1
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Golysheva EA, Boyle AL, Biondi B, Ruzza P, Kros A, Raap J, Toniolo C, Formaggio F, Dzuba SA. Probing the E/K Peptide Coiled-Coil Assembly by Double Electron-Electron Resonance and Circular Dichroism. Biochemistry 2020; 60:19-30. [PMID: 33320519 DOI: 10.1021/acs.biochem.0c00773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Double electron-electron resonance (DEER, also known as PELDOR) and circular dichroism (CD) spectroscopies were explored for the purpose of studying the specificity of the conformation of peptides induced by their assembly into a self-recognizing system. The E and K peptides are known to form a coiled-coil heterodimer. Two paramagnetic TOAC α-amino acid residues were incorporated into each of the peptides (denoted as K** and E**), and a three-dimensional structural investigation in the presence or absence of their unlabeled counterparts E and K was performed. The TOAC spin-labels, replacing two Ala residues in each compound, are covalently and quasi-rigidly connected to the peptide backbone. They are known not to disturb the native structure, so that any conformational change can easily be monitored and assigned. DEER spectroscopy enables the measurement of the intramolecular electron spin-spin distance distribution between the two TOAC labels, within a length range of 1.5-8 nm. This method allows the individual conformational changes for the K**, K**/E, E**, and E**/K molecules to be investigated in glassy frozen solutions. Our data reveal that the conformations of the E** and K** peptides are strongly influenced by the presence of their counterparts. The results are discussed with those from CD spectroscopy and with reference to the already reported nuclear magnetic resonance data. We conclude that the combined DEER/TOAC approach allows us to obtain accurate and reliable information about the conformation of the peptides before and after their assembly into coiled-coil heterodimers. Applications of this induced fit method to other two-component, but more complex, systems, like a receptor and antagonists, a receptor and a hormone, and an enzyme and a ligand, are discussed.
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Affiliation(s)
- Elena A Golysheva
- Novosibirsk State University, Novosibirsk 630090, Russian Federation.,V. V. Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk 630090, Russian Federation
| | - Aimee L Boyle
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Paolo Ruzza
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Alexander Kros
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Sergei A Dzuba
- Novosibirsk State University, Novosibirsk 630090, Russian Federation.,V. V. Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk 630090, Russian Federation
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2
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Pandidan S, Mechler A. Nano-viscosimetry analysis of the membrane disrupting action of the bee venom peptide melittin. Sci Rep 2019; 9:10841. [PMID: 31346251 PMCID: PMC6658469 DOI: 10.1038/s41598-019-47325-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/10/2019] [Indexed: 12/30/2022] Open
Abstract
Melittin is one of the most studied α-helical cationic membrane disrupting peptides. It is the main component of bee venom, however it is considered an antimicrobial peptide for its ability to kill bacteria. Melittin is believed to act by opening large toroidal pores in the plasma membrane of the targeted cells/bacteria, although this is questioned by some authors. Little is known, however, about the molecular mechanism leading to this activity. In this study the mechanism of action of melittin was studied by dye leakage and quartz crystal microbalance fingerprinting analysis in biomimetic model membranes. The results revealed the existence of multiple stages in the membrane disrupting action with characteristic differences between different membrane types. In bacterial-mimetic (charged) lipid mixtures the viscoelastic fingerprints suggest a surface-acting mechanism, whereas in mammalian-mimetic (neutral) membranes melittin appears to penetrate the bilayer already at low concentrations. In domain-forming mixed membranes melittin shows a preference for the domain containing predominantly zwitterionic lipids. The results confirm membrane poration but are inconsistent with the insertion-to-toroidal pore pathway. Therefore hypotheses of the two membrane disrupting pathways were developed, describing the membrane disruption as either surface tension modulation leading to toroidal pore formation, or linear aggregation leading to fissure formation in the membrane.
