1
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Eichler C, Himmelstoß M, Plangger R, Weber LI, Hartl M, Kreutz C, Micura R. Advances in RNA Labeling with Trifluoromethyl Groups. Chemistry 2023; 29:e202302220. [PMID: 37534701 PMCID: PMC10947337 DOI: 10.1002/chem.202302220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/04/2023]
Abstract
Fluorine labeling of ribonucleic acids (RNA) in conjunction with 19 F NMR spectroscopy has emerged as a powerful strategy for spectroscopic analysis of RNA structure and dynamics, and RNA-ligand interactions. This study presents the first syntheses of 2'-OCF3 guanosine and uridine phosphoramidites, their incorporation into oligoribonucleotides by solid-phase synthesis and a comprehensive study of their properties. NMR spectroscopic analysis showed that the 2'-OCF3 modification is associated with preferential C2'-endo conformation of the U and G ribose in single-stranded RNA. When paired to the complementary strand, slight destabilization of the duplex caused by the modification was revealed by UV melting curve analysis. Moreover, the power of the 2'-OCF3 label for NMR spectroscopy is demonstrated by dissecting RNA pseudoknot folding and its binding to a small molecule. Furthermore, the 2'-OCF3 modification has potential for applications in therapeutic oligonucleotides. To this end, three 2'-OCF3 modified siRNAs were tested in silencing of the BASP1 gene which indicated enhanced performance for one of them. Importantly, together with earlier work, the present study completes the set of 2'-OCF3 nucleoside phosphoramidites to all four standard nucleobases (A, U, C, G) and hence enables applications that utilize the favorable properties of the 2'-OCF3 group without any restrictions in placing the modification into the RNA target sequence.
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Affiliation(s)
- Clemens Eichler
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Maximilian Himmelstoß
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Plangger
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Leonie I. Weber
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Markus Hartl
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Christoph Kreutz
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
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2
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Strandberg E, Wadhwani P, Bürck J, Anders P, Mink C, van den Berg J, Ciriello RAM, Melo MN, Castanho MARB, Bardají E, Ulmschneider JP, Ulrich AS. Temperature-Dependent Re-alignment of the Short Multifunctional Peptide BP100 in Membranes Revealed by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations. Chembiochem 2023; 24:e202200602. [PMID: 36454659 DOI: 10.1002/cbic.202200602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/02/2022]
Abstract
BP100 is a cationic undecamer peptide with antimicrobial and cell-penetrating activities. The orientation of this amphiphilic α-helix in lipid bilayers was examined under numerous conditions using solid-state 19 F, 15 N and 2 H NMR. At high temperatures in saturated phosphatidylcholine lipids, BP100 lies flat on the membrane surface, as expected. Upon lowering the temperature towards the lipid phase transition, the helix is found to flip into an upright transmembrane orientation. In thin bilayers, this inserted state was stable at low peptide concentration, but thicker membranes required higher peptide concentrations. In the presence of lysolipids, the inserted state prevailed even at high temperature. Molecular dynamics simulations suggest that BP100 monomer insertion can be stabilized by snorkeling lysine side chains. These results demonstrate that even a very short helix like BP100 can span (and thereby penetrate through) a cellular membrane under suitable conditions.
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Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Patrick Anders
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Christian Mink
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.,Present address: Syngenta Crop Protection AG, 4333, Münchwilen, Switzerland
| | - Jonas van den Berg
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Raffaele A M Ciriello
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Manuel N Melo
- Instituto de Medicina Molecular Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal.,Present address: ITQB Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Miguel A R B Castanho
- Instituto de Medicina Molecular Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Eduard Bardají
- LIPPSO, Department of Chemistry, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Jakob P Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany.,Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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3
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Membranolytic Mechanism of Amphiphilic Antimicrobial β-Stranded [KL]n Peptides. Biomedicines 2022; 10:biomedicines10092071. [PMID: 36140173 PMCID: PMC9495826 DOI: 10.3390/biomedicines10092071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Amphipathic peptides can act as antibiotics due to membrane permeabilization. KL peptides with the repetitive sequence [Lys-Leu]n-NH2 form amphipathic β-strands in the presence of lipid bilayers. As they are known to kill bacteria in a peculiar length-dependent manner, we suggest here several different functional models, all of which seem plausible, including a carpet mechanism, a β-barrel pore, a toroidal wormhole, and a β-helix. To resolve their genuine mechanism, the activity of KL peptides with lengths from 6–26 amino acids (plus some inverted LK analogues) was systematically tested against bacteria and erythrocytes. Vesicle leakage assays served to correlate bilayer thickness and peptide length and to examine the role of membrane curvature and putative pore diameter. KL peptides with 10–12 amino acids showed the best therapeutic potential, i.e., high antimicrobial activity and low hemolytic side effects. Mechanistically, this particular window of an optimum β-strand length around 4 nm (11 amino acids × 3.7 Å) would match the typical thickness of a lipid bilayer, implying the formation of a transmembrane pore. Solid-state 15N- and 19F-NMR structure analysis, however, showed that the KL backbone lies flat on the membrane surface under all conditions. We can thus refute any of the pore models and conclude that the KL peptides rather disrupt membranes by a carpet mechanism. The intriguing length-dependent optimum in activity can be fully explained by two counteracting effects, i.e., membrane binding versus amyloid formation. Very short KL peptides are inactive, because they are unable to bind to the lipid bilayer as flexible β-strands, whereas very long peptides are inactive due to vigorous pre-aggregation into β-sheets in solution.
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4
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Wadhwani P, Sekaran S, Strandberg E, Bürck J, Chugh A, Ulrich AS. Membrane Interactions of Latarcins: Antimicrobial Peptides from Spider Venom. Int J Mol Sci 2021; 22:ijms221810156. [PMID: 34576320 PMCID: PMC8470881 DOI: 10.3390/ijms221810156] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/26/2022] Open
Abstract
A group of seven peptides from spider venom with diverse sequences constitute the latarcin family. They have been described as membrane-active antibiotics, but their lipid interactions have not yet been addressed. Using circular dichroism and solid-state 15N-NMR, we systematically characterized and compared the conformation and helix alignment of all seven peptides in their membrane-bound state. These structural results could be correlated with activity assays (antimicrobial, hemolysis, fluorescence vesicle leakage). Functional synergy was not observed amongst any of the latarcins. In the presence of lipids, all peptides fold into amphiphilic α-helices as expected, the helices being either surface-bound or tilted in the bilayer. The most tilted peptide, Ltc2a, possesses a novel kind of amphiphilic profile with a coiled-coil-like hydrophobic strip and is the most aggressive of all. It indiscriminately permeabilizes natural membranes (antimicrobial, hemolysis) as well as artificial lipid bilayers through the segregation of anionic lipids and possibly enhanced motional averaging. Ltc1, Ltc3a, Ltc4a, and Ltc5a are efficient and selective in killing bacteria but without causing significant bilayer disturbance. They act rather slowly or may even translocate towards intracellular targets, suggesting more subtle lipid interactions. Ltc6a and Ltc7, finally, do not show much antimicrobial action but can nonetheless perturb model bilayers.
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Affiliation(s)
- Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Germany; (P.W.); (E.S.); (J.B.)
| | - Saiguru Sekaran
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, Delhi 110016, India; (S.S.); (A.C.)
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Germany; (P.W.); (E.S.); (J.B.)
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Germany; (P.W.); (E.S.); (J.B.)
| | - Archana Chugh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, Delhi 110016, India; (S.S.); (A.C.)
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Germany; (P.W.); (E.S.); (J.B.)
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
- Correspondence:
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5
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Himmelstoß M, Erharter K, Renard E, Ennifar E, Kreutz C, Micura R. 2'- O-Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy. Chem Sci 2020; 11:11322-11330. [PMID: 34094374 PMCID: PMC8162808 DOI: 10.1039/d0sc04520a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/18/2020] [Indexed: 11/21/2022] Open
Abstract
New RNA modifications are needed to advance our toolbox for targeted manipulation of RNA. In particular, the development of high-performance reporter groups facilitating spectroscopic analysis of RNA structure and dynamics, and of RNA-ligand interactions has attracted considerable interest. To this end, fluorine labeling in conjunction with 19F-NMR spectroscopy has emerged as a powerful strategy. Appropriate probes for RNA previously focused on single fluorine atoms attached to the 5-position of pyrimidine nucleobases or at the ribose 2'-position. To increase NMR sensitivity, trifluoromethyl labeling approaches have been developed, with the ribose 2'-SCF3 modification being the most prominent one. A major drawback of the 2'-SCF3 group, however, is its strong impact on RNA base pairing stability. Interestingly, RNA containing the structurally related 2'-OCF3 modification has not yet been reported. Therefore, we set out to overcome the synthetic challenges toward 2'-OCF3 labeled RNA and to investigate the impact of this modification. We present the syntheses of 2'-OCF3 adenosine and cytidine phosphoramidites and their incorporation into oligoribonucleotides by solid-phase synthesis. Importantly, it turns out that the 2'-OCF3 group has only a slight destabilizing effect when located in double helical regions which is consistent with the preferential C3'-endo conformation of the 2'-OCF3 ribose as reflected in the 3 J (H1'-H2') coupling constants. Furthermore, we demonstrate the exceptionally high sensitivity of the new label in 19F-NMR analysis of RNA structure equilibria and of RNA-small molecule interactions. The study is complemented by a crystal structure at 0.9 Å resolution of a 27 nt hairpin RNA containing a single 2'-OCF3 group that well integrates into the minor groove. The new label carries high potential to outcompete currently applied fluorine labels for nucleic acid NMR spectroscopy because of its significantly advanced performance.
