1
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Toke O. Three Decades of REDOR in Protein Science: A Solid-State NMR Technique for Distance Measurement and Spectral Editing. Int J Mol Sci 2023; 24:13637. [PMID: 37686450 PMCID: PMC10487747 DOI: 10.3390/ijms241713637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Solid-state NMR (ss-NMR) is a powerful tool to investigate noncrystallizable, poorly soluble molecular systems, such as membrane proteins, amyloids, and cell walls, in environments that closely resemble their physical sites of action. Rotational-echo double resonance (REDOR) is an ss-NMR methodology, which by reintroducing heteronuclear dipolar coupling under magic angle spinning conditions provides intramolecular and intermolecular distance restraints at the atomic level. In addition, REDOR can be exploited as a selection tool to filter spectra based on dipolar couplings. Used extensively as a spectroscopic ruler between isolated spins in site-specifically labeled systems and more recently as a building block in multidimensional ss-NMR pulse sequences allowing the simultaneous measurement of multiple distances, REDOR yields atomic-scale information on the structure and interaction of proteins. By extending REDOR to the determination of 1H-X dipolar couplings in recent years, the limit of measurable distances has reached ~15-20 Å, making it an attractive method of choice for the study of complex biomolecular assemblies. Following a methodological introduction including the most recent implementations, examples are discussed to illustrate the versatility of REDOR in the study of biological systems.
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Affiliation(s)
- Orsolya Toke
- Laboratory for NMR Spectroscopy, Structural Research Centre, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, H-1117 Budapest, Hungary
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2
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Du Y, Su Y. 19F Solid-state NMR characterization of pharmaceutical solids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 120:101796. [PMID: 35688018 DOI: 10.1016/j.ssnmr.2022.101796] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Solid-state NMR has been increasingly recognized as a high-resolution and versatile spectroscopic tool to characterize drug substances and products. However, the analysis of pharmaceutical materials is often carried out at natural isotopic abundance and a relatively low drug loading in multi-component systems and therefore suffers from challenges of low sensitivity. The fact that fluorinated therapeutics are well represented in pipeline drugs and commercial products offers an excellent opportunity to utilize fluorine as a molecular probe for pharmaceutical analysis. We aim to review recent advancements of 19F magic angle spinning NMR methods in modern drug research and development. Applications to polymorph screening at the micromolar level, structural elucidation, and investigation of molecular interactions at the Ångström to submicron resolution in drug delivery, stability, and quality will be discussed.
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Affiliation(s)
- Yong Du
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, United States
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, United States; Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, IN, 47907, United States; Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, United States; Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, United States.
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3
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Shcherbakov AA, Medeiros-Silva J, Tran N, Gelenter MD, Hong M. From Angstroms to Nanometers: Measuring Interatomic Distances by Solid-State NMR. Chem Rev 2021; 122:9848-9879. [PMID: 34694769 DOI: 10.1021/acs.chemrev.1c00662] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Internuclear distances represent one of the main structural constraints in molecular structure determination using solid-state NMR spectroscopy, complementing chemical shifts and orientational restraints. Although a large number of magic-angle-spinning (MAS) NMR techniques have been available for distance measurements, traditional 13C and 15N NMR experiments are inherently limited to distances of a few angstroms due to the low gyromagnetic ratios of these nuclei. Recent development of fast MAS triple-resonance 19F and 1H NMR probes has stimulated the design of MAS NMR experiments that measure distances in the 1-2 nm range with high sensitivity. This review describes the principles and applications of these multiplexed multidimensional correlation distance NMR experiments, with an emphasis on 19F- and 1H-based distance experiments. Representative applications of these long-distance NMR methods to biological macromolecules as well as small molecules are reviewed.
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Affiliation(s)
- Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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4
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Su J, Marrink SJ, Melo MN. Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane Domains. Front Cell Dev Biol 2020; 8:350. [PMID: 32509780 PMCID: PMC7248343 DOI: 10.3389/fcell.2020.00350] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/20/2020] [Indexed: 01/14/2023] Open
Abstract
We performed coarse-grained simulations of the antimicrobial peptides Magainin-2, BP100, MSI-103, and MSI-78 on a phase-separated membrane to study their preference for the different domains. All the peptides displayed a clear preference for the liquid-disordered (Ld) phase over the liquid-ordered (Lo) one. For BP100, MSI-103, and MSI-78 there was a further preference of the peptides for the domain interface. The peptides' preference toward the disordered phase was shown to reflect a penalization of lipid-lipid interaction enthalpy in the Lo phase, when in the vicinity of peptides. Similar results were observed at the two studied concentrations, although Ld phase saturation at the higher concentration drove some of the peptide excess to the Lo phase. Magainin-2 and MSI-103 were found to dimerize, in agreement with available experimental data. Interestingly, at high concentrations of Magainin-2 toroidal pores spontaneously formed in the Ld phase. We performed additional simulations to characterize this phenomenon, which is likely related to Magainin-2's membranolytic action.
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Affiliation(s)
- Juanjuan Su
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Siewert J. Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Manuel N. Melo
- Multiscale Modeling Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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5
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Locke GM, Bernhard SSR, Senge MO. Nonconjugated Hydrocarbons as Rigid-Linear Motifs: Isosteres for Material Sciences and Bioorganic and Medicinal Chemistry. Chemistry 2019; 25:4590-4647. [PMID: 30387906 DOI: 10.1002/chem.201804225] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/20/2018] [Indexed: 01/02/2023]
Abstract
Nonconjugated hydrocarbons, like bicyclo[1.1.1]pentane, bicyclo[2.2.2]octane, triptycene, and cubane are a unique class of rigid linkers. Due to their similarity in size and shape they are useful mimics of classic benzene moieties in drugs, so-called bioisosteres. Moreover, they also fulfill an important role in material sciences as linear linkers, in order to arrange various functionalities in a defined spatial manner. In this Review article, recent developments and usages of these special, rectilinear systems are discussed. Furthermore, we focus on covalently linked, nonconjugated linear arrangements and discuss the physical and chemical properties and differences of individual linkers, as well as their application in material and medicinal sciences.