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Affiliation(s)
- Sara Pandidan
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Adam Mechler
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
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3
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Kundu A, Verma PK, Cho M. Water Structure and Dynamics in the Stern Layer of Micelles: Femtosecond Mid-Infrared Pump-Probe Spectroscopy Study. J Phys Chem B 2019; 123:5238-5245. [PMID: 31145621 DOI: 10.1021/acs.jpcb.9b03183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular-level understanding of the water structure and dynamics in the Stern layer of micelles is important to elucidate the active role of water in biological processes on membrane surfaces. Micelles and reverse micelles are considered to be excellent membrane model systems. Here, to address the question of whether or not the spatial confinement effect on water in reverse micelles and nanometric water pool systems plays a role in modulating water dynamics, we consider four different aqueous micelle solutions and study the water dynamics in the Stern layer of micelles using a femtosecond mid-infrared pump-probe spectroscopy technique. Vibrational energy relaxation and rotational dynamics of the O?D stretch mode of HDO and the azido stretch mode of hydrazoic acid are critically dependent on the charge, polarity, and chemical structure of the surfactant head group. In particular, water molecules in the Stern layer of micelles, which are not in spatially confined environments, are notably different from those in bulk water. This finding clearly indicates that changes in the vibrational and rotational dynamics of water molecules, even in spatially confined systems, are mainly induced by surface effects instead of spatial confinement effects. We believe that the present experimental results are of importance for understanding water-involved biochemical processes on biological membranes.
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Affiliation(s)
- Achintya Kundu
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea.,Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| | - Pramod Kumar Verma
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea.,Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea.,Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
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4
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Milov AD, Tsvetkov YD, Raap J, De Zotti M, Formaggio F, Toniolo C. Review conformation, self-aggregation, and membrane interaction of peptaibols as studied by pulsed electron double resonance spectroscopy. Biopolymers 2016; 106:6-24. [DOI: 10.1002/bip.22713] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/29/2015] [Accepted: 08/09/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Alexander D. Milov
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk 630090 Russian Federation
| | - Yuri D. Tsvetkov
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk 630090 Russian Federation
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University; 2300 RA Leiden The Netherlands
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | | | - Claudio Toniolo
- Department of Chemistry; University of Padova; Padova 35131 Italy
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5
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Bobone S, De Zotti M, Bortolotti A, Biondi B, Ballano G, Palleschi A, Toniolo C, Formaggio F, Stella L. The fluorescence and infrared absorption probepara-cyanophenylalanine: Effect of labeling on the behavior of different membrane-interacting peptides. Biopolymers 2015; 104:521-32. [DOI: 10.1002/bip.22674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/30/2015] [Accepted: 05/04/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Sara Bobone
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Marta De Zotti
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Annalisa Bortolotti
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Gema Ballano
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Claudio Toniolo
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Lorenzo Stella
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
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6
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De Zotti M, Ballano G, Jost M, Salnikov ES, Bechinger B, Oancea S, Crisma M, Toniolo C, Formaggio F. Solution synthesis, conformational analysis, and antimicrobial activity of three alamethicin F50/5 analogs bearing a trifluoroacetyl label. Chem Biodivers 2015; 11:1163-91. [PMID: 25146762 DOI: 10.1002/cbdv.201300394] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Indexed: 11/07/2022]
Abstract
We prepared, by solution-phase methods, and fully characterized three analogs of the membrane-active peptaibiotic alamethicin F50/5, bearing a single trifluoroacetyl (Tfa) label at the N-terminus, at position 9 (central region) or at position 19 (C-terminus), and with the three Gln at positions 7, 18, and 19 replaced by Glu(OMe) residues. To add the Tfa label at position 9 or 19, a γ-trifluoroacetylated α,γ-diaminobutyric acid (Dab) residue was incorporated as a replacement for the original Val(9) or Glu(OMe)(19) amino acid. We performed a detailed conformational analysis of the three analogs (using FT-IR absorption, CD, 2D-NMR, and X-ray diffraction), which clearly showed that Tfa labeling does not introduce any dramatic backbone modification in the predominantly α-helical structure of the parent peptaibiotic. The results of an initial solid-state (19)F-NMR study on one of the analogs favor the conclusion that the Tfa group is a very promising reporter for the analysis of peptaibioticmembrane interactions. Finally, we found that the antimicrobial activities of the three newly synthesized analogs depend on the position of the Tfa label in the peptide sequence.
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Affiliation(s)
- Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova.
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7
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Pike SJ, Boddaert T, Raftery J, Webb SJ, Clayden J. Participation of non-aminoisobutyric acid (Aib) residues in the 310 helical conformation of Aib-rich foldamers: a solid state study. NEW J CHEM 2015. [DOI: 10.1039/c4nj01547a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
310 helical conformations that extend over 21 Å result when selected non-Aib terminal and central residues are incorporated into Aib-rich foldamers.