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Affiliation(s)
- Maximilian Himmelstoß
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
| | - Kevin Erharter
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
| | - Eva Renard
- Université de Strasbourg, Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Eric Ennifar
- Université de Strasbourg, Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Christoph Kreutz
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
| | - Ronald Micura
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
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6
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Phosphate-dependent aggregation of [KL] n peptides affects their membranolytic activity. Sci Rep 2020; 10:12300. [PMID: 32704013 PMCID: PMC7378186 DOI: 10.1038/s41598-020-69162-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/25/2020] [Indexed: 11/25/2022] Open
Abstract
In this study, we investigate how the length of amphiphilic β-sheet forming peptides affects their interaction with membranes. Four polycationic model peptides with lengths from 6 to 18 amino acids were constructed from simple Lys-Leu repeats, giving [KL]n=3,5,7,9. We found that (1) they exhibit a pronounced antimicrobial activity with an intriguing length dependent maximum for [KL]5 with 10 amino acids; (2) their hemolytic effect, on the other hand, increases steadily with peptide length. CD analysis (3) and TEM (4) show that all peptides-except for the short [KL]3-aggregate into amyloid-like fibrils in the presence of phosphate ions, which in turn has a critical effect on the results in (1) and (2). In fact, (5) vesicle leakage reveals an intrinsic membrane-perturbing activity (at constant peptide mass) of [KL]5 > [KL]9 > [KL]7 in phosphate buffer, which changes to [KL]5 ≈ [KL]7 ≈ [KL]9 in PIPES. A specific interaction with phosphate ions thus explains the subtle balance between two counteracting effects: phosphate-induced unproductive pre-aggregation in solution versus monomeric membrane binding and vigorous lipid perturbation due to self-assembly of the bound peptides within the bilayer. This knowledge can now be used to control and optimize the peptides in further applications.
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7
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Drouin M, Wadhwani P, Grage SL, Bürck J, Reichert J, Tremblay S, Mayer MS, Diel C, Staub A, Paquin JF, Ulrich AS. Monofluoroalkene-Isostere as a 19 F NMR Label for the Peptide Backbone: Synthesis and Evaluation in Membrane-Bound PGLa and (KIGAKI) 3. Chemistry 2020; 26:1511-1517. [PMID: 31867761 DOI: 10.1002/chem.201905054] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/18/2019] [Indexed: 12/12/2022]
Abstract
Solid-state 19 F NMR is a powerful method to study the interactions of biologically active peptides with membranes. So far, in labelled peptides, the 19 F-reporter group has always been installed on the side chain of an amino acid. Given the fact that monofluoroalkenes are non-hydrolyzable peptide bond mimics, we have synthesized a monofluoroalkene-based dipeptide isostere, Val-Ψ[(Z)-CF=CH]-Gly, and inserted it in the sequence of two well-studied antimicrobial peptides: PGLa and (KIGAKI)3 are representatives of an α-helix and a β-sheet. The conformations and biological activities of these labeled peptides were studied to assess the suitability of monofluoroalkenes for 19 F NMR structure analysis.
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Affiliation(s)
- Myriam Drouin
- PROTEO, CCVC, Département de chimie, Université Laval, 1045 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021, Karlsruhe, Germany
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021, Karlsruhe, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021, Karlsruhe, Germany
| | - Johannes Reichert
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021, Karlsruhe, Germany
| | - Sébastien Tremblay
- PROTEO, CCVC, Département de chimie, Université Laval, 1045 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Marie Sabine Mayer
- PROTEO, CCVC, Département de chimie, Université Laval, 1045 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada.,Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021, Karlsruhe, Germany
| | - Christian Diel
- PROTEO, CCVC, Département de chimie, Université Laval, 1045 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada.,Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021, Karlsruhe, Germany
| | - Alexander Staub
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021, Karlsruhe, Germany
| | - Jean-François Paquin
- PROTEO, CCVC, Département de chimie, Université Laval, 1045 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021, Karlsruhe, Germany
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8
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Petkov P, Lilkova E, Ilieva N, Litov L. Self-Association of Antimicrobial Peptides: A Molecular Dynamics Simulation Study on Bombinin. Int J Mol Sci 2019; 20:ijms20215450. [PMID: 31683755 PMCID: PMC6862524 DOI: 10.3390/ijms20215450] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/26/2019] [Accepted: 10/28/2019] [Indexed: 12/29/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a diverse group of membrane-active peptides which play a crucial role as mediators of the primary host defense against microbial invasion. Many AMPs are found to be fully or partially disordered in solution and to acquire secondary structure upon interaction with a lipid membrane. Here, we report molecular dynamics simulations studies on the solution behaviour of a specific AMP, bombinin H2. We show that in monomeric form in water solution the peptide is somewhat disordered and preferably adopts a helix-loop-helix conformation. However, when more than a single monomer is placed in the solution, the peptides self-associate in aggregates. Within the aggregate, the peptides provide each other with an amphipathic environment that mimics the water–membrane interface, which allows them to adopt a single-helix structure. We hypothesise that this is the mechanism by which bombinin H2 and, possibly, other small linear AMPs reach the target membrane in a functional folded state and are able to effectively exert their antimicrobial action on it.
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Affiliation(s)
- Peicho Petkov
- Faculty of Physics, Atomic Physics Department, Sofia University "St. Kliment Ohridski", 5 J. Bouchier Blvd, 1164 Sofia, Bulgaria.
| | - Elena Lilkova
- Institute of Information and Communication Technologies at the Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 25A, 1113 Sofia, Bulgaria.
| | - Nevena Ilieva
- Institute of Information and Communication Technologies at the Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 25A, 1113 Sofia, Bulgaria.
- Institute of Informatics and Mathematics at the Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 8, 1113 Sofia, Bulgaria.
| | - Leandar Litov
- Faculty of Physics, Atomic Physics Department, Sofia University "St. Kliment Ohridski", 5 J. Bouchier Blvd, 1164 Sofia, Bulgaria.
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9
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The investigation of the dipole-dipole action direction and molecular space configuration effect during the dipole–dipole induced azobenzene supramolecular self-assembly. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2019.123742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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10
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Yin Z, Moriwaki H, Abe H, Miwa T, Han J, Soloshonok VA. Large-Scale Asymmetric Synthesis of Fmoc-( S)-2-Amino-6,6,6-Trifluorohexanoic Acid. ChemistryOpen 2019; 8:701-704. [PMID: 31183311 PMCID: PMC6554705 DOI: 10.1002/open.201900131] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/12/2019] [Indexed: 11/18/2022] Open
Abstract
Here we report the first large-scale synthesis of Fmoc-(S)-2-amino-6,6,6-trifluorohexanoic acid via asymmetric alkylation of chiral Ni(II)-complex of glycine Schiff base with CF3(CH2)3I. The synthesis was performed on over 100 g scale and can be recommended as the most advanced procedure for reliable preparation of large amounts of enantiomerically pure Fmoc-(S)-2-amino-6,6,6-trifluorohexanoic acid for protein engineering and drug design. Chiral auxiliary used in this protocol can be >90 % recovered and reused.
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Affiliation(s)
- Zizhen Yin
- College of Chemical EngineeringNanjing Forestry UniversityNanjing210037China
| | - Hiroki Moriwaki
- Hamari Chemicals Ltd.1-4-29 Kunijima, Higashi-Yodogawa-kuOsaka533-0024Japan
| | - Hidenori Abe
- Hamari Chemicals Ltd.1-4-29 Kunijima, Higashi-Yodogawa-kuOsaka533-0024Japan
| | - Toshio Miwa
- Hamari Chemicals Ltd.1-4-29 Kunijima, Higashi-Yodogawa-kuOsaka533-0024Japan
| | - Jianlin Han
- College of Chemical EngineeringNanjing Forestry UniversityNanjing210037China
| | - Vadim A. Soloshonok
- Department of Organic Chemistry I, Faculty of ChemistryUniversity of the Basque Country UPV/EHUPaseo Manuel Lardizábal 320018San SebastiánSpain
- IKERBASQUEBasque Foundation for ScienceMaría Díaz de Haro 3, Plaza Bizkaia48013BilbaoSpain
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11
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Abstract
In this work we report a convenient asymmetric synthesis of Fmoc-(S)-6,6,6-trifluoro-norleucine via alkylation reaction of chiral glycine equivalent. The target amino acid of 99% enantiomeric purity was prepared with 82.4% total yield (three steps).