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Affiliation(s)
- Gemma M Locke
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin, 2, Ireland
| | - Stefan S R Bernhard
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin, 2, Ireland
| | - Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin, 2, Ireland
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6
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King MJ, Bennett AL, Almeida PF, Lee HS. Coarse-grained simulations of hemolytic peptide δ-lysin interacting with a POPC bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:3182-3194. [PMID: 27720634 DOI: 10.1016/j.bbamem.2016.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/17/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
δ-lysin, secreted by a Gram-positive bacterium Staphylococcus aureus, is a 26-residue membrane active peptide that shares many common features with antimicrobial peptides (AMPs). However, it possesses a few unique features that differentiate itself from typical AMPs. In particular, δ-lysin has zero net charge, even though it has many charged residues, and it preferentially lyses eukaryotic cells over bacterial cells. Here, we present the results of coarse-grained molecular dynamics simulations of δ-lysin interacting with a zwitterionic membrane over a wide range of peptide concentrations. When the peptides concentration is low, spontaneous dimerization of peptides is observed on the membrane surface, but deep insertion of peptides or pore formation was not observed. However, the calculated free energy of peptide insertion suggests that a small fraction of peptides is likely to be present inside the membrane at the peptide concentrations typically seen in dye efflux experiments. When the simulations with multiple peptides are carried out with a single pre-inserted transmembrane peptide, spontaneous pore formation occurs with a peptide-to-lipid ratio (P/L) as low as P/L=1:42. Inter-peptide salt bridges among the transmembrane peptides seem to play a role in creating compact pores with very low level of hydration. More importantly, the transmembrane peptides making up the pore are constantly pushed to the opposite side of the membrane when the mass imbalance between the two sides of membrane is significant. Thus, the pore is very dynamic, allowing multiple peptides to translocate across the membrane simultaneously.
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Affiliation(s)
- Mariah J King
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States
| | - Ashley L Bennett
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States
| | - Paulo F Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States
| | - Hee-Seung Lee
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States.
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7
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Kokhan SO, Tymtsunik AV, Grage SL, Afonin S, Babii O, Berditsch M, Strizhak AV, Bandak D, Platonov MO, Komarov IV, Ulrich AS, Mykhailiuk PK. Design, Synthesis, and Application of an Optimized Monofluorinated Aliphatic Label for Peptide Studies by Solid-State 19
F NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Serhii O. Kokhan
- Enamine Ltd; Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Andriy V. Tymtsunik
- Enamine Ltd; Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Stephan L. Grage
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Marina Berditsch
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | | | | | | | - Igor V. Komarov
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Pavel K. Mykhailiuk
- Enamine Ltd; Chervonotkatska 78 02094 Kyiv Ukraine
- Chemistry Department; Taras Shevchenko National University of Kyiv; Volodymyrska 64 01601 Kyiv Ukraine
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8
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Kokhan SO, Tymtsunik AV, Grage SL, Afonin S, Babii O, Berditsch M, Strizhak AV, Bandak D, Platonov MO, Komarov IV, Ulrich AS, Mykhailiuk PK. Design, Synthesis, and Application of an Optimized Monofluorinated Aliphatic Label for Peptide Studies by Solid‐State
19
F NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:14788-14792. [DOI: 10.1002/anie.201608116] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Serhii O. Kokhan
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies Taras Shevchenko National University of Kyiv Volodymyrska 60 01601 Kyiv Ukraine
| | - Andriy V. Tymtsunik
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies Taras Shevchenko National University of Kyiv Volodymyrska 60 01601 Kyiv Ukraine
| | - Stephan L. Grage
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Marina Berditsch
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | | | | | | | - Igor V. Komarov
- Institute of High Technologies Taras Shevchenko National University of Kyiv Volodymyrska 60 01601 Kyiv Ukraine
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Pavel K. Mykhailiuk
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine
- Chemistry Department Taras Shevchenko National University of Kyiv Volodymyrska 64 01601 Kyiv Ukraine
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9
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Fillion M, Auger M. Oriented samples: a tool for determining the membrane topology and the mechanism of action of cationic antimicrobial peptides by solid-state NMR. Biophys Rev 2015; 7:311-320. [PMID: 28510228 PMCID: PMC5425733 DOI: 10.1007/s12551-015-0167-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/05/2015] [Indexed: 01/12/2023] Open
Abstract
Overuse and misuse of antibiotics have led bacteria to acquire several mechanisms of resistance. In response to this, researchers have identified natural antimicrobial peptides as promising candidates to fight against multiresistant bacteria. However, their mode of action is still unclear, and a better understanding of the mode of action of these peptides is of primary importance to develop new peptides displaying high antibacterial activity and low hemolytic activity. One of the main features that defines the mechanism of action is the membrane topology of the peptide. Among the spectroscopic techniques, solid-state NMR is the technique of choice for determining the location of the peptide within the membrane. It can be achieved by performing experiments with oriented samples. In the literature, the two most common types of oriented samples are bicelles and phospholipids mechanically oriented between glass plates. The mode of perturbation of the membrane-active peptide can be studied by phosphorus-31 and deuterium NMR. On the other hand, several experiments such as nitrogen-15 and fluorine solid-state NMR, that require labeled peptides, can give valuable information on the membrane topology of the peptide. The combination of the latter techniques allows the determination of a precise topology, thus a better knowledge of the molecular determinants involved in the membrane interactions of antimicrobial peptides.