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Affiliation(s)
- Sarah J. Pike
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | | | - James Raftery
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Simon J. Webb
- School of Chemistry
- University of Manchester
- Manchester
- UK
- Manchester Institute of Biotechnology
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8
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Pike SJ, Diemer V, Raftery J, Webb SJ, Clayden J. Designing foldamer-foldamer interactions in solution: the roles of helix length and terminus functionality in promoting the self-association of aminoisobutyric acid oligomers. Chemistry 2014; 20:15981-90. [PMID: 25280242 DOI: 10.1002/chem.201403626] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 12/11/2022]
Abstract
The biological activity of antibiotic peptaibols has been linked to their ability to aggregate, but the structure-activity relationship for aggregation is not well understood. Herein, we report a systematic study of a class of synthetic helical oligomer (foldamer) composed of aminoisobutyric acid (Aib) residues, which mimic the folding behavior of peptaibols. NMR spectroscopic analysis was used to quantify the dimerization constants in solution, which showed hydrogen-bond donors at the N terminus promoted aggregation more effectively than similar modifications at the C terminus. Elongation of the peptide chain also favored aggregation. The geometry of aggregation in solution was investigated by means of titrations with [D6]DMSO and 2D NOE NMR spectroscopy, which allowed the NH protons most involved in intermolecular hydrogen bonds in solution to be identified. X-ray crystallography studies of two oligomers allowed a comparison of the inter- and intramolecular hydrogen-bonding interactions in the solid state and in solution and gave further insight into the geometry of foldamer-foldamer interactions. These solution-based and solid-state studies indicated that the preferred geometry for aggregation is through head-to-tail interactions between the N and C termini of adjacent Aib oligomers.
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Affiliation(s)
- Sarah J Pike
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL (UK), Fax: (+44) 161-275-4939
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9
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Milov AD, Samoilova RI, Tsvetkov YD, Peggion C, Formaggio F, Toniolo C. Peptides on the Surface. PELDOR Data for Spin-Labeled Alamethicin F50/5 Analogues on Organic Sorbent. J Phys Chem B 2014; 118:7085-90. [DOI: 10.1021/jp503691n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Alexander D. Milov
- V.V.
Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
| | - Rimma I. Samoilova
- V.V.
Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
| | - Yuri D. Tsvetkov
- V.V.
Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
| | - Cristina Peggion
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
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10
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Milov AD, Tsvetkov YD, Bortolus M, Maniero AL, Gobbo M, Toniolo C, Formaggio F. Synthesis and conformational properties of a TOAC doubly spin-labeled analog of the medium-length, membrane active peptaibiotic ampullosporin a as revealed by cd, fluorescence, and EPR spectroscopies. Biopolymers 2014; 102:40-8. [DOI: 10.1002/bip.22362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/10/2013] [Accepted: 07/12/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Alexander D. Milov
- Institute of Chemical Kinetics and Combustion; Novosibirsk 630090 Russian Federation
| | - Yuri D. Tsvetkov
- Institute of Chemical Kinetics and Combustion; Novosibirsk 630090 Russian Federation
| | - Marco Bortolus
- Department of Chemical Sciences; University of Padova; 35131 Padova Italy
| | - Anna Lisa Maniero
- Department of Chemical Sciences; University of Padova; 35131 Padova Italy
| | - Marina Gobbo
- Department of Chemical Sciences; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
| | - Claudio Toniolo
- Department of Chemical Sciences; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
| | - Fernando Formaggio
- Department of Chemical Sciences; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
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11
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Kredics L, Szekeres A, Czifra D, Vágvölgyi C, Leitgeb B. Recent results in alamethicin research. Chem Biodivers 2013; 10:744-71. [PMID: 23681724 DOI: 10.1002/cbdv.201200390] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 12/20/2022]
Affiliation(s)
- László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged.
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12
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Möbius K, Lubitz W, Savitsky A. High-field EPR on membrane proteins - crossing the gap to NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 75:1-49. [PMID: 24160760 DOI: 10.1016/j.pnmrs.2013.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 06/02/2023]
Abstract
In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented.
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Affiliation(s)
- Klaus Möbius
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany; Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany.