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12
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Locke GM, Bernhard SSR, Senge MO. Nonconjugated Hydrocarbons as Rigid-Linear Motifs: Isosteres for Material Sciences and Bioorganic and Medicinal Chemistry. Chemistry 2019; 25:4590-4647. [PMID: 30387906 DOI: 10.1002/chem.201804225] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/20/2018] [Indexed: 01/02/2023]
Abstract
Nonconjugated hydrocarbons, like bicyclo[1.1.1]pentane, bicyclo[2.2.2]octane, triptycene, and cubane are a unique class of rigid linkers. Due to their similarity in size and shape they are useful mimics of classic benzene moieties in drugs, so-called bioisosteres. Moreover, they also fulfill an important role in material sciences as linear linkers, in order to arrange various functionalities in a defined spatial manner. In this Review article, recent developments and usages of these special, rectilinear systems are discussed. Furthermore, we focus on covalently linked, nonconjugated linear arrangements and discuss the physical and chemical properties and differences of individual linkers, as well as their application in material and medicinal sciences.
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Affiliation(s)
- Gemma M Locke
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin, 2, Ireland
| | - Stefan S R Bernhard
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin, 2, Ireland
| | - Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin, 2, Ireland
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13
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Reißer S, Strandberg E, Steinbrecher T, Elstner M, Ulrich AS. Best of Two Worlds? How MD Simulations of Amphiphilic Helical Peptides in Membranes Can Complement Data from Oriented Solid-State NMR. J Chem Theory Comput 2018; 14:6002-6014. [PMID: 30289704 DOI: 10.1021/acs.jctc.8b00283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane alignment of helical amphiphilic peptides in oriented phospholipid bilayers can be obtained as ensemble and time averages from solid state 2H NMR by fitting the quadrupolar splittings to ideal α-helices. At the same time, molecular dynamics (MD) simulations can provide atomistic insight into peptide-membrane systems. Here, we evaluate the potential of MD simulations to complement the experimental NMR data that is available on three exemplary systems: the natural antimicrobial peptide PGLa and the two designer-made peptides MSI-103 and KIA14, whose sequences were derived from PGLa. Each peptide was simulated for 1 μs in a DMPC lipid bilayer. We calculated from the MD simulations the local angles which define the side chain geometry with respect to the peptide helix. The peptide orientation was then calculated (i) directly from the simulation, (ii) from back-calculated MD-derived NMR splittings, and (iii) from experimental 2H NMR splittings. Our findings are that (1) the membrane orientation and secondary structure of the peptides found in the NMR analysis are generally well reproduced by the simulations; (2) the geometry of the side chains with respect to the helix backbone can deviate significantly from the ideal structure depending on the specific residue, but on average all side chains have the same orientation; and (3) for all of our peptides, the azimuthal rotation angle found from the MD-derived splittings is about 15° smaller than the experimental value.
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Affiliation(s)
- Sabine Reißer
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
| | - Thomas Steinbrecher
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Anne S Ulrich
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany.,Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
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14
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Reißer S, Prock S, Heinzmann H, Ulrich AS. Protein ORIGAMI: A program for the creation of 3D paper models of folded peptides. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:403-409. [PMID: 29984554 DOI: 10.1002/bmb.21132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/20/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
Protein ORIGAMI (http://ibg.kit.edu/protein_origami) is a browser-based web application that allows the user to create straightforward 3D paper models of folded peptides for research, teaching and presentations. An amino acid sequence can be turned into α-helices, β-strands and random coils that can be printed out and folded into properly scaled models, with a color code denoting the biophysical characteristics of each amino acid residue (hydrophobicity, charge, etc.). These models provide an intuitive visual and tactile understanding of peptide interactions with other partners, such as helix-helix assembly, oligomerization, membrane binding, or pore formation. Helices can also be displayed as a helical wheel or helical mesh in 2D graphics, to be used in publications or presentations. The highly versatile programme Protein ORIGAMI is also suited to create less conventional helices with arbitrary pitch (e.g., 310 -helix, π-helix, or left-handed helices). Noncanonical amino acids, labels and different terminal modifications can be defined and displayed at will, and different protonation states can be shown. In addition to the web application, the program source code can be downloaded and installed locally on a PC. The printed paper models can be readily used for daily research and discussions, just as for educational purposes and teaching. © 2018 by The International Union of Biochemistry and Molecular Biology, 46:403-409, 2018.
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Affiliation(s)
- Sabine Reißer
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Karlsruhe, 76133, Germany
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, 34136, Italy
| | - Sebastian Prock
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Karlsruhe, 76133, Germany
| | - Hartmut Heinzmann
- Institute of Biological Interfaces (IBG-2), KIT, Karlsruhe, 76012, Germany
| | - Anne S Ulrich
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Karlsruhe, 76133, Germany
- Institute of Biological Interfaces (IBG-2), KIT, Karlsruhe, 76012, Germany
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15
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Serra I, Casu M, Ceccarelli M, Gameiro P, Rinaldi AC, Scorciapino MA. Effects of amphipathic profile regularization on structural order and interaction with membrane models of two highly cationic branched peptides with β-sheet propensity. Peptides 2018; 105:28-36. [PMID: 29800587 DOI: 10.1016/j.peptides.2018.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/17/2018] [Accepted: 05/22/2018] [Indexed: 11/21/2022]
Abstract
Antimicrobial peptides attracted increasing interest in last decades due to the rising concern of multi-drug resistant pathogens. Dendrimeric peptides are branched molecules with multiple copies of one peptide functional unit bound to the central core. Compared to linear analogues, they usually show improved activity and lower susceptibility to proteases. Knowledge of structure-function relationship is fundamental to tailor their properties. This work is focused on SB056, the smallest example of dendrimeric peptide, whose amino acid sequence is WKKIRVRLSA. Two copies are bound to the α- and ε- nitrogen of one lysine core. An 8-aminooctanamide was added at the C-terminus to improve membrane affinity. Its propensity for β-type structures is also interesting, since helical peptides were already thoroughly studied. Moreover, SB056 maintains activity at physiological osmolarity, a typical limitation of natural peptides. An optimized analogue with improved performance was designed, β-SB056, which differs only in the relative position of the first two residues (KWKIRVRLSA). This produced remarkable differences. Structure order and aggregation behavior were characterized by using complementary techniques and membrane models with different negative charge. Infrared spectroscopy showed different propensity for ordered β-sheets. Lipid monolayers' surface pressure was measured to estimate the area/peptide and the ability to perturb lipid packing. Fluorescence spectroscopy was applied to compare peptide insertion into the lipid bilayer. Such small change in primary structure produced fundamental differences in their aggregation behavior. A regular amphipathic peptide's primary structure was responsible for ordered β-sheets in a charge independent fashion, in contrast to unordered aggregates formed by the former analogue.
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Affiliation(s)
- Ilaria Serra
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato (CA), Italy
| | - Mariano Casu
- Department of Physics, University of Cagliari, Monserrato (CA), Italy
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, Monserrato (CA), Italy
| | - Paula Gameiro
- Department of Chemistry and Biochemistry, Requimte, LAQV, University of Porto, Portugal
| | - Andrea C Rinaldi
- Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari, Monserrato (CA), Italy
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16
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Strandberg E, Grau-Campistany A, Wadhwani P, Bürck J, Rabanal F, Ulrich AS. Helix Fraying and Lipid-Dependent Structure of a Short Amphipathic Membrane-Bound Peptide Revealed by Solid-State NMR. J Phys Chem B 2018; 122:6236-6250. [DOI: 10.1021/acs.jpcb.8b02661] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Ariadna Grau-Campistany
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Francesc Rabanal
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
- KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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17
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Lu M, Sarkar S, Wang M, Kraus J, Fritz M, Quinn CM, Bai S, Holmes ST, Dybowski C, Yap GPA, Struppe J, Sergeyev IV, Maas W, Gronenborn AM, Polenova T. 19F Magic Angle Spinning NMR Spectroscopy and Density Functional Theory Calculations of Fluorosubstituted Tryptophans: Integrating Experiment and Theory for Accurate Determination of Chemical Shift Tensors. J Phys Chem B 2018; 122:6148-6155. [PMID: 29756776 DOI: 10.1021/acs.jpcb.8b00377] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 19F chemical shift is a sensitive NMR probe of structure and electronic environment in organic and biological molecules. In this report, we examine chemical shift parameters of 4F-, 5F-, 6F-, and 7F-substituted crystalline tryptophan by magic angle spinning (MAS) solid-state NMR spectroscopy and density functional theory. Significant narrowing of the 19F lines was observed under fast MAS conditions, at spinning frequencies above 50 kHz. The parameters characterizing the 19F chemical shift tensor are sensitive to the position of the fluorine in the aromatic ring and, to a lesser extent, the chirality of the molecule. Accurate calculations of 19F magnetic shielding tensors require the PBE0 functional with a 50% admixture of a Hartree-Fock exchange term, as well as taking account of the local crystal symmetry. The methodology developed will be beneficial for 19F-based MAS NMR structural analysis of proteins and protein assemblies.
