregates show rotational-mobility correlation times tau(r) of 0.87 and 5.9 ns, resp. Based on these values and analysis of dipole-dipole interactions of the TOAC labels in the aggregates, as determined by PELDOR, the average number N of alamethicin molecules in the aggregates is estimated to be less than nine. A distance-distribution function between spin labels in the supramolecular aggregate was obtained. This function exhibits two maxima: a broad one at a distance of 3.0 nm, and a wide one at a distance of ca. 7 nm. A molecular-dynamics (MD)-based model of the aggregate, consisting of two parallel tetramers, each composed of four molecules arranged in a 'head-to-tail' fashion, is proposed, accounting for the observed distances and their distribution.
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Affiliation(s)
- Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation
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35
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Ogrel A, Heerma W, Versluis K, Lugtenburg J, Raap J. Mass Spectrometric Analysis of Site Specific Deuterated Zervamicins. ANAL LETT 2006. [DOI: 10.1080/00032719708001825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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36
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Raap J, Hollander J, Ovchinnikova TV, Swischeva NV, Skladnev D, Kiihne S. Trans and surface membrane bound zervamicin IIB: 13C-MAOSS-NMR at high spinning speed. J Biomol NMR 2006; 35:285-93. [PMID: 16937243 DOI: 10.1007/s10858-006-9045-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Accepted: 06/21/2006] [Indexed: 05/11/2023]
Abstract
Interactions between (15)N-labelled peptides or proteins and lipids can be investigated using membranes aligned on a thin polymer film, which is rolled into a cylinder and inserted into the MAS-NMR rotor. This can be spun at high speed, which is often useful at high field strengths. Unfortuantely, substrate films like commercially available polycarbonate or PEEK produce severe overlap with peptide and protein signals in (13)C-MAOSS NMR spectra. We show that a simple house hold foil support allows clear observation of the carbonyl, aromatic and C(alpha) signals of peptides and proteins as well as the ester carbonyl and choline signals of phosphocholine lipids. The utility of the new substrate is validated in applications to the membrane active peptide zervamicin IIB. The stability and macroscopic ordering of thin PC10 bilayers was compared with that of thicker POPC bilayers, both supported on the household foil. Sidebands in the (31)P-spectra showed a high degree of alignment of both the supported POPC and PC10 lipid molecules. Compared with POPC, the PC10 lipids are slightly more disordered, most likely due to the increased mobilities of the shorter lipid molecules. This mobility prevents PC10 from forming stable vesicles for MAS studies. The (13)C-peptide peaks were selectively detected in a (13)C-detected (1)H-spin diffusion experiment. Qualitative analysis of build-up curves obtained for different mixing times allowed the transmembrane peptide in PC10 to be distinguished from the surface bound topology in POPC. The (13)C-MAOSS results thus independently confirms previous findings from (15)N spectroscopy [Bechinger, B., Skladnev, D.A., Ogrel, A., Li, X., Rogozhkina, E.V., Ovchinnikova, T.V., O'Neil, J.D.J. and Raap, J. (2001) Biochemistry, 40, 9428-9437]. In summary, application of house hold foil opens the possibility of measuring high resolution (13)C-NMR spectra of peptides and proteins in well ordered membranes, which are required to determine the secondary and supramolecular structures of membrane active peptides, proteins and aggregates.
