1
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Biondi B, Syryamina VN, Rocchio G, Barbon A, Formaggio F, Toniolo C, Raap J, Dzuba SA. Is Cys(MTSL) the Best α-Amino Acid Residue to Electron Spin Labeling of Synthetically Accessible Peptide Molecules with Nitroxides? ACS OMEGA 2022; 7:5154-5165. [PMID: 35187331 PMCID: PMC8851612 DOI: 10.1021/acsomega.1c06227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Electron paramagnetic resonance spectroscopy, particularly its pulse technique double electron-electron resonance (DEER) (also termed PELDOR), is rapidly becoming an extremely useful tool for the experimental determination of side chain-to-side chain distances between free radicals in molecules fundamental for life, such as polypeptides. Among appropriate probes, the most popular are undoubtedly nitroxide electron spin labels. In this context, suitable biosynthetically derived, helical regions of proteins, along with synthetic peptides with amphiphilic properties and antibacterial activities, are the most extensively investigated compounds. A strict requirement for a precise distance measurement has been identified in a minimal dynamic flexibility of the two nitroxide-bearing α-amino acid side chains. To this end, in this study, we have experimentally compared in detail the side-chain mobility properties of the two currently most widely utilized residues, namely, Cys(MTSL) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, two double-labeled, chemically synthesized 20-mer peptide molecules have been adopted as appropriate templates for our investigation on the determination of the model intramolecular separations. These double-Cys(MTSL) and double-TOAC compounds are both analogues of the almost completely rigid backbone peptide ruler which we have envisaged and 3D structurally analyzed as our original, unlabeled compound. Here, we have clearly found that the TOAC side-chain labels are largely more 3D structurally restricted than the MTSL labels. From this result, we conclude that the TOAC residue offers more precise information than the Cys(MTSL) residue on the side chain-to-side chain distance distribution in synthetically accessible peptide molecules.
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Affiliation(s)
- Barbara Biondi
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Victoria N. Syryamina
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
| | - Gabriele Rocchio
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Antonio Barbon
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Jan Raap
- Leiden
Institute of Chemistry, Gorlaeus Laboratories,
Leiden University, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
- Department
of Physics, Novosibirsk State University, 630090 Novosibirsk, Russian Federation
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2
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Golysheva EA, Boyle AL, Biondi B, Ruzza P, Kros A, Raap J, Toniolo C, Formaggio F, Dzuba SA. Probing the E/K Peptide Coiled-Coil Assembly by Double Electron-Electron Resonance and Circular Dichroism. Biochemistry 2020; 60:19-30. [PMID: 33320519 DOI: 10.1021/acs.biochem.0c00773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Double electron-electron resonance (DEER, also known as PELDOR) and circular dichroism (CD) spectroscopies were explored for the purpose of studying the specificity of the conformation of peptides induced by their assembly into a self-recognizing system. The E and K peptides are known to form a coiled-coil heterodimer. Two paramagnetic TOAC α-amino acid residues were incorporated into each of the peptides (denoted as K** and E**), and a three-dimensional structural investigation in the presence or absence of their unlabeled counterparts E and K was performed. The TOAC spin-labels, replacing two Ala residues in each compound, are covalently and quasi-rigidly connected to the peptide backbone. They are known not to disturb the native structure, so that any conformational change can easily be monitored and assigned. DEER spectroscopy enables the measurement of the intramolecular electron spin-spin distance distribution between the two TOAC labels, within a length range of 1.5-8 nm. This method allows the individual conformational changes for the K**, K**/E, E**, and E**/K molecules to be investigated in glassy frozen solutions. Our data reveal that the conformations of the E** and K** peptides are strongly influenced by the presence of their counterparts. The results are discussed with those from CD spectroscopy and with reference to the already reported nuclear magnetic resonance data. We conclude that the combined DEER/TOAC approach allows us to obtain accurate and reliable information about the conformation of the peptides before and after their assembly into coiled-coil heterodimers. Applications of this induced fit method to other two-component, but more complex, systems, like a receptor and antagonists, a receptor and a hormone, and an enzyme and a ligand, are discussed.
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Affiliation(s)
- Elena A Golysheva
- Novosibirsk State University, Novosibirsk 630090, Russian Federation.,V. V. Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk 630090, Russian Federation
| | - Aimee L Boyle
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Paolo Ruzza
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Alexander Kros
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy.,Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Sergei A Dzuba
- Novosibirsk State University, Novosibirsk 630090, Russian Federation.,V. V. Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk 630090, Russian Federation
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3
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Sahu ID, Lorigan GA. Electron Paramagnetic Resonance as a Tool for Studying Membrane Proteins. Biomolecules 2020; 10:E763. [PMID: 32414134 PMCID: PMC7278021 DOI: 10.3390/biom10050763] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins possess a variety of functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is extremely difficult to probe the structure and dynamic properties of membrane proteins using traditional biophysical techniques, particularly in their native environments. Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a very powerful and rapidly growing biophysical technique to study pertinent structural and dynamic properties of membrane proteins with no size restrictions. In this review, we will briefly discuss the most commonly used EPR techniques and their recent applications for answering structure and conformational dynamics related questions of important membrane protein systems.
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Affiliation(s)
- Indra D. Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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4
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Zurlo E, Gorroño Bikandi I, Meeuwenoord NJ, Filippov DV, Huber M. Tracking amyloid oligomerization with monomer resolution using a 13-amino acid peptide with a backbone-fixed spin label. Phys Chem Chem Phys 2019; 21:25187-25195. [PMID: 31696167 DOI: 10.1039/c9cp01060b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amyloid oligomers are suspected as toxic agents in neurodegenerative disease, and are transient and often heterogeneous, making them difficult to detect. Here we show an approach to track the development of amyloid oligomers in situ by room temperature, continuous wave (cw) 9 and 95 GHz EPR. Three amyloid peptides with the 2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid (TOAC) spin label were synthesized by solid phase peptide synthesis: T0EZ (TKVKVLGDVIEVGG) with TOAC (T) at the N-terminus, T5EZ with TOAC in the middle (KVKVTGDVIEVG) and T12EZ with TOAC at the C-terminus (KVKVLGDVIEVTG). These sequences are derived from the K11V (KVKVLGDVIEV) amyloid peptide, which self-aggregates to oligomers with a β-sheet configuration (A. Laganowsky, et al., Science, 2012, 335, 1228-1231). To monitor oligomerization, the rotational correlation time (τr) is measured by cw-EPR. For the backbone-fixed TOAC label that is devoid of local mobility τr should reflect the rotation and thereby the size of the peptide, resp. oligomer. For T5EZ a good match between the measured τr and the size of the peptide is obtained, showing the validity of the approach. One of the three peptides (T0EZ) aggregates (circular dichroism), whereas the other two do not. Since also the respective MTSL (S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl methanesulfonothioate) labelled peptides fail to aggregate, molecular crowding due to the label, rather than the helix-inducing properties of TOAC, seems to be responsible. Following in situ oligomer formation of T0EZ by the change in rotational correlation time, two oligomers are observed, a 5-6 mer and a 15-18 mer. The EPR approach, particularly 95 GHz EPR, enables following oligomerization of one monomer at a time, suggesting that the cw-EPR approach presented is a novel tool to follow amyloid oligomerization with high resolution.