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13
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Bortolus M, De Zotti M, Formaggio F, Maniero AL. Alamethicin in bicelles: Orientation, aggregation, and bilayer modification as a function of peptide concentration. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2620-7. [DOI: 10.1016/j.bbamem.2013.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/24/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022]
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14
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Milov AD, Tsvetkov YD, De Zotti M, Prinzivalli C, Biondi B, Formaggio F, Toniolo C, Gobbo M. Aggregation modes of the spin mono-labeled tylopeptin B and heptaibin peptaibiotics in frozen solutions of weak polarity as studied by PELDOR spectroscopy. J STRUCT CHEM+ 2013. [DOI: 10.1134/s0022476613070056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Yang P, Wu FG, Chen Z. Dependence of Alamethicin Membrane Orientation on the Solution Concentration. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2013; 117:3358-3365. [PMID: 23565299 PMCID: PMC3613978 DOI: 10.1021/jp3099522] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Alamethicin has been extensively studied as an antimicrobial peptide and is widely used as a simple model for ion channel proteins. It has been shown that the antimicrobial activity of peptides is related to their membrane orientation. In this study, we determined the relationship between the solution concentration of alamethicin and its membrane orientation in lipid bilayers using sum frequency generation (SFG) vibrational spectroscopy. Our SFG results indicated that the alamethicin molecules more or less lay down on the surface of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayers at a low peptide concentration of 0.84 μM; the α-helix segment tilts at about 88°, and 310-helix segment tilts at about 58° versus the surface normal. However, when the peptide concentration was increased to 15.6 μM, we observed that alamethicin molecules further inserted into the lipid bilayers: the α-helical component changes its orientation to make a 37° tilt from the lipid bilayer normal, and the 310-helical component tilts at about 50° versus the surface normal. This is in agreement with the barrel-stave mode for the alamethicin-cell membrane interaction as reported previously. Additionally, we have also studied membrane orientation of alamethicin as a function of peptide concentration with SFG. Our results showed that the membrane orientation of the alamethicin α-helical component changed substantially with the increase of the alamethicin concentration, while the membrane orientation of the 310-helical component remained more or less the same.
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Affiliation(s)
| | | | - Zhan Chen
- To whom correspondence should be addressed. Fax: 734-647-4865.
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16
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Matalon E, Kaminker I, Zimmermann H, Eisenstein M, Shai Y, Goldfarb D. Topology of the trans-membrane peptide WALP23 in model membranes under negative mismatch conditions. J Phys Chem B 2013; 117:2280-93. [PMID: 23311473 DOI: 10.1021/jp310056h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The organization and orientation of membrane-inserted helices is important for better understanding the mode of action of membrane-active peptides and of protein-membrane interactions. Here we report on the application of ESEEM (electron spin-echo envelope modulation) and DEER (double electron-electron resonance) techniques to probe the orientation and oligomeric state of an α-helical trans-membrane model peptide, WALP23, under conditions of negative mismatch between the hydrophobic cores of the model membrane and the peptide. Using ESEEM, we measured weak dipolar interactions between spin-labeled WALP23 and (2)H nuclei of either the solvent (D2O) or of lipids specifically deuterated at the choline group. The ESEEM data obtained from the deuterated lipids were fitted using a model that provided the spin label average distance from a layer of (2)H nuclei in the hydrophilic region of the membrane and the density of the (2)H nuclei in the layer. DEER was used to probe oligomerization through the dipolar interaction between two spin-labels on different peptides. We observed that the center of WALP23 does not coincide with the bilayer midplane and its N-terminus is more buried than the C-terminus. In addition, the ESEEM data fitting yielded a (2)H layer density that was much lower than expected. The DEER experiments revealed the presence of oligomers, the presence of which was attributable to the negative mismatch and the electrostatic dipole of the peptide. A discussion of a possible arrangement of the individual helices in the oligomers that is consistent with the ESEEM and DEER data is presented.