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Affiliation(s)
- J Raap
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
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Karstens WFJ, Berger HJFF, Van Haren ER, Lugtenburg J, Raap J. Enantioselective synthesis of isotopically labelled L-α-amino acids preparation of 13C-, 18O-and 2H-labelled L-serines and L-threonines. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580361108] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Salnikov ES, Erilov DA, Milov AD, Tsvetkov YD, Peggion C, Formaggio F, Toniolo C, Raap J, Dzuba SA. Location and aggregation of the spin-labeled peptide trichogin GA IV in a phospholipid membrane as revealed by pulsed EPR. Biophys J 2006; 91:1532-40. [PMID: 16751238 PMCID: PMC1518643 DOI: 10.1529/biophysj.105.075887] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lipopeptaibol trichogin GA IV is a 10 amino acid-long residue and alpha-aminoisobutyric acid-rich antibiotic peptide of fungal origin. TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) spin-labeled analogs of this membrane active peptide were investigated in hydrated bilayers of dipalmitoylphosphatidylcholine by electron spin echo envelope modulation (ESEEM) spectroscopy and pulsed electron-electron double resonance (PELDOR). Since, the ESEEM of the spin label appears to be strongly dependent on the presence of water molecules penetrated into the membrane, this phenomenon was used to study the location of this peptide in the membrane. This was achieved by comparing the ESEEM spectra for peptides labeled at different positions along the amino acid sequence with spectra known for lipids with spin labels at different positions along the hydrocarbon chain. To increase the ESEEM amplitude and to distinguish the hydrogen nuclei of water from lipid protons, membranes were hydrated with deuterated water. The PELDOR spectroscopy technique was chosen to study peptide aggregation and to determine the mutual distance distribution of the spin-labeled peptides in the membrane. The location of the peptide in the membrane and its aggregation state were found to be dependent on the peptide concentration. At a low peptide/lipid molar ratio (less than 1:100) the nonaggregated peptide chain of the trichogin molecules lie parallel to the membrane surface, with TOAC at the 4th residue located near the 9th-11th carbon positions of the sn-2 lipid chain. Increasing this ratio up to 1:20 leads to a change in peptide orientation, with the N-terminus of the peptide buried deeper into membrane. Under these conditions peptide aggregates are formed with a mean aggregate number of about N = 2. The aggregates are further characterized by a broad range of intermolecular distances (1.5-4 nm) between the labels at the N-terminal residues. The major population exhibits a distance of approximately 2.5 nm, which is of the same order as the length of the helical peptide. We suggest that the constituting monomers of the dimer are antiparallel oriented.
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Affiliation(s)
- E S Salnikov
- Institute of Chemical Kinetics and Combustion, Academy of Sciences, 630090 Novosibirsk, Russia
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Milov AD, Samoilova RI, Tsvetkov YD, Peggion C, Formaggio F, Toniolo C, Raap J. Aggregation of spin-labeled alamethicin in low-polarity solutions as studied by PELDOR spectroscopy. Dokl Phys Chem 2006. [DOI: 10.1134/s0012501606010064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kropacheva TN, Salnikov ES, Nguyen HH, Reissmann S, Yakimenko ZA, Tagaev AA, Ovchinnikova TV, Raap J. Membrane association and activity of 15/16-membered peptide antibiotics: zervamicin IIB, ampullosporin A and antiamoebin I. Biochim Biophys Acta 2005; 1715:6-18. [PMID: 16084799 DOI: 10.1016/j.bbamem.2005.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Revised: 06/14/2005] [Accepted: 07/07/2005] [Indexed: 11/23/2022]
Abstract
Permeabilization of the phospholipid membrane, induced by the antibiotic peptides zervamicin IIB (ZER), ampullosporin A (AMP) and antiamoebin I (ANT) was investigated in a vesicular model system. Membrane-perturbing properties of these 15/16 residue peptides were examined by measuring the K(+) transport across phosphatidyl choline (PC) membrane and by dissipation of the transmembrane potential. The membrane activities are found to decrease in the order ZER>AMP>>ANT, which correlates with the sequence of their binding affinities. To follow the insertion of the N-terminal Trp residue of ZER and AMP, the environmental sensitivity of its fluorescence was explored as well as the fluorescence quenching by water-soluble (iodide) and membrane-bound (5- and 16-doxyl stearic acids) quenchers. In contrast to AMP, the binding affinity of ZER as well as the depth of its Trp penetration is strongly influenced by the thickness of the membrane (diC(16:1)PC, diC(18:1)PC, C(16:0)/C(18:1)PC, diC(20:1)PC). In thin membranes, ZER shows a higher tendency to transmembrane alignment. In thick membranes, the in-plane surface association of these peptaibols results in a deeper insertion of the Trp residue of AMP which is in agreement with model calculations on the localization of both peptide molecules at the hydrophilic-hydrophobic interface. The observed differences between the membrane affinities/activities of the studied peptaibols are discussed in relation to their hydrophobic and amphipathic properties.