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Affiliation(s)
- E Zurlo
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
| | - I Gorroño Bikandi
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
| | - N J Meeuwenoord
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, 2300 RA Leiden, The Netherlands
| | - D V Filippov
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, 2300 RA Leiden, The Netherlands
| | - M Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
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5
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Sahu ID, Lorigan GA. Site-Directed Spin Labeling EPR for Studying Membrane Proteins. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3248289. [PMID: 29607317 PMCID: PMC5828257 DOI: 10.1155/2018/3248289] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/21/2017] [Indexed: 01/13/2023]
Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy is a rapidly expanding powerful biophysical technique to study the structural and dynamic properties of membrane proteins in a native environment. Membrane proteins are responsible for performing important functions in a wide variety of complicated biological systems that are responsible for the survival of living organisms. In this review, a brief introduction of the most popular SDSL EPR techniques and illustrations of recent applications for studying pertinent structural and dynamic properties on membrane proteins will be discussed.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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6
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Bortolus M, Dalzini A, Maniero AL, Panighel G, Siano A, Toniolo C, De Zotti M, Formaggio F. Insights into peptide-membrane interactions of newly synthesized, nitroxide-containing analogs of the peptaibiotic trichogin GAIV using EPR. Biopolymers 2017; 108. [DOI: 10.1002/bip.22913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/21/2016] [Accepted: 06/29/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Marco Bortolus
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | - Annalisa Dalzini
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | | | - Giacomo Panighel
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | - Alvaro Siano
- Department of Chemistry; University of Padova; Padova 35131 Italy
- Departamento de Química Orgánica; Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL); 3000 Santa Fe Argentina
| | - Claudio Toniolo
- Department of Chemistry; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
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7
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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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8
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Abstract
Membrane proteins are very important in controlling bioenergetics, functional activity, and initializing signal pathways in a wide variety of complicated biological systems. They also represent approximately 50% of the potential drug targets. EPR spectroscopy is a very popular and powerful biophysical tool that is used to study the structural and dynamic properties of membrane proteins. In this article, a basic overview of the most commonly used EPR techniques and examples of recent applications to answer pertinent structural and dynamic related questions on membrane protein systems will be presented.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States of America
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States of America
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9
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Lemmin T, Dimitrov M, Fraering PC, Dal Peraro M. Perturbations of the straight transmembrane α-helical structure of the amyloid precursor protein affect its processing by γ-secretase. J Biol Chem 2014; 289:6763-6774. [PMID: 24469457 PMCID: PMC3945338 DOI: 10.1074/jbc.m113.470781] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 01/14/2014] [Indexed: 01/30/2023] Open
Abstract
The amyloid precursor protein (APP) is a widely expressed type I transmembrane (TM) glycoprotein present at the neuronal synapse. The proteolytic cleavage by γ-secretase of its C-terminal fragment produces amyloid-β (Aβ) peptides of different lengths, the deposition of which is an early indicator of Alzheimer disease. At present, there is no consensus on the conformation of the APP-TM domain at the biological membrane. Although structures have been determined by NMR in detergent micelles, their conformation is markedly different. Here we show by using molecular simulations that the APP-TM region systematically prefers a straight α-helical conformation once embedded in a membrane bilayer. However, APP-TM is highly flexible, and its secondary structure is strongly influenced by the surrounding lipid environment, as when enclosed in detergent micelles. This behavior is confirmed when analyzing in silico the atomistic APP-TM population observed by residual dipolar couplings and double electron-electron resonance spectroscopy. These structural and dynamic features are critical in the proteolytic processing of APP by the γ-secretase enzyme, as suggested by a series of Gly(700) mutants. Affecting the hydration and flexibility of APP-TM, these mutants invariantly show an increase in the production of Aβ38 compared with Aβ40 peptides, which is reminiscent of the effect of γ-secretase modulators inhibitors.
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Affiliation(s)
- Thomas Lemmin
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Mitko Dimitrov
- Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Patrick C Fraering
- Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
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10
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Ji M, Ruthstein S, Saxena S. Paramagnetic metal ions in pulsed ESR distance distribution measurements. Acc Chem Res 2014; 47:688-95. [PMID: 24289139 DOI: 10.1021/ar400245z] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The use of pulsed electron spin resonance (ESR) to measure interspin distance distributions has advanced biophysical research. The three major techniques that use pulsed ESR are relaxation rate based distance measurements, double quantum coherence (DQC), and double electron electron resonance (DEER). Among these methods, the DEER technique has become particularly popular largely because it is easy to implement on commercial instruments and because programs are available to analyze experimental data. Researchers have widely used DEER to measure the structure and conformational dynamics of molecules labeled with the methanethiosulfonate spin label (MTSSL). Recently, researchers have exploited endogenously bound paramagnetic metal ions as spin probes as a way to determine structural constraints in metalloproteins. In this context Cu(2+) has served as a useful paramagnetic metal probe at X-band for DEER based distance measurements. Sample preparation is simple, and a coordinated-Cu(2+) ion offers limited spatial flexibility, making it an attractive probe for DEER experiments. On the other hand, Cu(2+) has a broad absorption ESR spectrum at low temperature, which leads to two potential complications. First, the Cu(2+)-based DEER time domain data has lower signal to noise ratio compared with MTSSL. Second, accurate distance distribution analysis often requires high-quality experimental data at different external magnetic fields or with different frequency offsets. In this Account, we summarize characteristics of Cu(2+)-based DEER distance distribution measurements and data analysis methods. We highlight a novel application of such measurements in a protein-DNA complex to identify the metal ion binding site and to elucidate its chemical mechanism of function. We also survey the progress of research on other metal ions in high frequency DEER experiments.