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Affiliation(s)
- Matthieu Fillion
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Michèle Auger
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada.
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10
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Hydrophobic mismatch demonstrated for membranolytic peptides, and their use as molecular rulers to measure bilayer thickness in native cells. Sci Rep 2015; 5:9388. [PMID: 25807192 PMCID: PMC5224518 DOI: 10.1038/srep09388] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/20/2015] [Indexed: 11/16/2022] Open
Abstract
Hydrophobic mismatch is a well-recognized principle in the interaction of transmembrane proteins with lipid bilayers. This concept was extended here to amphipathic membranolytic α-helices. Nine peptides with lengths between 14 and 28 amino acids were designed from repeated KIAGKIA motifs, and their helical nature was confirmed by circular dichroism spectroscopy. Biological assays for antimicrobial activity and hemolysis, as well as fluorescence vesicle leakage and solid-state NMR spectroscopy, were used to correlate peptide length with membranolytic activity. These data show that the formation of transmembrane pores is only possible under the condition of hydrophobic matching: the peptides have to be long enough to span the hydrophobic bilayer core to be able to induce vesicle leakage, kill bacteria, and cause hemolysis. By correlating the threshold lengths for biological activity with the biophysical results on model vesicles, the peptides could be utilized as molecular rulers to measure the membrane thickness in different cells.
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11
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Control and role of pH in peptide–lipid interactions in oriented membrane samples. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:833-41. [DOI: 10.1016/j.bbamem.2014.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 12/22/2022]
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12
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Wadhwani P, Strandberg E, van den Berg J, Mink C, Bürck J, Ciriello RA, Ulrich AS. Dynamical structure of the short multifunctional peptide BP100 in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:940-9. [DOI: 10.1016/j.bbamem.2013.11.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/25/2013] [Accepted: 11/01/2013] [Indexed: 11/26/2022]
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13
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Cegelski L. REDOR NMR for drug discovery. Bioorg Med Chem Lett 2013; 23:5767-75. [PMID: 24035486 PMCID: PMC4038398 DOI: 10.1016/j.bmcl.2013.08.064] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 11/19/2022]
Abstract
Rotational-echo double-resonance (REDOR) NMR is a powerful and versatile solid-state NMR measurement that has been recruited to elucidate drug modes of action and to drive the design of new therapeutics. REDOR has been implemented to examine composition, structure, and dynamics in diverse macromolecular and whole-cell systems, including taxol-bound microtubules, enzyme-cofactor-inhibitor ternary complexes, and antibiotic-whole-cell complexes. The REDOR approach involves the integrated design of specific isotopic labeling strategies and the selection of appropriate REDOR experiments. By way of example, this digest illustrates the versatility of the REDOR approach, with an emphasis on the practical considerations of experimental design and data interpretation.
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Affiliation(s)
- Lynette Cegelski
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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14
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Ulmschneider JP, Smith JC, Ulmschneider MB, Ulrich AS, Strandberg E. Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations. Biophys J 2013; 103:472-482. [PMID: 22947863 DOI: 10.1016/j.bpj.2012.06.040] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 06/27/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022] Open
Abstract
The membrane-active antimicrobial peptide PGLa from Xenopus laevis is known from solid-state (2)H-, (15)N-, and (19)F-NMR spectroscopy to occupy two distinct α-helical surface adsorbed states in membranes: a surface-bound S-state with a tilt angle of ~95° at low peptide/lipid molar ratio (P/L = 1:200), and an obliquely tilted T-state with a tilt angle of 127° at higher peptide concentration (P/L = 1:50). Using a rapid molecular-dynamics insertion protocol in combination with microsecond-scale simulation, we have characterized the structure of both states in detail. As expected, the amphiphilic peptide resides horizontally on the membrane surface in a monomeric form at a low P/L, whereas the T-state is seen in the simulations to be a symmetric antiparallel dimer, with close contacts between small glycine and alanine residues at the interface. The computed tilt angles and azimuthal rotations, as well as the quadrupolar splittings predicted from the simulations agree with the experimental NMR data. The simulations reveal many structural details previously inaccessible, such as the immersion depth of the peptide in the membrane and the packing of the dimerization interface. The study highlights the ability and limitations of current state-of-the-art multimicrosecond all-atom simulations of membrane-active peptides to complement experimental data from solid-state NMR.