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Affiliation(s)
- Erez Matalon
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel 76100
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17
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Ye S, Li H, Wei F, Jasensky J, Boughton AP, Yang P, Chen Z. Observing a model ion channel gating action in model cell membranes in real time in situ: membrane potential change induced alamethicin orientation change. J Am Chem Soc 2012; 134:6237-43. [PMID: 22420296 PMCID: PMC3328217 DOI: 10.1021/ja2110784] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ion channels play crucial roles in transport and regulatory functions of living cells. Understanding the gating mechanisms of these channels is important to understanding and treating diseases that have been linked to ion channels. One potential model peptide for studying the mechanism of ion channel gating is alamethicin, which adopts a split α/3(10)-helix structure and responds to changes in electric potential. In this study, sum frequency generation vibrational spectroscopy (SFG-VS), supplemented by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), has been applied to characterize interactions between alamethicin (a model for larger channel proteins) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayers in the presence of an electric potential across the membrane. The membrane potential difference was controlled by changing the pH of the solution in contact with the bilayer and was measured using fluorescence spectroscopy. The orientation angle of alamethicin in POPC lipid bilayers was then determined at different pH values using polarized SFG amide I spectra. Assuming that all molecules adopt the same orientation (a δ distribution), at pH = 6.7 the α-helix at the N-terminus and the 3(10)-helix at the C-terminus tilt at about 72° (θ(1)) and 50° (θ(2)) versus the surface normal, respectively. When pH increases to 11.9, θ(1) and θ(2) decrease to 56.5° and 45°, respectively. The δ distribution assumption was verified using a combination of SFG and ATR-FTIR measurements, which showed a quite narrow distribution in the angle of θ(1) for both pH conditions. This indicates that all alamethicin molecules at the surface adopt a nearly identical orientation in POPC lipid bilayers. The localized pH change in proximity to the bilayer modulates the membrane potential and thus induces a decrease in both the tilt and the bend angles of the two helices in alamethicin. This is the first reported application of SFG to the study of model ion channel gating mechanisms in model cell membranes.
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Affiliation(s)
- Shuji Ye
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, P.R.China 230026
| | - Hongchun Li
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, P.R.China 230026
| | - Feng Wei
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, P.R.China 230026
| | - Joshua Jasensky
- Department of Biophysics, University of Michigan, AnnArbor, MI 48109, USA
| | - Andrew P. Boughton
- Department of Chemistry, University of Michigan, AnnArbor, MI 48109, USA
| | - Pei Yang
- Department of Chemistry, University of Michigan, AnnArbor, MI 48109, USA
| | - Zhan Chen
- Department of Biophysics, University of Michigan, AnnArbor, MI 48109, USA
- Department of Chemistry, University of Michigan, AnnArbor, MI 48109, USA
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The spin label amino acid TOAC and its uses in studies of peptides: chemical, physicochemical, spectroscopic, and conformational aspects. Biophys Rev 2012; 4:45-66. [PMID: 22347893 PMCID: PMC3271205 DOI: 10.1007/s12551-011-0064-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 12/20/2011] [Indexed: 01/21/2023] Open
Abstract
We review work on the paramagnetic amino acid 2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid, TOAC, and its applications in studies of peptides and peptide synthesis. TOAC was the first spin label probe incorporated in peptides by means of a peptide bond. In view of the rigid character of this cyclic molecule and its attachment to the peptide backbone via a peptide bond, TOAC incorporation has been very useful to analyze backbone dynamics and peptide secondary structure. Many of these studies were performed making use of EPR spectroscopy, but other physical techniques, such as X-ray crystallography, CD, fluorescence, NMR, and FT-IR, have been employed. The use of double-labeled synthetic peptides has allowed the investigation of their secondary structure. A large number of studies have focused on the interaction of peptides, both synthetic and biologically active, with membranes. In the latter case, work has been reported on ligands and fragments of GPCR, host defense peptides, phospholamban, and β-amyloid. EPR studies of macroscopically aligned samples have provided information on the orientation of peptides in membranes. More recent studies have focused on peptide–protein and peptide–nucleic acid interactions. Moreover, TOAC has been shown to be a valuable probe for paramagnetic relaxation enhancement NMR studies of the interaction of labeled peptides with proteins. The growth of the number of TOAC-related publications suggests that this unnatural amino acid will find increasing applications in the future.