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Affiliation(s)
- Ming Ji
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sharon Ruthstein
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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11
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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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12
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Sahu ID, McCarrick RM, Lorigan GA. Use of electron paramagnetic resonance to solve biochemical problems. Biochemistry 2013; 52:5967-84. [PMID: 23961941 PMCID: PMC3839053 DOI: 10.1021/bi400834a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a very powerful biophysical tool that can provide valuable structural and dynamic information about a wide variety of biological systems. The intent of this review is to provide a general overview for biochemists and biological researchers of the most commonly used EPR methods and how these techniques can be used to answer important biological questions. The topics discussed could easily fill one or more textbooks; thus, we present a brief background on several important biological EPR techniques and an overview of several interesting studies that have successfully used EPR to solve pertinent biological problems. The review consists of the following sections: an introduction to EPR techniques, spin-labeling methods, and studies of naturally occurring organic radicals and EPR active transition metal systems that are presented as a series of case studies in which EPR spectroscopy has been used to greatly further our understanding of several important biological systems.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
| | | | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
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13
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Stone KM, Voska J, Kinnebrew M, Pavlova A, Junk MJN, Han S. Structural insight into proteorhodopsin oligomers. Biophys J 2013; 104:472-81. [PMID: 23442869 DOI: 10.1016/j.bpj.2012.11.3831] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 11/05/2012] [Accepted: 11/19/2012] [Indexed: 10/27/2022] Open
Abstract
Oligomerization has important functional implications for many membrane proteins. However, obtaining structural insight into oligomeric assemblies is challenging, as they are large and resist crystallization. We focus on proteorhodopsin (PR), a protein with seven transmembrane α-helices that was found to assemble to hexamers in densely packed lipid membrane, or detergent-solubilized environments. Yet, the structural organization and the subunit interface of these PR oligomers were unknown. We used site-directed spin-labeling together with electron spin-resonance lineshape and Overhauser dynamic nuclear polarization analysis to construct a model for the specific orientation of PR subunits within the hexameric complex. We found intersubunit distances to average 16 Å between neighboring 55 residues and that residues 177 are >20 Å apart from each other. These distance constraints show that PR has a defined and radial orientation within a hexamer, with the 55-site of the A-B loop facing the hexamer core and the 177-site of the E-F loop facing the hexamer exterior. Dynamic nuclear polarization measurements of the local solvent dynamics complement the electron spin-resonance-based distance analysis, by resolving whether protein surfaces at positions 55, 58, and 177 are exposed to solvent, or covered by protein-protein or protein-detergent contacts.
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Affiliation(s)
- Katherine M Stone
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California, USA
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14
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Jeschke G. Conformational dynamics and distribution of nitroxide spin labels. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 72:42-60. [PMID: 23731861 DOI: 10.1016/j.pnmrs.2013.03.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 06/02/2023]
Abstract
Long-range distance measurements based on paramagnetic relaxation enhancement (PRE) in NMR, quantification of surface water dynamics near biomacromolecules by Overhauser dynamic nuclear polarization (DNP) and sensitivity enhancement by solid-state DNP all depend on introducing paramagnetic species into an otherwise diamagnetic NMR sample. The species can be introduced by site-directed spin labeling, which offers precise control for positioning the label in the sequence of a biopolymer. However, internal flexibility of the spin label gives rise to dynamic processes that potentially influence PRE and DNP behavior and leads to a spatial distribution of the electron spin even in solid samples. Internal dynamics of spin labels and their static conformational distributions have been studied mainly by electron paramagnetic resonance spectroscopy and molecular dynamics simulations, with a large body of results for the most widely applied methanethiosulfonate spin label MTSL. These results are critically discussed in a unifying picture based on rotameric states of the group that carries the spin label. Deficiencies in our current understanding of dynamics and conformations of spin labeled groups and of their influence on NMR observables are highlighted and directions for further research suggested.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zürich, Laboratory Physical Chemistry, Zürich, Switzerland.
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15
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Dzuba SA, Raap J. Spin-Echo Electron Paramagnetic Resonance (EPR) Spectroscopy of a Pore-Forming (Lipo)Peptaibol in Model and Bacterial Membranes. Chem Biodivers 2013; 10:864-75. [DOI: 10.1002/cbdv.201200387] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 11/08/2022]
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16
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Gatto E, Venanzi M. Self-assembled monolayers formed by helical peptide building blocks: a new tool for bioinspired nanotechnology. Polym J 2013. [DOI: 10.1038/pj.2013.27] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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The spin label amino acid TOAC and its uses in studies of peptides: chemical, physicochemical, spectroscopic, and conformational aspects. Biophys Rev 2012; 4:45-66. [PMID: 22347893 PMCID: PMC3271205 DOI: 10.1007/s12551-011-0064-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 12/20/2011] [Indexed: 01/21/2023] Open
Abstract
We review work on the paramagnetic amino acid 2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid, TOAC, and its applications in studies of peptides and peptide synthesis. TOAC was the first spin label probe incorporated in peptides by means of a peptide bond. In view of the rigid character of this cyclic molecule and its attachment to the peptide backbone via a peptide bond, TOAC incorporation has been very useful to analyze backbone dynamics and peptide secondary structure. Many of these studies were performed making use of EPR spectroscopy, but other physical techniques, such as X-ray crystallography, CD, fluorescence, NMR, and FT-IR, have been employed. The use of double-labeled synthetic peptides has allowed the investigation of their secondary structure. A large number of studies have focused on the interaction of peptides, both synthetic and biologically active, with membranes. In the latter case, work has been reported on ligands and fragments of GPCR, host defense peptides, phospholamban, and β-amyloid. EPR studies of macroscopically aligned samples have provided information on the orientation of peptides in membranes. More recent studies have focused on peptide–protein and peptide–nucleic acid interactions. Moreover, TOAC has been shown to be a valuable probe for paramagnetic relaxation enhancement NMR studies of the interaction of labeled peptides with proteins. The growth of the number of TOAC-related publications suggests that this unnatural amino acid will find increasing applications in the future.
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De Zotti M, Biondi B, Peggion C, Formaggio F, Park Y, Hahm KS, Toniolo C. Trichogin GA IV: a versatile template for the synthesis of novel peptaibiotics. Org Biomol Chem 2011; 10:1285-99. [PMID: 22179201 DOI: 10.1039/c1ob06178j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trichogin GA IV, isolated from the fungus Trichoderma longibrachiatum, is the prototype of lipopeptaibols, the sub-class of short-length peptaibiotics exhibiting membrane-modifying properties. This peptaibol is predominantly folded in a mixed 3(10)-/α- helical conformation with a clear, albeit modest, amphiphilic character, which is likely to be responsible for its capability to perturb bacterial membranes and to induce cell death. In previous papers, we reported on the interesting biological properties of trichogin GA IV, namely its good activity against Gram positive bacteria, in particular methicillin-resistant S. aureus strains, its stability towards proteolytic degradation, and its low hemolytic activity. Aiming at broadening the antimicrobial activity spectrum by increasing the peptide helical amphiphilicity, in this work we synthesized, by solution and solid-phase methodologies, purified and fully characterized a set of trichogin GA IV analogs in which the four Gly residues at positions 2, 5, 6, 9, lying in the poorly hydrophilic face of the helical structure, are substituted by one (position 2, 5, 6 or 9), two (positions 5 and 6), three (positions 2, 5, and 9), and four (positions 2, 5, 6, and 9) Lys residues. The conformational preferences of the Lys-containing analogs were assessed by FT-IR absorption, CD and 2D-NMR techniques in aqueous, organic, and membrane-mimetic environments. Interestingly, it turns out that the presence of charged residues induces a transition of the helical conformation adopted by the peptaibols (from 3(10)- to α-helix) as a function of pH in a reversible process. The role played in the analogs by the markedly increased amphiphilicity was further tested by fluorescence leakage experiments in model membranes, protease resistance, antibacterial and antifungal activities, cytotoxicity, and hemolysis. Taken together, our biological results provide evidence that some of the least substituted among these analogs are good candidates for the development of new membrane-active antimicrobial agents.