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Affiliation(s)
| | | | | | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany; Institute of Organic Chemistry and CFN, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
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15
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Brender JR, McHenry AJ, Ramamoorthy A. Does cholesterol play a role in the bacterial selectivity of antimicrobial peptides? Front Immunol 2012; 3:195. [PMID: 22822405 PMCID: PMC3398343 DOI: 10.3389/fimmu.2012.00195] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 06/21/2012] [Indexed: 12/12/2022] Open
Affiliation(s)
- Jeffrey R Brender
- Biophysics and Department of Chemistry, University of Michigan Ann Arbor, MI, USA
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16
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Wadhwani P, Reichert J, Bürck J, Ulrich AS. Antimicrobial and cell-penetrating peptides induce lipid vesicle fusion by folding and aggregation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:177-87. [PMID: 22080286 PMCID: PMC3269571 DOI: 10.1007/s00249-011-0771-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 10/06/2011] [Accepted: 10/20/2011] [Indexed: 11/28/2022]
Abstract
According to their distinct biological functions, membrane-active peptides are generally classified as antimicrobial (AMP), cell-penetrating (CPP), or fusion peptides (FP). The former two classes are known to have some structural and physicochemical similarities, but fusogenic peptides tend to have rather different features and sequences. Nevertheless, we found that many CPPs and some AMPs exhibit a pronounced fusogenic activity, as measured by a lipid mixing assay with vesicles composed of typical eukaryotic lipids. Compared to the HIV fusion peptide (FP23) as a representative standard, all designer-made peptides showed much higher lipid-mixing activities (MSI-103, MAP, transportan, penetratin, Pep1). Native sequences, on the other hand, were less fusogenic (magainin 2, PGLa, gramicidin S), and pre-aggregated ones were inactive (alamethicin, SAP). The peptide structures were characterized by circular dichroism before and after interacting with the lipid vesicles. A striking correlation between the extent of conformational change and the respective fusion activities was found for the series of peptides investigated here. At the same time, the CD data show that lipid mixing can be triggered by any type of conformation acquired upon binding, whether α-helical, β-stranded, or other. These observations suggest that lipid vesicle fusion can simply be driven by the energy released upon membrane binding, peptide folding, and possibly further aggregation. This comparative study of AMPs, CPPs, and FPs emphasizes the multifunctional aspects of membrane-active peptides, and it suggests that the origin of a peptide (native sequence or designer-made) may be more relevant to define its functional range than any given name.
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Affiliation(s)
- Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021, Karlsruhe, Germany
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17
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A kinked antimicrobial peptide from Bombina maxima. II. Behavior in phospholipid bilayers. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:463-70. [DOI: 10.1007/s00249-010-0668-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 12/03/2010] [Accepted: 12/23/2010] [Indexed: 10/18/2022]
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18
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Kijac A, Shih AY, Nieuwkoop AJ, Schulten K, Sligar SG, Rienstra CM. Lipid-protein correlations in nanoscale phospholipid bilayers determined by solid-state nuclear magnetic resonance. Biochemistry 2010; 49:9190-8. [PMID: 20804175 PMCID: PMC3136391 DOI: 10.1021/bi1013722] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanodiscs are examples of discoidal nanoscale lipid-protein particles that have been extremely useful for the biochemical and biophysical characterization of membrane proteins. They are discoidal lipid bilayer fragments encircled and stabilized by two amphipathic helical proteins named membrane scaffolding protein (MSP), ~10 nm in size. Nanodiscs are homogeneous, easily prepared with reproducible success, amenable to preparations with a variety of lipids, and stable over a range of temperatures. Here we present solid-state nuclear magnetic resonance (SSNMR) studies on lyophilized, rehydrated POPC Nanodiscs prepared with uniformly (13)C-, (15)N-labeled MSP1D1 (Δ1-11 truncated MSP). Under these conditions, by SSNMR we directly determine the gel-to-liquid crystal lipid phase transition to be at 3 ± 2 °C. Above this phase transition, the lipid (1)H signals have slow transverse relaxation, enabling filtering experiments as previously demonstrated for lipid vesicles. We incorporate this approach into two- and three-dimensional heteronuclear SSNMR experiments to examine the MSP1D1 residues interfacing with the lipid bilayer. These (1)H-(13)C and (1)H-(13)C-(13)C correlation spectra are used to identify and quantify the number of lipid-correlated and solvent-exposed residues by amino acid type, which furthermore is compared with molecular dynamics studies of MSP1D1 in Nanodiscs. This study demonstrates the utility of SSNMR experiments with Nanodiscs for examining lipid-protein interfaces and has important applications for future structural studies of membrane proteins in physiologically relevant formulations.
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Affiliation(s)
- Aleksandra Kijac
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Amy Y. Shih
- Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Andrew J. Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Klaus Schulten
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Stephen G. Sligar
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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19
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Epand RF, Maloy WL, Ramamoorthy A, Epand RM. Probing the "charge cluster mechanism" in amphipathic helical cationic antimicrobial peptides. Biochemistry 2010; 49:4076-84. [PMID: 20387900 DOI: 10.1021/bi100378m] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Clustering of anionic lipids away from zwitterionic ones by cationic antimicrobial agents has recently been established as a mechanism of action of natural small, flexible peptides as well as non-natural synthetic peptide mimics. One of the largest classes of antimicrobial peptides consists of peptides that form cationic amphipathic helices on membranes and whose toxic action is dependent on the formation of pores in the membrane or through the "carpet" mechanism. We have evaluated the role of anionic lipid clustering for five of these peptides, i.e., MSI-78, MSI-103, MSI-469, MSI-843, and MSI-1254, with different sequences and properties. We determined whether these amphipathic helical cationic antimicrobial peptides cluster anionic lipids from zwitterionic ones and if this property is related to the species specificity of their toxicity. All five of these peptides were capable of lipid clustering, in contrast to the well-studied amphipathic helical antimicrobial peptide, magainin 2, which does not. We ascribe this difference to the lower density of positive charges in magainin 2. Peptides that efficiently cluster anionic lipids generally have a ratio of MIC for Staphylococcus aureus to that for Escherichia coli of >1. The addition of an N-terminal octyl chain did not preclude anionic charge clustering, although the ratio of MIC for S. aureus to that for E. coli was somewhat lowered. In most Gram-positive bacteria, there is a predominance of anionic lipids in the cytoplasmic membrane. In Gram-negative bacteria, however, clustering of anionic lipids away from zwitterionic ones is emerging as an important contributing mechanism of bacterial toxicity for some antimicrobial agents.