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Gordon-Grossman M, Zimmermann H, Wolf SG, Shai Y, Goldfarb D. Investigation of Model Membrane Disruption Mechanism by Melittin using Pulse Electron Paramagnetic Resonance Spectroscopy and Cryogenic Transmission Electron Microscopy. J Phys Chem B 2011; 116:179-88. [DOI: 10.1021/jp207159z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rajca A, Kathirvelu V, Roy SK, Pink M, Rajca S, Sarkar S, Eaton SS, Eaton GR. A spirocyclohexyl nitroxide amino acid spin label for pulsed EPR spectroscopy distance measurements. Chemistry 2010; 16:5778-82. [PMID: 20391558 DOI: 10.1002/chem.200903102] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Site-directed spin labeling and EPR spectroscopy offer accurate, sensitive tools for the characterization of structure and function of macromolecules and their assemblies. A new rigid spin label, spirocyclohexyl nitroxide alpha-amino acid and its N-(9-fluorenylmethoxycarbonyl) derivative, have been synthesized, which exhibit slow enough spin-echo dephasing to permit accurate distance measurements by pulsed EPR spectroscopy at temperatures up to 125 K in 1:1 water/glycerol and at higher temperatures in matrices with higher glass transition temperatures. Distance measurements in the liquid nitrogen temperature range are less expensive than those that require liquid helium, which will greatly facilitate applications of pulsed EPR spectroscopy to the study of structure and conformation of peptides and proteins.
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Affiliation(s)
- Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA.
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21
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Ye S, Nguyen KT, Chen Z. Interactions of alamethicin with model cell membranes investigated using sum frequency generation vibrational spectroscopy in real time in situ. J Phys Chem B 2010; 114:3334-40. [PMID: 20163089 PMCID: PMC2844632 DOI: 10.1021/jp911174d] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Structures of membrane-associated peptides and molecular interactions between peptides and cell membrane bilayers govern biological functions of these peptides. Sum frequency generation (SFG) vibrational spectroscopy has been demonstrated to be a powerful technique to study such structures and interactions at the molecular level. In this research, SFG has been applied, supplemented by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), to characterize the interactions between alamethicin (a model for larger channel proteins) and different lipid bilayers in the absence of membrane potential. The orientation of alamethicin in lipid bilayers has been determined using SFG amide I spectra detected with different polarization combinations. It was found that alamethicin adopts a mixed alpha-helical and 3(10)-helical structure in fluid-phase lipid bilayers. The helix (mainly alpha-helix) at the N-terminus tilts at about 63 degrees versus the surface normal in a fluid-phase 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine-1,1,2,2-d4-N,N,N-trimethyl-d9 (d-DMPC)/1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer. The 3(10)-helix at the C-terminus (beyond the Pro14 residue) tilts at about 43 degrees versus the surface normal. This is the first time to apply SFG to study a 3(10)-helix experimentally. When interacting with a gel-phase lipid bilayer, alamethicin lies down on the gel-phase bilayer surface or aggregates or both, which does not have significant insertion into the lipid bilayer.
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Affiliation(s)
- Shuji Ye
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, P.R. China 230026
| | - Khoi Tan Nguyen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhan Chen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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Milov AD, Samoilova RI, Tsvetkov YD, De Zotti M, Formaggio F, Toniolo C, Handgraaf JW, Raap J. Structure of self-aggregated alamethicin in ePC membranes detected by pulsed electron-electron double resonance and electron spin echo envelope modulation spectroscopies. Biophys J 2009; 96:3197-209. [PMID: 19383464 DOI: 10.1016/j.bpj.2009.01.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 01/14/2009] [Accepted: 01/15/2009] [Indexed: 11/17/2022] Open
Abstract
PELDOR spectroscopy was exploited to study the self-assembled super-structure of the [Glu(OMe)(7,18,19)]alamethicin molecules in vesicular membranes at peptide to lipid molar ratios in the range of 1:70-1:200. The peptide molecules were site-specifically labeled with TOAC electron spins. From the magnetic dipole-dipole interaction between the nitroxides of the monolabeled constituents and the PELDOR decay patterns measured at 77 K, intermolecular-distance distribution functions were obtained and the number of aggregated molecules (n approximately 4) was estimated. The distance distribution functions exhibit a similar maximum at 2.3 nm. In contrast to Alm16, for Alm1 and Alm8 additional maxima were recorded at 3.2 and approximately 5.2 nm. From ESEEM experiments and based on the membrane polarity profiles, the penetration depths of the different spin-labeled positions into the membrane were qualitatively estimated. It was found that the water accessibility of the spin-labels follows the order TOAC-1 > TOAC-8 approximately TOAC-16. The geometric data obtained are discussed in terms of a penknife molecular model. At least two peptide chains are aligned parallel and eight ester groups of the polar Glu(OMe)(18,19) residues are suggested to stabilize the self-aggregate superstructure.
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Affiliation(s)
- Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation
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