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Affiliation(s)
- Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131, Padova, Italy
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Sepkhanova I, Drescher M, Meeuwenoord NJ, Limpens RWAL, Koning RI, Filippov DV, Huber M. Monitoring Alzheimer Amyloid Peptide Aggregation by EPR. APPLIED MAGNETIC RESONANCE 2009; 36:209-222. [PMID: 19946595 PMCID: PMC2779421 DOI: 10.1007/s00723-009-0019-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Revised: 12/28/2008] [Indexed: 05/28/2023]
Abstract
Plaques containing the aggregated beta-Amyloid (Abeta) peptide in the brain are the main indicators of Alzheimer's disease. Fibrils, the building blocks of plaques, can also be produced in vitro and consist of a regular arrangement of the peptide. The initial steps of fibril formation are not well understood and could involve smaller aggregates (oligomers) of Abeta. Such oligomers have even been implicated as the toxic agents. Here, a method to study oligomers on the time scale of aggregation is suggested. We have labeled the 40 residue Abeta peptide variant containing an N-terminal cysteine (cys-Abeta) with the MTSL [1-oxyl-2,2,5,5-tetramethyl-Delta-pyrroline-3-methyl] methanethiosulfonate spin label (SL-Abeta). Fibril formation in solutions of pure SL-Abeta and of SL-Abeta mixed with Abeta was shown by Congo-red binding and electron microscopy. Continuous-wave 9 GHz electron paramagnetic resonance reveals three fractions of different spin-label mobility: one attributed to monomeric Abeta, one to a multimer (8-15 monomers), and the last one to larger aggregates or fibrils. The approach, in principle, allows detection of oligomers on the time scale of aggregation.
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Affiliation(s)
- I. Sepkhanova
- Huygens Laboratory, Department of Molecular Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
| | - M. Drescher
- Huygens Laboratory, Department of Molecular Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
| | - N. J. Meeuwenoord
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - R. W. A. L. Limpens
- Section Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - R. I. Koning
- Section Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - D. V. Filippov
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - M. Huber
- Huygens Laboratory, Department of Molecular Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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Ghimire H, McCarrick RM, Budil DE, Lorigan GA. Significantly improved sensitivity of Q-band PELDOR/DEER experiments relative to X-band is observed in measuring the intercoil distance of a leucine zipper motif peptide (GCN4-LZ). Biochemistry 2009; 48:5782-4. [PMID: 19476379 DOI: 10.1021/bi900781u] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pulsed electron double resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy is a very powerful structural biology tool in which the dipolar coupling between two unpaired electron spins (site-directed nitroxide spin-labels) is measured. These measurements are typically conducted at X-band (9.4 GHz) microwave excitation using the four-pulse DEER sequence and can often require up to 12 h of signal averaging for biological samples (depending on the spin-label concentration). In this work, we present for the first time a substantial increase in DEER sensitivity obtained by collecting DEER spectra at Q-band (34 GHz), when compared to X-band. The huge boost in sensitivity (factor of 13) demonstrated at Q-band represents a 169-fold decrease in data collection time, reveals a greatly improved frequency spectrum and higher-quality distance data, and significantly increases sample throughput. Thus, the availability of Q-band DEER spectroscopy should have a major impact on structural biology studies using site-directed spin labeling EPR techniques.
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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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22
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Sicoli G, Mathis G, Aci-Sèche S, Saint-Pierre C, Boulard Y, Gasparutto D, Gambarelli S. Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling. Nucleic Acids Res 2009; 37:3165-76. [PMID: 19304747 PMCID: PMC2691821 DOI: 10.1093/nar/gkp165] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 02/05/2009] [Accepted: 03/01/2009] [Indexed: 12/23/2022] Open
Abstract
Double electron-electron resonance (DEER) was applied to determine nanometre spin-spin distances on DNA duplexes that contain selected structural alterations. The present approach to evaluate the structural features of DNA damages is thus related to the interspin distance changes, as well as to the flexibility of the overall structure deduced from the distance distribution. A set of site-directed nitroxide-labelled double-stranded DNA fragments containing defined lesions, namely an 8-oxoguanine, an abasic site or abasic site analogues, a nick, a gap and a bulge structure were prepared and then analysed by the DEER spectroscopic technique. New insights into the application of 4-pulse DEER sequence are also provided, in particular with respect to the spin probes' positions and the rigidity of selected systems. The lesion-induced conformational changes observed, which were supported by molecular dynamics studies, confirm the results obtained by other, more conventional, spectroscopic techniques. Thus, the experimental approaches described herein provide an efficient method for probing lesion-induced structural changes of nucleic acids.
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Affiliation(s)
- Giuseppe Sicoli
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Gérald Mathis
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Samia Aci-Sèche
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Christine Saint-Pierre
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Yves Boulard
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Didier Gasparutto
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Serge Gambarelli
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
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Ruthstein S, Raitsimring AM, Bitton R, Frydman V, Godt A, Goldfarb D. Distribution of guest molecules in Pluronic micelles studied by double electron electron spin resonance and small angle X-ray scattering. Phys Chem Chem Phys 2009; 11:148-60. [DOI: 10.1039/b812475b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Milov AD, Samoilova RI, Tsvetkov YD, De Zotti M, Toniolo C, Raap J. PELDOR Conformational Analysis of bis-Labeled Alamethicin Aggregated in Phospholipid Vesicles. J Phys Chem B 2008; 112:13469-72. [DOI: 10.1021/jp8046714] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander D. Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Rimma I. Samoilova
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Yuri D. Tsvetkov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Marta De Zotti
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Claudio Toniolo
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jan Raap
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
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25
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Gatto E, Stella L, Formaggio F, Toniolo C, Lorenzelli L, Venanzi M. Electroconductive and photocurrent generation properties of self-assembled monolayers formed by functionalized, conformationally-constrained peptides on gold electrodes. J Pept Sci 2008; 14:184-91. [PMID: 18035859 DOI: 10.1002/psc.973] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The electroconductive properties and photocurrent generation capabilities of self-assembled monolayers formed by conformationally-constrained hexapeptides were studied by cyclic voltammetry, chronoamperometry, and photocurrent generation experiments. Lipoic acid was covalently linked to the N-terminus of the peptides investigated to exploit the high affinity of the disulfide group to the gold substrates. Smart functionalization of the peptide scaffold with a redox-active (TOAC) or a photosensitizer (Trp) amino acid allowed us to study the efficiency of peptide-based self-assembled monolayers to mediate electron transfer and photoinduced electron transfer processes on gold substrates. Interdigitated microelectrodes have shown higher film stability under photoexcitation, lower dark currents, and higher sensitivity with respect to standard gold electrodes.