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Affiliation(s)
- T N Kropacheva
- Chemistry Department, Udmurt State University, Izhevsk, Russia
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Shenkarev ZO, Paramonov AS, Balashova TA, Yakimenko ZA, Baru MB, Mustaeva LG, Raap J, Ovchinnikova TV, Arseniev AS. High stability of the hinge region in the membrane-active peptide helix of zervamicin: paramagnetic relaxation enhancement studies. Biochem Biophys Res Commun 2005; 325:1099-105. [PMID: 15541401 DOI: 10.1016/j.bbrc.2004.10.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Indexed: 10/26/2022]
Abstract
Zervamicin IIB is a 16 amino acid peptaibol that forms voltage dependent ion channels with multilevel conductance states in planar lipid bilayers and vesicular systems. Stability of the hinge region and intermolecular interactions were investigated in the N- and C-terminally spin-labelled peptide analogues. Intermolecular and intramolecular paramagnetic enhancement indicates that zervamicin behaves as a rigid helical rod in methanol solution. There are no high amplitude hinge-bending motions, and the peptaibol is monomeric up to concentration 1.5 mM. Stability of the hinge region illustrates the helix stabilising propensity of the Pro residue in membrane mimic environments and implies absence of significant conformational rearrangement due to voltage peptaibol activation.
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Affiliation(s)
- Zakhar O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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Raap J, Erkelens K, Ogrel A, Skladnev DA, Brückner H. Fungal biosynthesis of non-ribosomal peptide antibiotics and α, α-dialkylated amino acid constituents. J Pept Sci 2005; 11:331-8. [PMID: 15635654 DOI: 10.1002/psc.621] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Zervamicins (Zrv) IIA and IIB are membrane modifying peptide antibiotics of fungal origin, characterized by a sequence of 15 amino acid residues. The primary structure of Zrv-IIA contains five alpha-aminoisobutyric acid residues at positions 4, 7, 9, 12 and 14 of the linear peptide. The sequence of Zrv-IIB is similar, but contains a D-isovaline at position 4. When the free amino acid Aib was added to the peptone-glucose culture medium, the fungus Emericellopsis salmosynnemata produced Zrv-IIA as the major secondary metabolite, whereas addition of DL-Iva to the culture led to a high production of Zrv-IIB. This observation is rationalized by a lack of selectivity of the non-ribosomal peptide synthetase with respect to the thiolester activated amino acid substrates during step 12 of peptide synthesis. Analysis of the configuration of the Iva residue of Zrv-IIB showed a high enantiomeric purity of the D-enantiomer, indicating a high stereoselectivity of the peptide synthetase for this substrate.When the culture was supplemented with [(15)N]DL-Iva, the nitrogen isotope was not only found at the D-Iva residue, but surprisingly also at the Aib residues as well as at the proteinogenic residues of Zrv. The partial catabolism of exogenous [(15)N]DL-Iva is explained by the assumption of a decarboxylation-dependent transamination reaction, catalysed by 2,2-dimethylglycine decarboxylase. The same enzyme might also be involved in the reversed carboxylation reactions of acetone and 2-butanone, during the anabolic biosynthesis of Aib and Iva, respectively. Zrv might possibly act as a thermodynamic sink to shift these equilibrium reactions towards the reversed side.
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Affiliation(s)
- Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, The Netherlands.
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Milov AD, Erilov DA, Salnikov ES, Tsvetkov YD, Formaggio F, Toniolo C, Raap J. Structure and spatial distribution of the spin-labelled lipopeptide trichogin GA IV in a phospholipid membrane studied by pulsed electron–electron double resonance (PELDOR). Phys Chem Chem Phys 2005; 7:1794-9. [DOI: 10.1039/b418414a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Siebum AG, Tsang RF, Steen R, Raap J, Lugtenburg J. Synthesis of (?-13C-,?-15N)-EnrichedL-Lysine ? Establishing Schemes for the Preparation of All Possible13C and15N Isotopomers ofL-Lysine,L-Ornithine, andL-Proline. European J Org Chem 2004. [DOI: 10.1002/ejoc.200400370] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Siebum A, Woo W, Raap J, Lugtenburg J. Access to Any Site-Directed Isotopomer of Methionine, Selenomethionine, Cysteine, and Selenocysteine− Use of Simple, Efficient Modular Synthetic Reaction Schemes for Isotope Incorporation. European J Org Chem 2004. [DOI: 10.1002/ejoc.200400063] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Milov AD, Tsvetkov YD, Formaggio F, Oancea S, Toniolo C, Raap J. Solvent effect on the distance distribution between spin labels in aggregated spin labeled trichogin GA IV dimer peptides as studied by pulsed electron–electron double resonance. Phys Chem Chem Phys 2004. [DOI: 10.1039/b313701e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Milov AD, Tsvetkov YD, Formaggio F, Oancea S, Toniolo C, Raap J. Aggregation of Spin Labeled Trichogin GA IV Dimers: Distance Distribution between Spin Labels in Frozen Solutions by PELDOR Data. J Phys Chem B 2003. [DOI: 10.1021/jp035057x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. D. Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Yu. D. Tsvetkov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - F. Formaggio