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Affiliation(s)
- Manman Lu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Sucharita Sarkar
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Jodi Kraus
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Matthew Fritz
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Shi Bai
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sean T Holmes
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Werner Maas
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States.,Department of Structural Biology , University of Pittsburgh School of Medicine , 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
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18
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Wadhwani P, Heidenreich N, Podeyn B, Bürck J, Ulrich AS. Antibiotic gold: tethering of antimicrobial peptides to gold nanoparticles maintains conformational flexibility of peptides and improves trypsin susceptibility. Biomater Sci 2018; 5:817-827. [PMID: 28275774 DOI: 10.1039/c7bm00069c] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptide-coated nanoparticles are valuable tools for diverse biological applications, such as drug delivery, molecular recognition, and antimicrobial action. The functionalization of pre-fabricated nanoparticles with free peptides in solution is inefficient either due to aggregation of the particles or due to the poor ligand exchange reaction. Here, we present a one-pot synthesis for preparing gold nanoparticles with a homogeneous distribution that are covered in situ with cationic peptides in a site-selective manner via Cys-residue at the N-terminus. Five representative peptides were selected, which are known to perturb cellular membranes and exert their antimicrobial and/or cell penetrating activity by folding into amphiphilic α-helical structures. When tethered to the nanoparticles at a single site, all peptides were found to switch their conformation from unordered state (in aqueous buffers) to their functionally relevant α-helical conformation in the presence of model membranes, as shown by circular dichroism spectroscopy. The conjugated peptides also maintained the same antibacterial activity as in the free form. Most importantly, when tethered to the gold nanoparticles the peptides showed an enormous increase in stability against trypsin digestion compared to the free forms, leading to a dramatic improvement of their lifetimes and activities. These findings suggest that site-selective surface tethering of peptides to gold nanoparticles has several advantages: (i) it does not prevent the peptides from folding into their biologically active conformation, (ii) such conjugation protects the peptides against protease digestion, and (iii) this way it is possible to prepare stable, water soluble antimicrobial nanoparticles as promising antibacterial agents.
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Affiliation(s)
- Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), 1Institute of Biological Interfaces (IBG-2) P.O.B. 3640, D 76021 Karlsruhe, Germany.
| | - Nico Heidenreich
- KIT, 2Institute of Organic Chemistry & CFN, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Benjamin Podeyn
- KIT, 2Institute of Organic Chemistry & CFN, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), 1Institute of Biological Interfaces (IBG-2) P.O.B. 3640, D 76021 Karlsruhe, Germany.
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), 1Institute of Biological Interfaces (IBG-2) P.O.B. 3640, D 76021 Karlsruhe, Germany. and KIT, 2Institute of Organic Chemistry & CFN, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
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19
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New insights into the influence of monofluorination on dimyristoylphosphatidylcholine membrane properties: A solid-state NMR study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:654-663. [DOI: 10.1016/j.bbamem.2017.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022]
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20
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Towards the use of monofluorinated dimyristoylphosphatidylcholines as 19F NMR reporters in bacterial model membranes. J Fluor Chem 2018. [DOI: 10.1016/j.jfluchem.2017.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Sequence length dependence in arginine/phenylalanine oligopeptides: Implications for self-assembly and cytotoxicity. Biophys Chem 2018; 233:1-12. [DOI: 10.1016/j.bpc.2017.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/13/2022]
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22
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Structure analysis of the membrane-bound dermcidin-derived peptide SSL-25 from human sweat. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2308-2318. [DOI: 10.1016/j.bbamem.2017.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 11/24/2022]
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23
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Babii O, Afonin S, Schober T, Komarov IV, Ulrich AS. Flexibility vs rigidity of amphipathic peptide conjugates when interacting with lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2505-2515. [PMID: 28958778 PMCID: PMC5667891 DOI: 10.1016/j.bbamem.2017.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/05/2017] [Accepted: 09/21/2017] [Indexed: 01/17/2023]
Abstract
For the first time, the photoisomerization of a diarylethene moiety (DAET) in peptide conjugates was used to probe the effects of molecular rigidity/flexibility on the structure and behavior of model peptides bound to lipid membranes. The DAET unit was incorporated into the backbones of linear peptide-based constructs, connecting two amphipathic sequences (derived from the β-stranded peptide (KIGAKI)3 and/or the α-helical peptide BP100). A β-strand-DAET-α-helix and an α-helix-DAET-α-helix models were synthesized and studied in phospholipid membranes. Light-induced photoisomerization of the linker allowed the generation of two forms of each conjugate, which differed in the conformational mobility of the junction between the α-helical and/or the β-stranded part of these peptidomimetic molecules. A detailed study of their structural, orientational and conformational behavior, both in isotropic solution and in phospholipid model membranes, was carried out using circular dichroism and solid-state 19F-NMR spectroscopy. The study showed that the rigid and flexible forms of the two conjugates had appreciably different structures only when embedded in an anisotropic lipid environment and only in the gel phase. The influence of the rigidity/flexibility of the studied conjugates on the lipid thermotropic phase transition was also investigated by differential scanning calorimetry. Both models were found to destabilize the lamellar gel phases. DAET building blocks can be used to study rigidity/flexibility effects in supramolecular model systems. Photoswitchable DAET linkers perturb only up to 3–4 adjacent amino acid residues. Membrane-bound amphiphilic secondary structure elements exert a negligible influence on each other when linked by DAET. The rigidity of peptide conjugates affected their structural behavior only in the lipid gel phase.
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Affiliation(s)
- Oleg Babii
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Sergii Afonin
- Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Tim Schober
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Igor V Komarov
- Taras Shevchenko National University of Kyiv, Institute of High Technologies, Volodymyrska 60, 01601 Kyiv, Ukraine.
| | - Anne S Ulrich
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany.
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24
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Afonin S, Kubyshkin V, Mykhailiuk PK, Komarov IV, Ulrich AS. Conformational Plasticity of the Cell-Penetrating Peptide SAP As Revealed by Solid-State 19F-NMR and Circular Dichroism Spectroscopies. J Phys Chem B 2017; 121:6479-6491. [PMID: 28608690 DOI: 10.1021/acs.jpcb.7b02852] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cell-penetrating peptide SAP, which was designed as an amphipathic poly-l-proline helix II (PPII), was suggested to self-assemble into regular fibrils that are relevant for its internalization. Herein we have analyzed the structure of SAP in the membrane-bound state by solid-state 19F-NMR, which revealed other structural states, in addition to the expected surface-aligned PPII. Trifluoromethyl-bicyclopentyl-glycine (CF3-Bpg) and two rigid isomers of trifluoromethyl-4,5-methanoprolines (CF3-MePro) were used as labels for 19F-NMR analysis. The equilibria between different conformations of SAP were studied and were found to be shifted by the substituents at Pro-11. Synchrotron-CD results suggested that substituting Pro-11 by CF3-MePro governed the coil-to-PPII equilibrium in solution and in the presence of a lipid bilayer. Using CD and 19F-NMR, we examined the slow kinetics of the association of SAP with membranes and the dependence of the SAP conformational dynamics on the lipid composition. The peptide did not bind to lipids in the solid ordered phase and aggregated only in the liquid ordered "raft"-like bilayers. Self-association could not be detected in solution or in the presence of liquid disordered membranes. Surface-bound amphipathic SAP in a nonaggregated state was structured as a mixture of nonideal extended conformations reflecting the equilibrium already present in solution, i.e., before binding to the membrane.
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Affiliation(s)
- Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology , P.O.B. 3640, 76021 Karlsruhe, Germany
| | - Vladimir Kubyshkin
- Institute of Organic Chemistry, Karlsruhe Institute of Technology , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Pavel K Mykhailiuk
- Institute of Organic Chemistry, Karlsruhe Institute of Technology , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.,Enamine Ltd. , Vul. Chervonotkatska 78, 02660 Kyiv, Ukraine
| | - Igor V Komarov
- Institute of High Technologies, Taras Shevchenko National University of Kyiv , Prosp. Glushkova 4-g, 02033 Kyiv, Ukraine
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology , P.O.B. 3640, 76021 Karlsruhe, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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25
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Palunas K, Sprenger K, Weidner T, Pfaendtner J. Effect of an ionic liquid/air Interface on the structure and dynamics of amphiphilic peptides. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Gagnon MC, Strandberg E, Grau-Campistany A, Wadhwani P, Reichert J, Bürck J, Rabanal F, Auger M, Paquin JF, Ulrich AS. Influence of the Length and Charge on the Activity of α-Helical Amphipathic Antimicrobial Peptides. Biochemistry 2017; 56:1680-1695. [PMID: 28282123 DOI: 10.1021/acs.biochem.6b01071] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrophobic mismatch is important for pore-forming amphipathic antimicrobial peptides, as demonstrated recently [Grau-Campistany, A., et al. (2015) Sci. Rep. 5, 9388]. A series of different length peptides have been generated with the heptameric repeat sequence KIAGKIA, called KIA peptides, and it was found that only those helices sufficiently long to span the hydrophobic thickness of the membrane could induce leakage in lipid vesicles; there was also a clear length dependence of the antimicrobial and hemolytic activities. For the original KIA sequences, the cationic charge increased with peptide length. The goal of this work is to examine whether the charge also has an effect on activity; hence, we constructed two further series of peptides with a sequence similar to those of the KIA peptides, but with a constant charge of +7 for all lengths from 14 to 28 amino acids. For both of these new series, a clear length dependence similar to that of KIA peptides was observed, indicating that charge has only a minor influence. Both series also showed a distinct threshold length for peptides to be active, which correlates directly with the thickness of the membrane. Among the longer peptides, the new series showed activities only slightly lower than those of the original KIA peptides of the same length that had a higher charge. Shorter peptides, in which Gly was replaced with Lys, showed activities similar to those of KIA peptides of the same length, but peptides in which Ile was replaced with Lys lost their helicity and were less active.