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Affiliation(s)
- Emanuela Gatto
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy
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26
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Yang Z, Becker J, Saxena S. On Cu(II)-Cu(II) distance measurements using pulsed electron electron double resonance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 188:337-43. [PMID: 17825593 DOI: 10.1016/j.jmr.2007.08.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Revised: 08/10/2007] [Accepted: 08/10/2007] [Indexed: 05/17/2023]
Abstract
The effects of orientational selectivity on the 4-pulse electron electron double resonance (PELDOR) ESR spectra of coupled Cu(II)-Cu(II) spins are presented. The data were collected at four magnetic fields on a poly-proline peptide containing two Cu(II) centers. The Cu(II)-PELDOR spectra of this peptide do not change appreciably with magnetic field at X-band. The data were analyzed by adapting the theory of Maryasov, Tsvetkov, and Raap [A.G. Maryasov, Y.D. Tsvetkov, J. Raap, Weakly coupled radical pairs in solids:ELDOR in ESE structure studies, Appl. Magn. Reson. 14 (1998) 101-113]. Simulations indicate that orientational effects are important for Cu(II)-PELDOR. Based on simulations, the field-independence of the PELDOR data for this peptide is likely due to two effects. First, for this peptide, the Cu(II) g-tensor(s) are in a very specific orientation with respect to the interspin vector. Second, the flexibility of the peptide washes out the orientation effects. These effects reduce the suitability of the poly-proline based peptide as a good model system to experimentally probe orientational effects in such experiments. An average Cu(II)-Cu(II) distance of 2.1-2.2 nm was determined, which is consistent with earlier double quantum coherence ESR results.
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Affiliation(s)
- Zhongyu Yang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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27
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Lubitz W, Reijerse E, van Gastel M. [NiFe] and [FeFe] Hydrogenases Studied by Advanced Magnetic Resonance Techniques. Chem Rev 2007; 107:4331-65. [PMID: 17845059 DOI: 10.1021/cr050186q] [Citation(s) in RCA: 423] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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28
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Milov AD, Samoilova RI, Tsvetkov YD, Formaggio F, Toniolo C, Raap J. Self-Aggregation of Spin-Labeled Alamethicin in ePC Vesicles Studied by Pulsed Electron−Electron Double Resonance. J Am Chem Soc 2007; 129:9260-1. [PMID: 17616195 DOI: 10.1021/ja072851d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation
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29
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Milov AD, Tsvetkov YD, Gorbunova EY, Mustaeva LG, Ovchinnikova TV, Handgraaf JW, Raap J. Solvent effects on the secondary structure of the membrane-active zervamicin determined by PELDOR spectroscopy. Chem Biodivers 2007; 4:1243-55. [PMID: 17589863 DOI: 10.1002/cbdv.200790107] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Zervamicin is a voltage-gated ion-channel-forming peptide. Channels are generally considered to be formed by first insertion of amphipathic molecules into the phospholipid bilayer, followed by self-assembly of a variable number of transmembrane helices. We have studied the length of the peptide structure to address the question whether this peptide is long enough to span the phospholipid bilayer. The pulsed electron-electron double resonance (PELDOR) spectroscopic technique was used to determine the length of the helical molecule in membrane-mimicking solvents. This was achieved from the distance-related dipole-dipole interaction between spin labels, which were located at both ends of the linear peptide chain. The data were obtained by using samples of frozen glassy solutions of MeOH, MeOH/toluene, and MeOH/CHCl(3). Contributions of inter- and intramolecular interactions of spin labels were separated to analyze the intramolecular interaction and the distance distribution function between the labels. It is shown that the main maximum of the distribution functions is located at a distance of ca. 3.3 nm, and this distance appears to be only slightly dependent on the solvent composition. The distribution function was observed to narrow after addition of either CHCl(3) or toluene to MeOH. This effect is rationalized in terms of a decreased mobility of the terminal amino acid residues. By molecular-dynamics simulations, it was shown that the conformation, corresponding with the predominant distance found by PELDOR, agrees well with the mixed alpha/3(10)-helical that was previously determined by NMR. However, in the case toluene was added to the MeOH solution to further increase the hydrophobicity of the environment of the membrane-active peptide, the distribution function gives rise to a minor fraction (7-8%) with a distance of 4.2 nm. This distance corresponds most likely to the more extended 2(7)-helix structure.
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Affiliation(s)
- Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, Russian Federation
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30
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Schiemann O, Piton N, Plackmeyer J, Bode BE, Prisner TF, Engels JW. Spin labeling of oligonucleotides with the nitroxide TPA and use of PELDOR, a pulse EPR method, to measure intramolecular distances. Nat Protoc 2007; 2:904-23. [PMID: 17446891 DOI: 10.1038/nprot.2007.97] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this protocol, we describe the facile synthesis of the nitroxide spin-label 2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene (TPA) and then its coupling to DNA/RNA through Sonogashira cross-coupling during automated solid-phase synthesis. Subsequently, we explain how to perform distance measurements between two such spin-labels on RNA/DNA using the pulsed electron paramagnetic resonance method pulsed electron double resonance (PELDOR). This combination of methods can be used to study global structure elements of oligonucleotides in frozen solution at RNA/DNA amounts of approximately 10 nmol. We especially focus on the Sonogashira cross-coupling step, the advantages of the ACE chemistry together with the appropriate parameters for the RNA synthesizer and on the PELDOR data analysis. This procedure is applicable to RNA/DNA strands of up to approximately 80 bases in length and PELDOR yields reliably spin-spin distances up to approximately 6.5 nm. The synthesis of TPA takes approximately 5 days and spin labeling together with purification approximately 4 days. The PELDOR measurements usually take approximately 16 h and data analysis from an hour up to several days depending on the extent of analysis.
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Affiliation(s)
- Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany.