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Affiliation(s)
- Raquel F Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre, Hamilton, Ontario L8N 3Z5, Canada
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20
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Afonin S, Grage SL, Ieronimo M, Wadhwani P, Ulrich AS. Temperature-dependent transmembrane insertion of the amphiphilic peptide PGLa in lipid bilayers observed by solid state 19F NMR spectroscopy. J Am Chem Soc 2009; 130:16512-4. [PMID: 19049452 DOI: 10.1021/ja803156d] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sergii Afonin
- Karlsruhe Institute of Technology, Institute of Biological Interfaces, P.O. Box 3640, 76021 Karlsruhe, Germany
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21
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Shi L, Traaseth NJ, Verardi R, Cembran A, Gao J, Veglia G. A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints. JOURNAL OF BIOMOLECULAR NMR 2009; 44:195-205. [PMID: 19597943 PMCID: PMC2824793 DOI: 10.1007/s10858-009-9328-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 05/15/2009] [Indexed: 05/11/2023]
Abstract
To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based potential, E (z) (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software for general use.
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Affiliation(s)
- Lei Shi
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nathaniel J. Traaseth
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
| | - Raffaello Verardi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
| | - Alessandro Cembran
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA. Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
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22
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Fernandez DI, Gehman JD, Separovic F. Membrane interactions of antimicrobial peptides from Australian frogs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:1630-8. [PMID: 19013126 DOI: 10.1016/j.bbamem.2008.10.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 10/08/2008] [Accepted: 10/12/2008] [Indexed: 10/21/2022]
Abstract
The membrane interactions of four antimicrobial peptides, aurein 1.2, citropin 1.1, maculatin 1.1 and caerin 1.1, isolated from Australian tree frogs, are reviewed. All four peptides are amphipathic alpha-helices with a net positive charge and range in length from 13 to 25 residues. Despite several similar sequence characteristics, these peptides compromise the integrity of model membrane bilayers via different mechanisms; the shorter peptides exhibit a surface interaction mechanism while the longer peptides may form pores in membranes.
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Affiliation(s)
- David I Fernandez
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne VIC 3010, Australia
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23
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Dürr UHN, Grage SL, Witter R, Ulrich AS. Solid state 19F NMR parameters of fluorine-labeled amino acids. Part I: aromatic substituents. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 191:7-15. [PMID: 18155936 DOI: 10.1016/j.jmr.2007.11.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 10/30/2007] [Accepted: 11/21/2007] [Indexed: 05/25/2023]
Abstract
Structural parameters of peptides and proteins in biomembranes can be directly measured by solid state NMR of selectively labeled amino acids. The 19F nucleus is a promising label to overcome the low sensitivity of 2H, 13C or 15N, and to serve as a background-free reporter group in biological compounds. To make the advantages of solid state 19F NMR fully available for structural studies of polypeptides, we have systematically measured the chemical shift anisotropies and relaxation properties of the most relevant aromatic and aliphatic 19F-labeled amino acids. In this first part of two consecutive contributions, six different 19F-substituents on representative aromatic side chains were characterized as polycrystalline powders by static and MAS experiments. The data are also compared with results on the same amino acids incorporated in synthetic peptides. The spectra show a wide variety of lineshapes, from which the principal values of the CSA tensors were extracted. In addition, temperature-dependent T(1) and T(2) relaxation times were determined by 19F NMR in the solid state, and isotropic chemical shifts and scalar couplings were obtained in solution.
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Affiliation(s)
- Ulrich H N Dürr
- Max-Planck-Institute for Biophysical Chemistry, Department of NMR-Based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany
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24
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Solid State NMR Structure Analysis of the Antimicrobial Peptide Gramicidin S in Lipid Membranes: Concentration-Dependent Re-alignment and Self-Assembly as a β-Barrel. Top Curr Chem (Cham) 2008; 273:139-54. [DOI: 10.1007/128_2007_20] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Oligomeric structure, dynamics, and orientation of membrane proteins from solid-state NMR. Structure 2007; 14:1731-40. [PMID: 17161364 DOI: 10.1016/j.str.2006.10.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2006] [Revised: 10/01/2006] [Accepted: 10/03/2006] [Indexed: 11/27/2022]
Abstract
Solid-state NMR is a versatile and powerful tool for determining the dynamic structure of membrane proteins at atomic resolution. I review the recent progress in determining the orientation, the internal and global protein dynamics, the oligomeric structure, and the ligand-bound structure of membrane proteins with both alpha-helical and beta sheet conformations. Examples are given that illustrate the insights into protein function that can be gained from the NMR structural information.