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Affiliation(s)
- Marie-Claude Gagnon
- Department of Chemistry, PROTEO, CGCC, Université Laval , 1045 avenue de la Médecine, Québec, Canada G1V 0A6.,Department of Chemistry, PROTEO, CERMA, CQMF, Université Laval , 1045 avenue de la Médecine, Québec, Canada G1V 0A6
| | - Erik Strandberg
- Karlsruhe Institute of Technology (KIT) , Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Ariadna Grau-Campistany
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona , Barcelona, Spain
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT) , Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Johannes Reichert
- Karlsruhe Institute of Technology (KIT) , Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT) , Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Francesc Rabanal
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona , Barcelona, Spain
| | - Michèle Auger
- Department of Chemistry, PROTEO, CERMA, CQMF, Université Laval , 1045 avenue de la Médecine, Québec, Canada G1V 0A6
| | - Jean-François Paquin
- Department of Chemistry, PROTEO, CGCC, Université Laval , 1045 avenue de la Médecine, Québec, Canada G1V 0A6
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT) , Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany.,KIT , Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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27
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Kokhan SO, Tymtsunik AV, Grage SL, Afonin S, Babii O, Berditsch M, Strizhak AV, Bandak D, Platonov MO, Komarov IV, Ulrich AS, Mykhailiuk PK. Design, Synthesis, and Application of an Optimized Monofluorinated Aliphatic Label for Peptide Studies by Solid-State 19
F NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Serhii O. Kokhan
- Enamine Ltd; Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Andriy V. Tymtsunik
- Enamine Ltd; Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Stephan L. Grage
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Marina Berditsch
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | | | | | | | - Igor V. Komarov
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Pavel K. Mykhailiuk
- Enamine Ltd; Chervonotkatska 78 02094 Kyiv Ukraine
- Chemistry Department; Taras Shevchenko National University of Kyiv; Volodymyrska 64 01601 Kyiv Ukraine
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28
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Kokhan SO, Tymtsunik AV, Grage SL, Afonin S, Babii O, Berditsch M, Strizhak AV, Bandak D, Platonov MO, Komarov IV, Ulrich AS, Mykhailiuk PK. Design, Synthesis, and Application of an Optimized Monofluorinated Aliphatic Label for Peptide Studies by Solid‐State
19
F NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:14788-14792. [DOI: 10.1002/anie.201608116] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Serhii O. Kokhan
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies Taras Shevchenko National University of Kyiv Volodymyrska 60 01601 Kyiv Ukraine
| | - Andriy V. Tymtsunik
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies Taras Shevchenko National University of Kyiv Volodymyrska 60 01601 Kyiv Ukraine
| | - Stephan L. Grage
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Marina Berditsch
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | | | | | | | - Igor V. Komarov
- Institute of High Technologies Taras Shevchenko National University of Kyiv Volodymyrska 60 01601 Kyiv Ukraine
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Pavel K. Mykhailiuk
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine
- Chemistry Department Taras Shevchenko National University of Kyiv Volodymyrska 64 01601 Kyiv Ukraine
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29
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Windisch D, Ziegler C, Grage SL, Bürck J, Zeitler M, Gor'kov PL, Ulrich AS. Hydrophobic Mismatch Drives the Interaction of E5 with the Transmembrane Segment of PDGF Receptor. Biophys J 2016; 109:737-49. [PMID: 26287626 PMCID: PMC4547410 DOI: 10.1016/j.bpj.2015.07.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 02/05/2023] Open
Abstract
The oncogenic E5 protein from bovine papillomavirus is a short (44 amino acids long) integral membrane protein that forms homodimers. It activates platelet-derived growth factor receptor (PDGFR) β in a ligand-independent manner by transmembrane helix-helix interactions. The nature of this recognition event remains elusive, as numerous mutations are tolerated in the E5 transmembrane segment, with the exception of one hydrogen-bonding residue. Here, we examined the conformation, stability, and alignment of the E5 protein in fluid lipid membranes of substantially varying bilayer thickness, in both the absence and presence of the PDGFR transmembrane segment. Quantitative synchrotron radiation circular dichroism analysis revealed a very long transmembrane helix for E5 of ∼26 amino acids. Oriented circular dichroism and solid-state 15N-NMR showed that the alignment and stability of this unusually long segment depend critically on the membrane thickness. When reconstituted alone in exceptionally thick DNPC lipid bilayers, the E5 helix was found to be inserted almost upright. In moderately thick bilayers (DErPC and DEiPC), it started to tilt and became slightly deformed, and finally it became aggregated in conventional DOPC, POPC, and DMPC membranes due to hydrophobic mismatch. On the other hand, when E5 was co-reconstituted with the transmembrane segment of PDGFR, it was able to tolerate even the most pronounced mismatch and was stabilized by binding to the receptor, which has the same hydrophobic length. As E5 is known to activate PDGFR within the thin membranes of the Golgi compartment, we suggest that the intrinsic hydrophobic mismatch of these two interaction partners drives them together. They seem to recognize each other by forming a closely packed bundle of mutually aligned transmembrane helices, which is further stabilized by a specific pair of hydrogen-bonding residues.
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Affiliation(s)
- Dirk Windisch
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Colin Ziegler
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcel Zeitler
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Peter L Gor'kov
- National High Magnetic Field Laboratory, Tallahassee, Florida
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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30
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Zerweck J, Strandberg E, Bürck J, Reichert J, Wadhwani P, Kukharenko O, Ulrich AS. Homo- and heteromeric interaction strengths of the synergistic antimicrobial peptides PGLa and magainin 2 in membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:535-47. [PMID: 27052218 DOI: 10.1007/s00249-016-1120-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/01/2016] [Accepted: 02/16/2016] [Indexed: 12/11/2022]
Abstract
PGLa and magainin 2 (MAG2) are amphiphilic α-helical frog peptides with synergistic antimicrobial activity. In vesicle leakage assays we observed the strongest synergy for equimolar mixtures of PGLa and MAG2. This result was consistent with solid-state (15)N-NMR data on the helix alignment in model membranes. The Hill coefficients determined from the vesicle leakage data showed that the heterodimeric (PGLa-MAG2) interactions were stronger than the homodimeric (PGLa-PGLa and MAG2-MAG2) interactions. This result was also reflected in the free energy of dimerization determined from oriented circular dichroism and quantitative solid-state (19)F-NMR analysis.
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Affiliation(s)
- Jonathan Zerweck
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Erik Strandberg
- KIT, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Jochen Bürck
- KIT, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Johannes Reichert
- KIT, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Parvesh Wadhwani
- KIT, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Olga Kukharenko
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany. .,KIT, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany.
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31
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Zamora-Carreras H, Strandberg E, Mühlhäuser P, Bürck J, Wadhwani P, Jiménez MÁ, Bruix M, Ulrich AS. Alanine scan and (2)H NMR analysis of the membrane-active peptide BP100 point to a distinct carpet mechanism of action. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1328-38. [PMID: 26975251 DOI: 10.1016/j.bbamem.2016.03.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/23/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
The short membrane-active peptide BP100 [KKLFKKILKYL-NH2] is known as an effective antimicrobial and cell penetrating agent. For a functional alanine scan each of the 11 amino acids was replaced with deuterated Ala-d3, one at a time. MIC assays showed that a substitution of Lys did not affect the antimicrobial activity, but it decreased when a hydrophobic residue was replaced. In most cases, a reduction in hydrophobicity led to a decrease in hemolysis, and some peptide analogues had an improved therapeutic index. Circular dichroism showed that BP100 folds as an amphiphilic α-helix in a bilayer. Its alignment was determined from (2)H NMR in oriented membranes of different composition. The azimuthal rotation angle was the same under all conditions, but the average helix tilt angle and the dynamical behavior of the peptide varied in a systematic manner. In POPC/POPG bilayers, with a negative spontaneous curvature, the peptide was found to lie flat on the bilayer surface, and with little wobble. In DMPC/DMPG, with a positive spontaneous curvature, BP100 at higher concentrations became tilted obliquely into the membrane, with the uncharged C-terminus inserted more deeply into the lipid bilayer, experiencing significant fluctuations in tilt angle. In DMPC/DMPG/lyso-MPC, with a pronounced positive spontaneous curvature, the helix tilted even further and became even more mobile. The 11-mer BP100 is obviously too short to form transmembrane pores. We conclude that BP100 operates via a carpet mechanism, whereby the C-terminus gets inserted into the hydrophobic core of the bilayer, which leads to membrane perturbation and induces transient permeability.