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31
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Schiemann O, Prisner TF. Long-range distance determinations in biomacromolecules by EPR spectroscopy. Q Rev Biophys 2007; 40:1-53. [PMID: 17565764 DOI: 10.1017/s003358350700460x] [Citation(s) in RCA: 423] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy provides a variety of tools to study structures and structural changes of large biomolecules or complexes thereof. In order to unravel secondary structure elements, domain arrangements or complex formation, continuous wave and pulsed EPR methods capable of measuring the magnetic dipole coupling between two unpaired electrons can be used to obtain long-range distance constraints on the nanometer scale. Such methods yield reliably and precisely distances of up to 80 A, can be applied to biomolecules in aqueous buffer solutions or membranes, and are not size limited. They can be applied either at cryogenic or physiological temperatures and down to amounts of a few nanomoles. Spin centers may be metal ions, metal clusters, cofactor radicals, amino acid radicals, or spin labels. In this review, we discuss the advantages and limitations of the different EPR spectroscopic methods, briefly describe their theoretical background, and summarize important biological applications. The main focus of this article will be on pulsed EPR methods like pulsed electron-electron double resonance (PELDOR) and their applications to spin-labeled biosystems.
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Affiliation(s)
- Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, J. W. Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany.
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32
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Milov AD, Samoilova MI, Tsvetkov YD, Jost M, Peggion C, Formaggio F, Crisma M, Toniolo C, Handgraaf JW, Raap J. Supramolecular Structure of Self-Assembling Alamethicin Analog Studied by ESR and PELDOR. Chem Biodivers 2007; 4:1275-98. [PMID: 17589866 DOI: 10.1002/cbdv.200790110] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Three analogs of alamethicin F50/5, labelled with the TOAC (='2,2,6,6-tetramethylpiperidin-1-oxyl-4-amino-4-carboxylic acid') spin label at positions 1 (Alm1), 8 (Alm8), and 16 (Alm16), resp., were studied by Electron-Spin-Resonance (ESR) and Pulsed Electron-Electron Double-Resonance (PELDOR) techniques in solvents of different polarity to investigate the self-assembly of amphipathic helical peptides in membrane-mimicking environments. In polar solvents, alamethicin forms homogeneous solutions. In the weakly polar chloroform/toluene 1 : 1 mixture, however, this peptide forms aggregates that are detectable at 293 K by ESR in liquid solution, as well as by PELDOR in frozen, glassy solution at 77 K. In liquid solution, free alamethicin molecules and their aggregates show rotational-mobility correlation times tau(r) of 0.87 and 5.9 ns, resp. Based on these values and analysis of dipole-dipole interactions of the TOAC labels in the aggregates, as determined by PELDOR, the average number N of alamethicin molecules in the aggregates is estimated to be less than nine. A distance-distribution function between spin labels in the supramolecular aggregate was obtained. This function exhibits two maxima: a broad one at a distance of 3.0 nm, and a wide one at a distance of ca. 7 nm. A molecular-dynamics (MD)-based model of the aggregate, consisting of two parallel tetramers, each composed of four molecules arranged in a 'head-to-tail' fashion, is proposed, accounting for the observed distances and their distribution.
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Affiliation(s)
- Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation
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33
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Hara H, Tenno T, Shirakawa M. Distance determination in human ubiquitin by pulsed double electron-electron resonance and double quantum coherence ESR methods. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 184:78-84. [PMID: 17046296 DOI: 10.1016/j.jmr.2006.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 09/01/2006] [Accepted: 09/08/2006] [Indexed: 05/12/2023]
Abstract
Recently, distance measurements by pulsed ESR (electron spin resonance) have been obtained using pulsed DEER (double electron-electron resonance) and DQC (double quantum coherence) in SDSL (site directed spin labeling) proteins. These methods can observe long range dipole interactions (15-80A). We applied these methods to human ubiquitin proteins. The distance between the 20th and the 35th cysteine was estimated in doubly spin labeled human ubiquitin. Pulsed DEER requires two microwave sources. However, a phase cycle is not usually required in this method. On the other hand, DQC-ESR at X-band ( approximately 9GHz) can acquire a large echo signal by using pulses of short duration and high power, but this method has an ESEEM (electron spin echo envelope modulation) problem. We used a commercial pulsed ESR spectrometer and compared these two methods.
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Affiliation(s)
- H Hara
- ESR Division, Bruker Biospin K.K., Ibaraki 305-0051, Japan.
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34
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Borbat PP, Freed JH. Measuring distances by pulsed dipolar ESR spectroscopy: spin-labeled histidine kinases. Methods Enzymol 2007; 423:52-116. [PMID: 17609127 DOI: 10.1016/s0076-6879(07)23003-4] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Applications of dipolar ESR spectroscopy to structural biology are rapidly expanding, and it has become a useful method that is aimed at resolving protein structure and functional mechanisms. The method of pulsed dipolar ESR spectroscopy (PDS) is outlined in the first half of the chapter, and it illustrates the simplicity and potential of this developing technology with applications to various biological systems. A more detailed description is presented of the implementation of PDS to reconstruct the ternary structure of a large dimeric protein complex from Thermotoga maritima, formed by the histidine kinase CheA and the coupling protein CheW. This protein complex is a building block of an extensive array composed of coupled supramolecular structures assembled from CheA/CheW proteins and transmembrane signaling chemoreceptors, which make up a sensor that is key to controlling the motility in bacterial chemotaxis. The reconstruction of the CheA/CheW complex has employed several techniques, including X-ray crystallography and pulsed ESR. Emphasis is on the role of PDS, which is part of a larger effort to reconstruct the entire signaling complex, including chemoreceptor, by means of PDS structural mapping. In order to precisely establish the mode of coupling of CheW to CheA and to globally map the complex, approximately 70 distances have already been determined and processed into molecular coordinates by readily available methods of distance geometry constraints.
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Affiliation(s)
- Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
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35
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Jun S, Becker JS, Yonkunas M, Coalson R, Saxena S. Unfolding of alanine-based peptides using electron spin resonance distance measurements. Biochemistry 2006; 45:11666-73. [PMID: 16981726 DOI: 10.1021/bi061195b] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a scheme for tagging an alanine-based peptide with a Cu(II) and a nitroxide to measure unfolding transitions. The enhancement in longitudinal relaxation rate of the nitroxide due to the presence of Cu(II) was measured at physiological temperatures by pulsed electron spin resonance (ESR). The change in relaxation rate provided the average interspin distance between the Cu(II) and the nitroxide. Control experiments on a proline-based peptide verify the robustness of the method. The change in interspin distances with temperature for the alanine-based peptide is in accord with the change in helicity measured by circular dichroism. The data provide an opportunity to examine the unfolding process in polyalanine peptides. The distance in the folded state is in concordance with molecular dynamics. However, the ESR experiment measures an average distance of 17 A in the unfolded state, whereas molecular dynamics indicates a distance of 42 A if the unfolded geometry was a polyproline type II helix. Therefore, ESR demonstrates that the unfolded state of this alanine-based peptide is not an ideal extended polyproline type II helix.