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26
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Ramamoorthy A, Kandasamy SK, Lee DK, Kidambi S, Larson RG. Structure, topology, and tilt of cell-signaling peptides containing nuclear localization sequences in membrane bilayers determined by solid-state NMR and molecular dynamics simulation studies. Biochemistry 2007; 46:965-75. [PMID: 17240980 PMCID: PMC2527728 DOI: 10.1021/bi061895g] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cell-signaling peptides have been extensively used to transport functional molecules across the plasma membrane into living cells. These peptides consist of a hydrophobic sequence and a cationic nuclear localization sequence (NLS). It has been assumed that the hydrophobic region penetrates the hydrophobic lipid bilayer and delivers the NLS inside the cell. To better understand the transport mechanism of these peptides, in this study, we investigated the structure, orientation, tilt of the peptide relative to the bilayer normal, and the membrane interaction of two cell-signaling peptides, SA and SKP. Results from CD and solid-state NMR experiments combined with molecular dynamics simulations suggest that the hydrophobic region is helical and has a transmembrane orientation with the helical axis tilted away from the bilayer normal. The influence of the hydrophobic mismatch, between the hydrophobic length of the peptide and the hydrophobic thickness of the bilayer, on the tilt angle of the peptides was investigated using thicker POPC and thinner DMPC bilayers. NMR experiments showed that the hydrophobic domain of each peptide has a tilt angle of 15 +/- 3 degrees in POPC, whereas in DMPC, 25 +/- 3 degree and 30 +/- 3 degree tilts were observed for SA and SKP peptides, respectively. These results are in good agreement with molecular dynamics simulations, which predict a tilt angle of 13.3 degrees (SA in POPC), 16.4 degrees (SKP in POPC), 22.3 degrees (SA in DMPC), and 31.7 degrees (SKP in DMPC). These results and simulations on the hydrophobic fragment of SA or SKP suggest that the tilt of helices increases with a decrease in bilayer thickness without changing the phase, order, and structure of the lipid bilayers.
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Affiliation(s)
- Ayyalusamy Ramamoorthy
- Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1055, USA.
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27
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Matsuoka S, Schaefer J. Double-quantum filtered rotational-echo double resonance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 183:252-8. [PMID: 17008112 DOI: 10.1016/j.jmr.2006.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 08/14/2006] [Accepted: 08/15/2006] [Indexed: 05/12/2023]
Abstract
The homonuclear scalar coupling of a directly bonded 13C-13C pair has been used to create a double-quantum filter (DQF) to remove the natural-abundance 13C background in 13C{15N} rotational-echo double-resonance (REDOR) experiments. The DQF scalar and REDOR dipolar evolution periods are coincident which is important for sensitivity in the event of weak 13C-15N dipolar coupling. Calculated and observed 13C{15N} DQF-REDOR dephasings were in agreement for a test sample of mixed recrystallized labeled alanines. Glycine metabolism in a single uniform-15N soybean leaf labeled for 6 min by 13CO2 was measured quantitatively by 13C{15N} DQF-REDOR with no background interferences.
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Affiliation(s)
- Shigeru Matsuoka
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
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28
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Grage SL, Suleymanova AV, Afonin S, Wadhwani P, Ulrich AS. Solid state NMR analysis of the dipolar couplings within and between distant CF3-groups in a membrane-bound peptide. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 183:77-86. [PMID: 16919983 DOI: 10.1016/j.jmr.2006.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Revised: 07/11/2006] [Accepted: 07/14/2006] [Indexed: 05/11/2023]
Abstract
Dipolar couplings contain information on internuclear distances as well as orientational constraints. To characterize the structure of the antimicrobial peptide gramicidin S when bound to model membranes, two rigid 4-CF3-phenylglycine labels were attached to the cyclic backbone such that they reflect the behavior of the entire peptide. By solid state 19F NMR we measured the homonuclear dipolar couplings of the two trifluoromethyl-groups in oriented membrane samples. Using the CPMG experiment, both the strong couplings within each CF3-group as well as the weak coupling between the two CF3-groups could be detected. An intra-CF3-group dipolar coupling of 86 Hz and a weak inter-group coupling of 20 Hz were obtained by lineshape simulation of the complex dipolar spectrum. It is thus possible to explore the large distance range provided by 19F-labels and to resolve weak dipolar couplings even in the presence of strong intra-CF3 couplings. We applied this approach to distinguish and assign two epimers of the labeled gramicidin S peptide on the basis of their distinct 19F dipolar coupling patterns.
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Affiliation(s)
- Stephan L Grage
- Institute of Biological Interfaces, Forschungszentrum Karlsruhe, P.O. Box 3640, 76021 Karlsruhe, Germany
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29
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The effect of binding of spider-derived antimicrobial peptides, oxyopinins, on lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:1475-82. [DOI: 10.1016/j.bbamem.2006.04.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 04/19/2006] [Accepted: 04/19/2006] [Indexed: 11/22/2022]
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30
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Toke O, Cegelski L, Schaefer J. Peptide antibiotics in action: Investigation of polypeptide chains in insoluble environments by rotational-echo double resonance. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:1314-29. [PMID: 16616889 DOI: 10.1016/j.bbamem.2006.02.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 02/16/2006] [Accepted: 02/28/2006] [Indexed: 11/22/2022]
Abstract
Rotational-echo double resonance (REDOR) is a solid-state NMR technique that has the capability of providing intra- and intermolecular distance and orientational restraints in non-crystallizable, poorly soluble heterogeneous molecular systems such as cell membranes and cell walls. In this review, we will present two applications of REDOR: the investigation of a magainin-related antimicrobial peptide in lipid bilayers and the study of a vancomycin-like glycopeptide in the cell walls of Staphylococcus aureus.