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Affiliation(s)
| | - Erik Strandberg
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Philipp Mühlhäuser
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - M Ángeles Jiménez
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Marta Bruix
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Anne S Ulrich
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany; KIT, Institute of Organic Chemistry and CFN, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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32
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Bürck J, Wadhwani P, Fanghänel S, Ulrich AS. Oriented Circular Dichroism: A Method to Characterize Membrane-Active Peptides in Oriented Lipid Bilayers. Acc Chem Res 2016; 49:184-92. [PMID: 26756718 DOI: 10.1021/acs.accounts.5b00346] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structures of membrane-bound polypeptides are intimately related to their functions and may change dramatically with the lipid environment. Circular dichroism (CD) is a rapid analytical method that requires relatively low amounts of material and no labeling. Conventional CD is routinely used to monitor the secondary structure of peptides and proteins in solution, for example, in the presence of ligands and other binding partners. In the case of membrane-active peptides and transmembrane proteins, these measurements can be applied to, and remain limited to, samples containing detergent micelles or small sonicated lipid vesicles. Such traditional CD analysis reveals only secondary structures. With the help of an oriented circular dichroism (OCD) setup, however, based on the preparation of macroscopically oriented lipid bilayers, it is possible to address the membrane alignment of a peptide in addition to its conformation. This approach has been mostly used for α-helical peptides so far, but other structural elements are conceivable as well. OCD analysis relies on Moffitt's theory, which predicts that the electronic transition dipole moments of the backbone amide bonds in helical polypeptides are polarized either parallel or perpendicular to the helix axis. The interaction of the electric field vector of the circularly polarized light with these transitions results in an OCD spectrum of a membrane-bound α-helical peptide, which exhibits a characteristic line shape and reflects the angle between the helix axis and the bilayer normal. For parallel alignment of a peptide helix with respect to the membrane surface (S-state), the corresponding "fingerprint" CD band around 208 nm will exhibit maximum negative amplitude. If the helix changes its alignment via an obliquely tilted (T-state) to a fully inserted transmembrane orientation (I-state), the ellipticity at 208 nm decreases and the value approaches zero due to the decreased interactions between the field and the transition dipole. Compared to conventional CD, OCD data are not only collected in the biologically relevant environment of a highly hydrated planar lipid bilayer (whose composition can be varied at will), but in addition it provides information about the tilt angle of the polypeptide in the membrane. It is the method of choice for screening numerous different conditions, such as peptide concentration, lipid composition, membrane additives, pH, temperature, and sample hydration. All these factors have been found to affect the peptide alignment in membrane, while having little or no influence on conformation. In many cases, the observed realignment could be related to biological action, such as pore formation by antimicrobial and cell-penetrating peptides, or to binding events of transmembrane segments of integral membrane proteins. Likewise, any lipid-induced conversion from α-helix to β-sheeted conformation is readily picked up by OCD and has been interpreted in terms of protein instability or amyloid-formation.
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Affiliation(s)
- Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Susanne Fanghänel
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
- Institute of Organic Chemistry, KIT, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
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33
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Li J, Chen Z, Zhou M, Jing J, Li W, Wang Y, Wu L, Wang L, Wang Y, Lee M. Polyoxometalate-Driven Self-Assembly of Short Peptides into Multivalent Nanofibers with Enhanced Antibacterial Activity. Angew Chem Int Ed Engl 2016; 55:2592-5. [DOI: 10.1002/anie.201511276] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Jingfang Li
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Zhijun Chen
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Mengcheng Zhou
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Jiangbo Jing
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Yang Wang
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Lixin Wu
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Liyan Wang
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Yanqiu Wang
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Myongsoo Lee
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
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34
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Li J, Chen Z, Zhou M, Jing J, Li W, Wang Y, Wu L, Wang L, Wang Y, Lee M. Polyoxometalate-Driven Self-Assembly of Short Peptides into Multivalent Nanofibers with Enhanced Antibacterial Activity. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511276] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jingfang Li
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Zhijun Chen
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Mengcheng Zhou
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Jiangbo Jing
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Yang Wang
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Lixin Wu
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Liyan Wang
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Yanqiu Wang
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
| | - Myongsoo Lee
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; Qianjin Avenue 2699 Changchun 130012 China
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35
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Girrbach M, Meliciani I, Waterkotte B, Berthold S, Oster A, Brurein F, Strunk T, Wadhwani P, Berensmeier S, Wenzel W, Schmitz K. A fluorescence polarization assay for the experimental validation of an in silico model of the chemokine CXCL8 binding to receptor-derived peptides. Phys Chem Chem Phys 2015; 16:8036-43. [PMID: 24647967 DOI: 10.1039/c3cp53850h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide based inhibitors of protein-protein interactions are of great interest in proteomics, structural biology and medicinal chemistry. Optimized inhibitors can be designed by experimental approaches or by computational prediction. Ideally, computational models are adjusted to the peptide-protein complex of interest according to experimental data obtained in specific binding experiments. The chemokine CXCL8 (interleukin-8) is an interesting target for drug discovery due to its role in inflammatory diseases. Given the available structural data and information on its receptor interactions it constitutes a basis for the rational design of inhibitor peptides. Starting from the reported structure of CXCL8 in complex with a peptide derived from its receptor CXCR1 we developed a computational docking procedure to estimate the changes in binding energy as a function of individual amino acid exchanges. This indicates whether the respective amino acid residue must be preserved or can be substituted to maintain or improve affinity, respectively. To validate and improve the assumptions made in this docking simulation we established a fluorescence polarization assay for receptor-derived peptides binding to CXCL8. A peptide library was tested comprising selected mutants characterized by docking simulations. A number of predictions regarding electrostatic interactions were confirmed by these experiments and it was revealed that the model needed to be corrected for backbone flexibility. Therefore, the assay presented here is a promising tool to systematically improve the computational model by iterative cycles of modeling, experimental validation and refinement of the algorithm, leading to a more reliable model and peptides with improved affinity.
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Affiliation(s)
- Maria Girrbach
- Karlsruhe Institute of Technology, Centre for Functional Nanostructures, Haid-und-Neu-Straße 6, 76131 Karlsruhe, Germany
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36
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Bürck J, Roth S, Windisch D, Wadhwani P, Moss D, Ulrich AS. UV-CD12: synchrotron radiation circular dichroism beamline at ANKA. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:844-52. [PMID: 25931105 PMCID: PMC4416691 DOI: 10.1107/s1600577515004476] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/03/2015] [Indexed: 05/25/2023]
Abstract
Synchrotron radiation circular dichroism (SRCD) is a rapidly growing technique for structure analysis of proteins and other chiral biomaterials. UV-CD12 is a high-flux SRCD beamline installed at the ANKA synchrotron, to which it had been transferred after the closure of the SRS Daresbury. The beamline covers an extended vacuum-UV to near-UV spectral range and has been open for users since October 2011. The current end-station allows for temperature-controlled steady-state SRCD spectroscopy, including routine automated thermal scans of microlitre volumes of water-soluble proteins down to 170 nm. It offers an excellent signal-to-noise ratio over the whole accessible spectral range. The technique of oriented circular dichroism (OCD) was recently implemented for determining the membrane alignment of α-helical peptides and proteins in macroscopically oriented lipid bilayers as mimics of cellular membranes. It offers improved spectral quality <200 nm compared with an OCD setup adapted to a bench-top instrument, and accelerated data collection by a factor of ∼3. In addition, it permits investigations of low hydrated protein films down to 130 nm using a rotatable sample cell that avoids linear dichroism artifacts.
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Affiliation(s)
- Jochen Bürck
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Siegmar Roth
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Dirk Windisch
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - David Moss
- ANKA Synchrotron Radiation Facility, Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
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37
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Strandberg E, Zerweck J, Horn D, Pritz G, Berditsch M, Bürck J, Wadhwani P, Ulrich AS. Influence of hydrophobic residues on the activity of the antimicrobial peptide magainin 2 and its synergy with PGLa. J Pept Sci 2015; 21:436-45. [PMID: 25898805 DOI: 10.1002/psc.2780] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Magainin 2 (MAG2) and PGLa are two related antimicrobial peptides found in the skin of the African frog Xenopus laevis with a pronounced synergistic activity, which act by permeabilizing bacterial membranes. To probe the influence of hydrophobic peptide-lipid and peptide-peptide interactions on the antimicrobial activity and on synergy, the sequence of MAG2 was modified by replacing single amino acids either with a small alanine or with the stiff and bulky hydrophobic 3-(trifluoromethyl)-L-bicyclopent-[1.1.1]-1-ylglycine side chain. The minimum inhibitory concentration of 14 MAG2 analogs was strongly influenced by these single substitutions: the antimicrobial activity was consistently improved when the hydrophobicity was increased on the hydrophobic face of the amphiphilic helix, while the activity decreased when the hydrophobicity was reduced. The synergy with PGLa, on the other hand, was rather insensitive to mutations of hydrophobic residues. It thus seems that the antimicrobial effect of MAG2 on its own depends strongly on the hydrophobicity of the peptide, while the synergy with PGLa does not depend on the overall hydrophobicity of MAG2.