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Affiliation(s)
- Sangmi Jun
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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36
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Pornsuwan S, Bird G, Schafmeister CE, Saxena S. Flexibility and lengths of bis-peptide nanostructures by electron spin resonance. J Am Chem Soc 2006; 128:3876-7. [PMID: 16551072 DOI: 10.1021/ja058143e] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the use of electron spin resonance (ESR) to determine long-range distances and flexibility in water-soluble bis-peptide molecular rods. Bis-peptide oligomers with 4-8 monomer units were synthesized. ESR determined that the end-to-end length of the peptides is linearly proportional to the number of monomers. The linear shape is, therefore, easily interpreted from the data. In addition, the flexibility of the rods was quantified directly from the ESR-determined distance distribution functions. Quantitative information on chain length and flexibility is important to develop the use of these oligomers as rodlike structural elements for applications such as bivalent display of ligands and as elements of future nanoscale devices.
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Affiliation(s)
- Soraya Pornsuwan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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37
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Ruthstein S, Potapov A, Raitsimring AM, Goldfarb D. Double Electron Electron Resonance as a Method for Characterization of Micelles. J Phys Chem B 2005; 109:22843-51. [PMID: 16853976 DOI: 10.1021/jp054450v] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Double electron electron resonance (DEER) is an experimental technique used to determine distance between electron spins. In this work, we show that it can be used to study the properties of micelles in solution, specifically their volume and the aggregation number. The feasibility of the method is tested on micelles of Pluronic block copolymers, PEO(x)-PPO(y)-PEO(x), built from chains of poly(ethylene oxide) (PEO), comprising the more hydrophilic corona, and a poly(propylene oxide) (PPO) block constituting the hydrophobic core. In this work, the dimensions of the hydrophobic core of micelles of Pluronic L64 (x = 13, y = 30), P123 (x = 20, y = 70), and F127 (x = 106, y = 70) and their aggregation number were studied. This was done using the spin-probe 4-hydroxy-tempo-benzoate (4HTB), which is hydrophobic and is localized in the hydrophobic core of the micelles and does not dissolve in aqueous solution. The measurements were carried out on frozen solutions, freeze quenched after equilibration at 50 degrees C. It was found that the hydrophobic core radii occupied by 4HTB in 7.5 wt % F127 and 6 wt % L64 are 4.0 +/- 0.05 and 3.8 +/- 0.1 nm, respectively, and the corresponding aggregation numbers are 57 +/- 2 and 206 +/- 14. The micelles of 6 wt % P123 were found to have a rod shape, and the addition of 4HTB at concentrations higher than 0.7 mM resulted in a phase transitioned to spherical micelles. Finally, this study also showed that the micelle structure is preserved upon rapid freezing.
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Affiliation(s)
- Sharon Ruthstein
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
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Elsässer C, Monien B, Haehnel W, Bittl R. Orientation of spin labels in de novo peptides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2005; 43 Spec no.:S26-33. [PMID: 16235214 DOI: 10.1002/mrc.1692] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A series of de novo synthesised peptides including the artificial rigid paramagnetic amino acid TOAC at two positions with different distances from two to seven in the primary structure have been investigated by 9- and 94-GHz EPR spectroscopy under solid-state conditions. From simulations of the spectra of such two-spin systems, the distance and relative orientation of the paramagnetic centres can be deduced. This yields structural information on the peptides. A quantitative analysis of the spectra of individual peptides in different solvents as well as a qualitative analysis of the spectra of the peptide series shows that the peptides do not assume conformations corresponding to any of the common helical structures in proteins.
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Affiliation(s)
- Celine Elsässer
- Freie Universität Berlin, Institut für Experimentalphysik, Arnimallee 14, 14195 Berlin, Germany
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39
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40
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Sartori E, Corvaja C, Oancea S, Formaggio F, Crisma M, Toniolo C. Linear Configuration of the Spins of a Stable Trinitroxide Radical Based on a Ternary Helical Peptide. Chemphyschem 2005; 6:1472-5. [PMID: 15999386 DOI: 10.1002/cphc.200500139] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Elena Sartori
- Department of Chemistry, University of Padova, via Marzolo, 1, 35131 Padova, Italy
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41
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Milov AD, Erilov DA, Salnikov ES, Tsvetkov YD, Formaggio F, Toniolo C, Raap J. Structure and spatial distribution of the spin-labelled lipopeptide trichogin GA IV in a phospholipid membrane studied by pulsed electron–electron double resonance (PELDOR). Phys Chem Chem Phys 2005; 7:1794-9. [DOI: 10.1039/b418414a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Bonora M, Becker J, Saxena S. Suppression of electron spin-echo envelope modulation peaks in double quantum coherence electron spin resonance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 170:278-283. [PMID: 15388091 DOI: 10.1016/j.jmr.2004.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2004] [Revised: 07/01/2004] [Indexed: 05/24/2023]
Abstract
We show the use of the observer blind spots effect for the elimination of electron spin-echo envelope modulation (ESEEM) peaks in double quantum coherence (DQC) electron spin resonance (ESR). The suppression of ESEEM facilitates the routine and unambiguous extraction of distances from DQC-ESR spectra. This is also the first demonstration of this challenging methodology on commercial instrumentation.
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Affiliation(s)
- Marco Bonora
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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43
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Peggion C, Formaggio F, Crisma M, Epand RF, Epand RM, Toniolo C. Trichogin: a paradigm for lipopeptaibols. J Pept Sci 2004; 9:679-89. [PMID: 14658789 DOI: 10.1002/psc.500] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Lipopeptaibols are members of a novel family of naturally occurring, short peptides with antimicrobial activity, characterized by a lipophilic acyl chain at the N-terminus, a high content of turn/helix inducing alpha-aminoisobutyric acid and a 1,2-amino alcohol at the C-terminus. Using solution methods, the prototypical lipopeptaibol trichogin GA IV and a large series of appropriately designed analogues were synthesized, which allow: (i) determination of the minimal lipid chain and peptide main-chain lengths for the onset of membrane activity, and (ii) exploitation of a number of physico-chemical techniques aimed at assessing the trichogin preferred conformation under a variety of conditions and at investigating its mechanism of interaction with the phospholipid membranes.
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Affiliation(s)
- Cristina Peggion
- Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy
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44
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Stella L, Mazzuca C, Venanzi M, Palleschi A, Didonè M, Formaggio F, Toniolo C, Pispisa B. Aggregation and water-membrane partition as major determinants of the activity of the antibiotic peptide trichogin GA IV. Biophys J 2004; 86:936-45. [PMID: 14747329 PMCID: PMC1303941 DOI: 10.1016/s0006-3495(04)74169-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Water-membrane partition and aggregation behavior are fundamental aspects of the biological activity of antibiotic peptides, natural compounds causing the death of pathogenic organisms by perturbing the permeability of their membranes. A synthetic fluorescent analog of the natural lipopeptaibol trichogin GA IV was used to study its interaction with model membranes. Time-resolved fluorescence data show that in water, an equilibrium between monomers and small aggregates is present, the two species having different affinity for membranes. Therefore, association curves are strongly dependent on peptide concentration. A similar heterogeneity is present in the membrane phase, which strongly suggests the occurrence of a monomer-aggregate equilibrium in this case, too. The relative population of each species was determined and a strong correlation between the concentration of membrane-bound aggregates and membrane leakage was found, thereby suggesting that liposome perturbation is due to peptide aggregates only. Light-scattering measurements demonstrate that leakage is not due to liposome micellization. Moreover, experiments with markers of different sizes show that molecules with a diameter of approximately 4 nm are released only to a minor extent. Overall, these results suggest that, within the concentration range explored, pore formation by peptide aggregates is the most likely mechanism of action for trichogin in membranes.