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - S. Oancea
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - C. Toniolo
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - J. Raap
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic 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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Alia, Hulsebosch B, van Gorkom HJ, Raap J, Lugtenburg J, Matysik J, de Groot HJ, Gast P. Probing the electronic structure of tyrosine radical YD in photosystem II by EPR spectroscopy using site specific isotope labelling in Spirodela oligorrhiza. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00326-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Milov AD, Tsvetkov YD, Formaggio F, Crisma M, Toniolo C, Raap J. Self-assembling and membrane modifying properties of a lipopeptaibol studied by CW-ESR and PELDOR spectroscopies. J Pept Sci 2003; 9:690-700. [PMID: 14664226 DOI: 10.1002/psc.513] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Trichogin GA IV is a short lipopeptaibol antibiotic that is capable of enhancing the transport of small cations through the phospholipid double layer of the membrane. The antibiotic activity of the undecapeptide is thought to be based on either its self-assembling or membrane-modifying property. The chemical equilibrium between self-aggregated and non-aggregated molecular states was studied by CW-ESR spectroscopy using solutions of TOAC nitroxide spin-labelled trichogin analogues in an apolar solvent to mimic the membrane bound state. At room temperature the two different sets of signals observed in the spectrum were attributed to the presence of both monomers and aggregates in the sample. The ESR spectra of the monomeric and aggregated forms were separated and the dependence of the fraction of monomeric peptide molecules on concentration was obtained over the range 5 x 10(-6) to 7 x 10(-4) M. A two-step aggregation mechanism is proposed: dimerization of peptide molecules followed by aggregation of dimers to assemblies of four peptide molecules per aggregate. The equilibrium constants were estimated for both steps. In addition, the lower lifetime limit was determined for dimers and tetramers. It is shown that when the peptide concentration exceeds 10(-5) M. the major part of the peptide molecules in solution has the form of tetrameric aggregates. Independently, the PELDOR technique was used to investigate the concentration dependence of the parameters of the dipole-dipole interaction between spin labels in frozen (77 K] glassy solutions of aggregates of mono-labelled TOAC analogues. The number of molecules in aggregates as well as the frequency and amplitude of PELDOR signal oscillations were found to be concentration independent in the range 5 x 10(-4) to 8 x 10(-3) M. In the frozen glassy solution state, the number of peptide molecules per aggregate was determined to be close to four, which is in agreement with the value obtained for spin-labelled trichogin at room temperature. The present data provide experimental evidence in favour of a self-assembling rather than a membrane-modifying ion conduction mechanism.
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Affiliation(s)
- A D Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation
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Abstract
Trichogin GA IV is a special member of a class of peptaibols that are linear peptide antibiotics of fungal origin, characterised by the presence of a variable number of alpha-aminoisobutyric acid residues, an acyl group at the N-terminus and a 1,2-amino alcohol at the C-terminus. Most of the peptaibols display ion-channel-forming or at least membrane-modifying properties. The 11-residue-long trichogin GA IV is not only one of shortest peptaibols, but it is also unique for its n-octanoyl group instead of the more common found acetyl group at the N-terminus. For the first time we have found that this lipopeptaibol is able to enhance conduction of monovalent cations through membranes of large unilamellar vesicles (LUVs). The influence of the [Leu-OMe]trichogin GA IV analogue (TRI) on ion permeation was studied under a variety of conditions (lipid composition, lipid-to-peptide ratio and a transmembrane potential). Parallel experiments were performed with the 16-residue long, channel-forming peptaibol, zervamicin (ZER). For the two peptides, the permeability between K(+) and Na(+) was found to be different. In addition, the ion diffusion rate dependencies on the peptide concentration are observed to be different. This might indicate that a different number of aggregated molecules are involved in the rate-limiting step, i.e. 3-4 (TRI) and 4-7 (ZER). In the presence of TRI, dissipation of the transmembrane potential, Delta psi, was observed with a rate to be dependent on the magnitude of both initial Delta psi and peptide concentration. Both peptides were activated by a cis-positive but not by cis-negative Delta psi. Under identical conditions the ion-conducting efficiency of zervamicin was 100-200 times higher than that of trichogin. Our results show that, unlike for zervamicin, the membrane-modifying activity of trichogin is not associated with a channel mechanism.
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Affiliation(s)
- T N Kropacheva
- Department of Chemistry, Udmurt State University, Izhevsk, Russia
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