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Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
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38
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Misiewicz J, Afonin S, Grage SL, van den Berg J, Strandberg E, Wadhwani P, Ulrich AS. Action of the multifunctional peptide BP100 on native biomembranes examined by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 61:287-98. [PMID: 25616492 DOI: 10.1007/s10858-015-9897-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/10/2015] [Indexed: 05/22/2023]
Abstract
Membrane composition is a key factor that regulates the destructive activity of antimicrobial peptides and the non-leaky permeation of cell penetrating peptides in vivo. Hence, the choice of model membrane is a crucial aspect in NMR studies and should reflect the biological situation as closely as possible. Here, we explore the structure and dynamics of the short multifunctional peptide BP100 using a multinuclear solid-state NMR approach. The membrane alignment and mobility of this 11 amino acid peptide was studied in various synthetic lipid bilayers with different net charge, fluidity, and thickness, as well as in native biomembranes harvested from prokaryotic and eukaryotic cells. (19)F-NMR provided the high sensitivity and lack of natural abundance background that are necessary to observe a labelled peptide even in protoplast membranes from Micrococcus luteus and in erythrocyte ghosts. Six selectively (19)F-labeled BP100 analogues gave remarkably similar spectra in all of the macroscopically oriented membrane systems, which were studied under quasi-native conditions of ambient temperature and full hydration. This similarity suggests that BP100 has the same surface-bound helical structure and high mobility in the different biomembranes and model membranes alike, independent of charge, thickness or cholesterol content of the system. (31)P-NMR spectra of the phospholipid components did not indicate any bilayer perturbation, so the formation of toroidal wormholes or micellarization can be excluded as a mechanism of its antimicrobial or cell penetrating action. However, (2)H-NMR analysis of the acyl chain order parameter profiles showed that BP100 leads to considerable membrane thinning and thereby local destabilization.
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Affiliation(s)
- Julia Misiewicz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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Hydrophobic mismatch demonstrated for membranolytic peptides, and their use as molecular rulers to measure bilayer thickness in native cells. Sci Rep 2015; 5:9388. [PMID: 25807192 PMCID: PMC5224518 DOI: 10.1038/srep09388] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/20/2015] [Indexed: 11/16/2022] Open
Abstract
Hydrophobic mismatch is a well-recognized principle in the interaction of transmembrane proteins with lipid bilayers. This concept was extended here to amphipathic membranolytic α-helices. Nine peptides with lengths between 14 and 28 amino acids were designed from repeated KIAGKIA motifs, and their helical nature was confirmed by circular dichroism spectroscopy. Biological assays for antimicrobial activity and hemolysis, as well as fluorescence vesicle leakage and solid-state NMR spectroscopy, were used to correlate peptide length with membranolytic activity. These data show that the formation of transmembrane pores is only possible under the condition of hydrophobic matching: the peptides have to be long enough to span the hydrophobic bilayer core to be able to induce vesicle leakage, kill bacteria, and cause hemolysis. By correlating the threshold lengths for biological activity with the biophysical results on model vesicles, the peptides could be utilized as molecular rulers to measure the membrane thickness in different cells.
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40
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Control and role of pH in peptide–lipid interactions in oriented membrane samples. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:833-41. [DOI: 10.1016/j.bbamem.2014.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 12/22/2022]
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41
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Manzo G, Scorciapino MA, Wadhwani P, Bürck J, Montaldo NP, Pintus M, Sanna R, Casu M, Giuliani A, Pirri G, Luca V, Ulrich AS, Rinaldi AC. Enhanced amphiphilic profile of a short β-stranded peptide improves its antimicrobial activity. PLoS One 2015; 10:e0116379. [PMID: 25617899 PMCID: PMC4305290 DOI: 10.1371/journal.pone.0116379] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 12/05/2014] [Indexed: 12/11/2022] Open
Abstract
SB056 is a novel semi-synthetic antimicrobial peptide with a dimeric dendrimer scaffold. Active against both Gram-negative and -positive bacteria, its mechanism has been attributed to a disruption of bacterial membranes. The branched peptide was shown to assume a β-stranded conformation in a lipidic environment. Here, we report on a rational modification of the original, empirically derived linear peptide sequence [WKKIRVRLSA-NH2, SB056-lin]. We interchanged the first two residues [KWKIRVRLSA-NH2, β-SB056-lin] to enhance the amphipathic profile, in the hope that a more regular β-strand would lead to a better antimicrobial performance. MIC values confirmed that an enhanced amphiphilic profile indeed significantly increases activity against both Gram-positive and -negative strains. The membrane binding affinity of both peptides, measured by tryptophan fluorescence, increased with an increasing ratio of negatively charged/zwitterionic lipids. Remarkably, β-SB056-lin showed considerable binding even to purely zwitterionic membranes, unlike the original sequence, indicating that besides electrostatic attraction also the amphipathicity of the peptide structure plays a fundamental role in binding, by stabilizing the bound state. Synchrotron radiation circular dichroism and solid-state 19F-NMR were used to characterize and compare the conformation and mobility of the membrane bound peptides. Both SB056-lin and β-SB056-lin adopt a β-stranded conformation upon binding POPC vesicles, but the former maintains an intrinsic structural disorder that also affects its aggregation tendency. Upon introducing some anionic POPG into the POPC matrix, the sequence-optimized β-SB056-lin forms well-ordered β-strands once electro-neutrality is approached, and it aggregates into more extended β-sheets as the concentration of anionic lipids in the bilayer is raised. The enhanced antimicrobial activity of the analogue correlates with the formation of these extended β-sheets, which also leads to a dramatic alteration of membrane integrity as shown by 31P-NMR. These findings are generally relevant for the design and optimization of other membrane-active antimicrobial peptides that can fold into amphipathic β-strands.
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Affiliation(s)
- Giorgia Manzo
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Mariano A. Scorciapino
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Nicola Pietro Montaldo
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Manuela Pintus
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Roberta Sanna
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Mariano Casu
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Andrea Giuliani
- Research & Development Unit, Spider Biotech S.r.l., I-10010 Colleretto Giacosa (TO), Italy
| | - Giovanna Pirri
- Research & Development Unit, Spider Biotech S.r.l., I-10010 Colleretto Giacosa (TO), Italy
| | - Vincenzo Luca
- Dipartimento di Scienze Biochimiche, “A. Rossi Fanelli”, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Andrea C. Rinaldi
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
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3D hydrophobic moment vectors as a tool to characterize the surface polarity of amphiphilic peptides. Biophys J 2015; 106:2385-94. [PMID: 24896117 DOI: 10.1016/j.bpj.2014.04.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 11/22/2022] Open
Abstract
The interaction of membranes with peptides and proteins is largely determined by their amphiphilic character. Hydrophobic moments of helical segments are commonly derived from their two-dimensional helical wheel projections, and the same is true for β-sheets. However, to the best of our knowledge, there exists no method to describe structures in three dimensions or molecules with irregular shape. Here, we define the hydrophobic moment of a molecule as a vector in three dimensions by evaluating the surface distribution of all hydrophilic and lipophilic regions over any given shape. The electrostatic potential on the molecular surface is calculated based on the atomic point charges. The resulting hydrophobic moment vector is specific for the instantaneous conformation, and it takes into account all structural characteristics of the molecule, e.g., partial unfolding, bending, and side-chain torsion angles. Extended all-atom molecular dynamics simulations are then used to calculate the equilibrium hydrophobic moments for two antimicrobial peptides, gramicidin S and PGLa, under different conditions. We show that their effective hydrophobic moment vectors reflect the distribution of polar and nonpolar patches on the molecular surface and the calculated electrostatic surface potential. A comparison of simulations in solution and in lipid membranes shows how the peptides undergo internal conformational rearrangement upon binding to the bilayer surface. A good correlation with solid-state NMR data indicates that the hydrophobic moment vector can be used to predict the membrane binding geometry of peptides. This method is available as a web application on http://www.ibg.kit.edu/HM/.
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43
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Bandak D, Babii O, Vasiuta R, Komarov IV, Mykhailiuk PK. Design and synthesis of novel 19F-amino acid: a promising 19F NMR label for peptide studies. Org Lett 2014; 17:226-9. [PMID: 25545327 DOI: 10.1021/ol503300m] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Novel aliphatic (19)F-substituted amino acid was designed as a (19)F NMR label for peptide studies. The synthesis was performed in 11 steps and 9% overall yield from a commercially available starting material. The key transformation was a decarboxylative fluorination of an aliphatic carboxylic acid with XeF2 in C6F6.