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Affiliation(s)
- Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, 00133 Rome, Italy
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45
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Bonora M, Pornsuwan S, Saxena S. Nitroxide Spin−Relaxation over the Entire Motional Range. J Phys Chem B 2004. [DOI: 10.1021/jp0365864] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marco Bonora
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Soraya Pornsuwan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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46
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Milov AD, Tsvetkov YD, Formaggio F, Oancea S, Toniolo C, Raap J. Solvent effect on the distance distribution between spin labels in aggregated spin labeled trichogin GA IV dimer peptides as studied by pulsed electron–electron double resonance. Phys Chem Chem Phys 2004. [DOI: 10.1039/b313701e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Milov AD, Tsvetkov YD, Formaggio F, Oancea S, Toniolo C, Raap J. Aggregation of Spin Labeled Trichogin GA IV Dimers: Distance Distribution between Spin Labels in Frozen Solutions by PELDOR Data. J Phys Chem B 2003. [DOI: 10.1021/jp035057x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. D. Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Yu. D. Tsvetkov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - F. Formaggio
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - S. Oancea
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - C. Toniolo
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - J. Raap
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation, Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
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48
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Schiemann O, Weber A, Edwards TE, Prisner TF, Sigurdsson ST. Nanometer distance measurements on RNA using PELDOR. J Am Chem Soc 2003; 125:3434-5. [PMID: 12643697 DOI: 10.1021/ja0274610] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A rapid increase in RNA structural studies has been seen in the past few years, in part due to the interest in the multitude of cellular functions performed by RNA. Electron paramagnetic resonance spectroscopy is a useful technique for studying biopolymer structure under physiologically relevant conditions. We present herein the use of pulsed electron double resonance for the determination of a 35 +/- 2 A distance between two spin label nitroxides that were linked to specific positions within an RNA.
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Affiliation(s)
- Olav Schiemann
- Institut für Physikalische und Theoretische Chemie, J. W. Goethe-Universität, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany.
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49
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Milov AD, Tsvetkov YD, Formaggio F, Crisma M, Toniolo C, Raap J. Self-assembling and membrane modifying properties of a lipopeptaibol studied by CW-ESR and PELDOR spectroscopies. J Pept Sci 2003; 9:690-700. [PMID: 14664226 DOI: 10.1002/psc.513] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Trichogin GA IV is a short lipopeptaibol antibiotic that is capable of enhancing the transport of small cations through the phospholipid double layer of the membrane. The antibiotic activity of the undecapeptide is thought to be based on either its self-assembling or membrane-modifying property. The chemical equilibrium between self-aggregated and non-aggregated molecular states was studied by CW-ESR spectroscopy using solutions of TOAC nitroxide spin-labelled trichogin analogues in an apolar solvent to mimic the membrane bound state. At room temperature the two different sets of signals observed in the spectrum were attributed to the presence of both monomers and aggregates in the sample. The ESR spectra of the monomeric and aggregated forms were separated and the dependence of the fraction of monomeric peptide molecules on concentration was obtained over the range 5 x 10(-6) to 7 x 10(-4) M. A two-step aggregation mechanism is proposed: dimerization of peptide molecules followed by aggregation of dimers to assemblies of four peptide molecules per aggregate. The equilibrium constants were estimated for both steps. In addition, the lower lifetime limit was determined for dimers and tetramers. It is shown that when the peptide concentration exceeds 10(-5) M. the major part of the peptide molecules in solution has the form of tetrameric aggregates. Independently, the PELDOR technique was used to investigate the concentration dependence of the parameters of the dipole-dipole interaction between spin labels in frozen (77 K] glassy solutions of aggregates of mono-labelled TOAC analogues. The number of molecules in aggregates as well as the frequency and amplitude of PELDOR signal oscillations were found to be concentration independent in the range 5 x 10(-4) to 8 x 10(-3) M. In the frozen glassy solution state, the number of peptide molecules per aggregate was determined to be close to four, which is in agreement with the value obtained for spin-labelled trichogin at room temperature. The present data provide experimental evidence in favour of a self-assembling rather than a membrane-modifying ion conduction mechanism.
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Affiliation(s)
- A D Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation
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50
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Kropacheva TN, Raap J. Ion transport across a phospholipid membrane mediated by the peptide trichogin GA IV. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1567:193-203. [PMID: 12488053 DOI: 10.1016/s0005-2736(02)00616-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trichogin GA IV is a special member of a class of peptaibols that are linear peptide antibiotics of fungal origin, characterised by the presence of a variable number of alpha-aminoisobutyric acid residues, an acyl group at the N-terminus and a 1,2-amino alcohol at the C-terminus. Most of the peptaibols display ion-channel-forming or at least membrane-modifying properties. The 11-residue-long trichogin GA IV is not only one of shortest peptaibols, but it is also unique for its n-octanoyl group instead of the more common found acetyl group at the N-terminus. For the first time we have found that this lipopeptaibol is able to enhance conduction of monovalent cations through membranes of large unilamellar vesicles (LUVs). The influence of the [Leu-OMe]trichogin GA IV analogue (TRI) on ion permeation was studied under a variety of conditions (lipid composition, lipid-to-peptide ratio and a transmembrane potential). Parallel experiments were performed with the 16-residue long, channel-forming peptaibol, zervamicin (ZER). For the two peptides, the permeability between K(+) and Na(+) was found to be different. In addition, the ion diffusion rate dependencies on the peptide concentration are observed to be different. This might indicate that a different number of aggregated molecules are involved in the rate-limiting step, i.e. 3-4 (TRI) and 4-7 (ZER). In the presence of TRI, dissipation of the transmembrane potential, Delta psi, was observed with a rate to be dependent on the magnitude of both initial Delta psi and peptide concentration. Both peptides were activated by a cis-positive but not by cis-negative Delta psi. Under identical conditions the ion-conducting efficiency of zervamicin was 100-200 times higher than that of trichogin. Our results show that, unlike for zervamicin, the membrane-modifying activity of trichogin is not associated with a channel mechanism.
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Affiliation(s)
- T N Kropacheva
- Department of Chemistry, Udmurt State University, Izhevsk, Russia
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