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Affiliation(s)
- Orsolya Toke
- Institute for Structural Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, Pusztaszeri út 59-67, H-1025 Budapest, Hungary
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31
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Mikhailiuk PK, Afonin S, Chernega AN, Rusanov EB, Platonov MO, Dubinina GG, Berditsch M, Ulrich AS, Komarov IV. Conformationally Rigid Trifluoromethyl-Substituted α-Amino Acid Designed for Peptide Structure Analysis by Solid-State19F NMR Spectroscopy. Angew Chem Int Ed Engl 2006; 45:5659-61. [PMID: 16865762 DOI: 10.1002/anie.200600346] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Pavel K Mikhailiuk
- Department of Chemistry, Kyiv National Taras Shevchenko University, Volodymyrska 64, 01033 Kyiv, Ukraine
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32
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Mikhailiuk PK, Afonin S, Chernega AN, Rusanov EB, Platonov MO, Dubinina GG, Berditsch M, Ulrich AS, Komarov IV. Conformationally Rigid Trifluoromethyl-Substituted α-Amino Acid Designed for Peptide Structure Analysis by Solid-State19F NMR Spectroscopy. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600346] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Umeyama M, Kira A, Nishimura K, Naito A. Interactions of bovine lactoferricin with acidic phospholipid bilayers and its antimicrobial activity as studied by solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:1523-8. [PMID: 16884683 DOI: 10.1016/j.bbamem.2006.06.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2006] [Revised: 06/10/2006] [Accepted: 06/12/2006] [Indexed: 10/24/2022]
Abstract
Bovine lactoferricin (LfcinB) is an antimicrobial peptide released by pepsin cleavage of lactoferrin. In this work, the interaction between LfcinB and acidic phospholipid bilayers with the weight percentage of 65% dimyristoylphosphatidylglycerol (DMPG), 10% cardiolipin (CL) and 25% dimyristoylphosphatidylcholine (DMPC) was investigated as a mimic of cell membrane of Staphylococcus aureus by means of quartz crystal microbalance (QCM) and solid-state (31)P and (1)H NMR spectroscopy. Moreover, we elucidated a molecular mechanism of the antimicrobial activity of LfcinB by means of potassium ion selective electrode (ISE). It turned out that affinity of LfcinB for acidic phospholipid bilayers was higher than that for neutral phospholipid bilayers. It was also revealed that the association constant of LfcinB was larger than that of lactoferrin as a result of QCM measurements. (31)P DD-static NMR spectra indicated that LfcinB interacted with acidic phospholipid bilayers and bilayer defects were observed in the bilayer systems because isotropic peaks were clearly appeared. Gel-to-liquid crystalline phase transition temperatures (Tc) in the mixed bilayer systems were determined by measuring the temperature variation of relative intensities of acyl chains in (1)H MAS NMR spectra. Tc values of the acidic phospholipid and LfcinB-acidic phospholipid bilayer systems were 21.5 degrees C and 24.0 degrees C, respectively. To characterize the bilayer defects, potassium ion permeation across the membrane was observed by ISE measurements. The experimental results suggest that LfcinB caused pores in the acidic phospholipid bilayers. Because these pores lead the permeability across the membrane, the molecular mechanism of the antimicrobial activity could be attributed to the pore formation in the bacterial membrane induced by LfcinB.
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Affiliation(s)
- Masako Umeyama
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
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34
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Dürr UHN, Sudheendra US, Ramamoorthy A. LL-37, the only human member of the cathelicidin family of antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:1408-25. [PMID: 16716248 DOI: 10.1016/j.bbamem.2006.03.030] [Citation(s) in RCA: 723] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 03/23/2006] [Accepted: 03/24/2006] [Indexed: 12/28/2022]
Abstract
Antimicrobial peptides and their precursor molecules form a central part of human and mammalian innate immunity. The underlying genes have been thoroughly investigated and compared for a considerable number of species, allowing for phylogenetic characterization. On the phenotypical side, an ever-increasing number of very varied and distinctive influences of antimicrobial peptides on the innate immune system are reported. The basic biophysical understanding of mammalian antimicrobial peptides, however, is still very limited. This is especially unsatisfactory since knowledge of structural properties will greatly help in the understanding of their immunomodulatory functions. The focus of this review article will be on LL-37, the only cathelicidin-derived antimicrobial peptide found in humans. LL-37 is a 37-residue, amphipathic, helical peptide found throughout the body and has been shown to exhibit a broad spectrum of antimicrobial activity. It is expressed in epithelial cells of the testis, skin, the gastrointestinal tract, and the respiratory tract, and in leukocytes such as monocytes, neutrophils, T cells, NK cells, and B cells. It has been found to have additional defensive roles such as regulating the inflammatory response and chemo-attracting cells of the adaptive immune system to wound or infection sites, binding and neutralizing LPS, and promoting re-epthelialization and wound closure. The article aims to report the known biophysical facts, with an emphasis on structural evidence, and to set them into relation with insights gained on phylogenetically related antimicrobial peptides in other species. The multitude of immuno-functional roles is only outlined. We believe that this review will aid the future work on the biophysical, biochemical and immunological investigations of this highly intriguing molecule.
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Affiliation(s)
- Ulrich H N Dürr
- Biophysics Research Division and Department of Chemistry, 930 N. University Avenue, University of Michigan, Ann Arbor, MI 48109-1055, USA
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35
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Tremouilhac P, Strandberg E, Wadhwani P, Ulrich AS. Conditions affecting the re-alignment of the antimicrobial peptide PGLa in membranes as monitored by solid state 2H-NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:1330-42. [PMID: 16716250 DOI: 10.1016/j.bbamem.2006.02.029] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 02/23/2006] [Accepted: 02/28/2006] [Indexed: 11/27/2022]
Abstract
The cationic antimicrobial peptide PGLa is electrostatically attracted to bacterial membranes, binds as an amphiphilic alpha-helix, and is thus able to permeabilize the lipid bilayer. Using solid state (2)H-NMR of non-perturbing Ala-d(3) labels on the peptide, we have characterized the helix alignment under a range of different conditions. Even at a very high peptide-to-lipid ratio (1:20) and in the presence of negatively charged lipids, there was no indication of a toroidal wormhole structure. Instead, PGLa re-aligns from a surface-bound S-state to an obliquely tilted T-state, which is presumably dimeric. An intermediate structure half-way between the S- and T-state was observed in fully hydrated multilamellar DMPC vesicles at 1:50, suggesting a fast exchange between the two states on the time scale of >50 kHz. We demonstrate that this equilibrium is shifted from the S- towards the T-state either upon (i) increasing the peptide concentration, (ii) adding negatively charged DMPG, or (iii) decreasing the level of hydration. The threshold concentration for re-alignment in DMPC is found to be between 1:200 and 1:100 in oriented samples at 96% humidity. In fully hydrated multilamellar DMPC vesicles, it shifts to an effective peptide-to-lipid ratio of 1:50 as some peptides are able to escape into the bulk water phase.