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Affiliation(s)
- Dmytro Bandak
- Department of Chemistry, Taras Shevchenko National University of Kyiv , Volodymyrska 64, Kyiv 01601, Ukraine
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44
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Vácha R, Linse S, Lund M. Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides. J Am Chem Soc 2014; 136:11776-82. [DOI: 10.1021/ja505502e] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Robert Vácha
- National
Centre for Biomolecular Research, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University, Kamenice
5, 625 00 Brno-Bohunice, Czech Republic
| | - Sara Linse
- Division
of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Mikael Lund
- Division
of Theoretical Chemistry, Lund University, Lund, Sweden
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45
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The cooperative behaviour of antimicrobial peptides in model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2870-81. [PMID: 25046254 DOI: 10.1016/j.bbamem.2014.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/27/2014] [Accepted: 07/01/2014] [Indexed: 01/24/2023]
Abstract
A systematic analysis of the hypothesis of the antimicrobial peptides' (AMPs) cooperative action is performed by means of full atomistic molecular dynamics simulations accompanied by circular dichroism experiments. Several AMPs from the aurein family (2.5,2.6, 3.1), have a similar sequence in the first ten amino acids, are investigated in different environments including aqueous solution, trifluoroethanol (TFE), palmitoyloleoylphosphatidylethanolamine (POPE), and palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayers. It is found that the cooperative effect is stronger in aqueous solution and weaker in TFE. Moreover, in the presence of membranes, the cooperative effect plays an important role in the peptide/lipid bilayer interaction. The action of AMPs is a competition of the hydrophobic interactions between the side chains of the peptides and the hydrophobic region of lipid molecules, as well as the intra peptide interaction. The aureins 2.5-COOH and 2.6-COOH form a hydrophobic aggregate to minimize the interaction between the hydrophobic group and the water. Once that the peptides reach the water/lipid interface the hydrophobic aggregate becomes smaller and the peptides start to penetrate into the membrane. In contrast, aurein 3.1-COOH forms only a transient aggregate which disintegrates once the peptides reached the membrane, and it shows no cooperativity in membrane penetration.
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46
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Fanghänel S, Wadhwani P, Strandberg E, Verdurmen WPR, Bürck J, Ehni S, Mykhailiuk PK, Afonin S, Gerthsen D, Komarov IV, Brock R, Ulrich AS. Structure analysis and conformational transitions of the cell penetrating peptide transportan 10 in the membrane-bound state. PLoS One 2014; 9:e99653. [PMID: 24937132 PMCID: PMC4061077 DOI: 10.1371/journal.pone.0099653] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/18/2014] [Indexed: 11/18/2022] Open
Abstract
Structure analysis of the cell-penetrating peptide transportan 10 (TP10) revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan) was found to exhibit prominent characteristics of (i) amphiphilic α-helices, (ii) intrinsically disordered peptides, as well as (iii) β-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state (19)F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L- or D-enantiomer of 3-(trifluoromethyl)-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg) as a reporter group for (19)F-NMR. Using the L-epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal α-helix is embedded in the membrane with an oblique tilt angle of ∼ 55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D-CF3-Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile β-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D-CF3-Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the α-helix counteracts the tendency of the unfolded N-terminus to self-assemble into β-pleated fibrils.
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Affiliation(s)
- Susanne Fanghänel
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
| | - Parvesh Wadhwani
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Erik Strandberg
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Wouter P. R. Verdurmen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jochen Bürck
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Sebastian Ehni
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
| | - Pavel K. Mykhailiuk
- Taras Shevchenko National University of Kyiv, Chemistry Department, Kyiv, Ukraine and Enamine Ltd., Kyiv, Ukraine
| | - Sergii Afonin
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | | | - Igor V. Komarov
- Taras Shevchenko National University of Kyiv, Institute of High Technologies, Kyiv, Ukraine
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
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Košutić M, Jud L, Da Veiga C, Frener M, Fauster K, Kreutz C, Ennifar E, Micura R. Surprising base pairing and structural properties of 2'-trifluoromethylthio-modified ribonucleic acids. J Am Chem Soc 2014; 136:6656-63. [PMID: 24766131 PMCID: PMC4021565 DOI: 10.1021/ja5005637] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The chemical synthesis of ribonucleic
acids (RNA) with novel chemical
modifications is largely driven by the motivation to identify eligible
functional probes for the various applications in life sciences. To
this end, we have a strong focus on the development of novel fluorinated
RNA derivatives that are powerful in NMR spectroscopic analysis of
RNA folding and RNA ligand interactions. Here, we report on the synthesis
of 2′-SCF3 pyrimidine nucleoside containing oligoribonucleotides
and the comprehensive investigation of their structure and base pairing
properties. While this modification has a modest impact on thermodynamic
stability when it resides in single-stranded regions, it was found
to be destabilizing to a surprisingly high extent when located in
double helical regions. Our NMR spectroscopic investigations on short
single-stranded RNA revealed a strong preference for C2′-endo
conformation of the 2′-SCF3 ribose unit. Together
with a recent computational study (L. Li, J. W. Szostak, J.
Am. Chem. Soc. 2014, 136, 2858–2865)
that estimated the extent of destabilization caused by a single C2′-endo
nucleotide within a native RNA duplex to amount to 6 kcal mol−1 because of disruption of the planar base pair structure,
these findings support the notion that the intrinsic preference for
C2′-endo conformation of 2′-SCF3 nucleosides
is most likely responsible for the pronounced destabilization of double
helices. Importantly, we were able to crystallize 2′-SCF3 modified RNAs and solved their X-ray structures at atomic
resolution. Interestingly, the 2′-SCF3 containing
nucleosides that were engaged in distinct mismatch arrangements, but
also in a standard Watson–Crick base pair, adopted the same
C3′-endo ribose conformations as observed in the structure
of the unmodified RNA. Likely, strong crystal packing interactions
account for this observation. In all structures, the fluorine atoms
made surprisingly close contacts to the oxygen atoms of the corresponding
pyrimidine nucleobase (O2), and the 2′-SCF3 moieties
participated in defined water-bridged hydrogen-bonding networks in
the minor groove. All these features allow a rationalization of the
structural determinants of the 2′-SCF3 nucleoside
modification and correlate them to base pairing properties.
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Affiliation(s)
- Marija Košutić
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , 6020 Innsbruck, Austria
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Tkachenko AN, Mykhailiuk PK, Radchenko DS, Babii O, Afonin S, Ulrich AS, Komarov IV. Design and Synthesis of a Monofluoro-Substituted Aromatic Amino Acid as a Conformationally Restricted19F NMR Label for Membrane-Bound Peptides. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301737] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Afonin S, Glaser RW, Sachse C, Salgado J, Wadhwani P, Ulrich AS. (19)F NMR screening of unrelated antimicrobial peptides shows that membrane interactions are largely governed by lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2260-8. [PMID: 24699372 DOI: 10.1016/j.bbamem.2014.03.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/23/2014] [Accepted: 03/24/2014] [Indexed: 02/07/2023]
Abstract
Many amphiphilic antimicrobial peptides permeabilize bacterial membranes via successive steps of binding, re-alignment and/or oligomerization. Here, we have systematically compared the lipid interactions of two structurally unrelated peptides: the cyclic β-pleated gramicidin S (GS), and the α-helical PGLa. (19)F NMR was used to screen their molecular alignment in various model membranes over a wide range of temperatures. Both peptides were found to respond to the phase state and composition of these different samples in a similar way. In phosphatidylcholines, both peptides first bind to the bilayer surface. Above a certain threshold concentration they can re-align and immerse more deeply into the hydrophobic core, which presumably involves oligomerization. Re-alignment is most favorable around the lipid chain melting temperature, and also promoted by decreasing bilayer thickness. The presence of anionic lipids has no influence in fluid membranes, but in the gel phase the alignment states are more complex. Unsaturated acyl chains and other lipids with intrinsic negative curvature prevent re-alignment, hence GS and PGLa do not insert into mixtures resembling bacterial membranes, nor into bacterial lipid extracts. Cholesterol, which is present in high concentrations in animal membranes, even leads to an expulsion of the peptides from the bilayer and prevents their binding altogether. However, a very low cholesterol content of 10% was found to promote binding and re-alignment of both peptides. Overall, these findings show that the ability of amphiphilic peptides to re-align and immerse into a membrane is determined by the physico-chemical properties of the lipids, such as spontaneous curvature. This idea is reinforced by the remarkably similar behavior observed here for two structurally unrelated molecules (with different conformation, size, shape, charge), which further suggests that their activity at the membrane level is largely governed by the properties of the constituent lipids, while the selectivity towards different cell types is additionally ruled by electrostatic attraction between peptide and cell surface. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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Affiliation(s)
- Sergii Afonin
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Ralf W Glaser
- Institute of Biochemistry and Biophysics, Friedrich-Schiller-Universität Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Carsten Sachse
- EMBL - European Molecular Biology Laboratory, Structural and Computational Biology, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Jesús Salgado
- Institute of Molecular Science (ICMol), University of Valencia, C/Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany; Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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50
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Wadhwani P, Strandberg E, van den Berg J, Mink C, Bürck J, Ciriello RA, Ulrich AS. Dynamical structure of the short multifunctional peptide BP100 in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:940-9. [DOI: 10.1016/j.bbamem.2013.11.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/25/2013] [Accepted: 11/01/2013] [Indexed: 11/26/2022]
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