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Affiliation(s)
- Pierre Tremouilhac
- Institute for Biological Interfaces, Forschungszentrum Karlsruhe, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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36
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Kandasamy SK, Larson RG. Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch. Biophys J 2006; 90:2326-43. [PMID: 16428278 PMCID: PMC1403172 DOI: 10.1529/biophysj.105.073395] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrophobic mismatch, which is the difference between the hydrophobic length of trans-membrane segments of a protein and the hydrophobic width of the surrounding lipid bilayer, is known to play a role in membrane protein function. We have performed molecular dynamics simulations of trans-membrane KALP peptides (sequence: GKK(LA)nLKKA) in phospholipid bilayers to investigate hydrophobic mismatch alleviation mechanisms. By varying systematically the length of the peptide (KALP15, KALP19, KALP23, KALP27, and KALP31) and the lipid hydrophobic length (DLPC, DMPC, and DPPC), a wide range of mismatch conditions were studied. Simulations of durations of 50-200 ns show that under positive mismatch, the system alleviates the mismatch predominantly by tilting the peptide and to a smaller extent by increased lipid ordering in the immediate vicinity of the peptide. Under negative mismatch, alleviation takes place by a combination of local bilayer bending and the snorkeling of the lysine residues of the peptide. Simulations performed at a higher peptide/lipid molar ratio (1:25) reveal slower dynamics of both the peptide and lipid relative to those at a lower peptide/lipid ratio (1:128). The lysine residues have favorable interactions with specific oxygen atoms of the phospholipid headgroups, indicating the preferred localization of these residues at the lipid/water interface.
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Affiliation(s)
- Senthil K Kandasamy
- Chemical Engineering Department, University of Michigan, Ann Arbor, Michigan, USA
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Cegelski L, Rice CV, O'Connor RD, Caruano AL, Tochtrop GP, Cai ZY, Covey DF, Schaefer J. Mapping the locations of estradiol and potent neuroprotective analogues in phospholipid bilayers by REDOR. Drug Dev Res 2006. [DOI: 10.1002/ddr.20048] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Strandberg E, Wadhwani P, Tremouilhac P, Dürr UHN, Ulrich AS. Solid-state NMR analysis of the PGLa peptide orientation in DMPC bilayers: structural fidelity of 2H-labels versus high sensitivity of 19F-NMR. Biophys J 2005; 90:1676-86. [PMID: 16339890 PMCID: PMC1367318 DOI: 10.1529/biophysj.105.073858] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structure and alignment of the amphipathic alpha-helical antimicrobial peptide PGLa in a lipid membrane is determined with high accuracy by solid-state 2H-NMR. Orientational constraints are derived from a series of eight alanine-3,3,3-d3-labeled peptides, in which either a native alanine is nonperturbingly labeled (4x), or a glycine (2x) or isoleucine (2x) is selectively replaced. The concentration dependent realignment of the alpha-helix from the surface-bound "S-state" to a tilted "T-state" by 30 degrees is precisely calculated using the quadrupole splittings of the four nonperturbing labels as constraints. The remaining, potentially perturbing alanine-3,3,3-d3 labels show only minor deviations from the unperturbed peptide structure and help to single out the unique solution. Comparison with previous 19F-NMR constraints from 4-CF3-phenylglycine labels shows that the structure and orientation of the PGLa peptide is not much disturbed even by these bulky nonnatural side chains, which contain CF3 groups that offer a 20-fold better NMR sensitivity than CD3 groups.
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Affiliation(s)
- Erik Strandberg
- Institute for Biological Interfaces, Forschungszentrum Karlsruhe, 76344 Eggenstein-Leopoldshafen, Germany
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Glaser RW, Sachse C, Dürr UHN, Wadhwani P, Afonin S, Strandberg E, Ulrich AS. Concentration-dependent realignment of the antimicrobial peptide PGLa in lipid membranes observed by solid-state 19F-NMR. Biophys J 2005; 88:3392-7. [PMID: 15695635 PMCID: PMC1305486 DOI: 10.1529/biophysj.104.056424] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The membrane-disruptive antimicrobial peptide PGLa is found to change its orientation in a dimyristoyl-phosphatidylcholine bilayer when its concentration is increased to biologically active levels. The alignment of the alpha-helix was determined by highly sensitive solid-state NMR measurements of (19)F dipolar couplings on CF(3)-labeled side chains, and supported by a nonperturbing (15)N label. At a low peptide/lipid ratio of 1:200 the amphiphilic peptide resides on the membrane surface in the so-called S-state, as expected. However, at high peptide concentration (>/=1:50 molar ratio) the helix axis changes its tilt angle from approximately 90 degrees to approximately 120 degrees , with the C-terminus pointing toward the bilayer interior. This tilted "T-state" represents a novel feature of antimicrobial peptides, which is distinct from a membrane-inserted I-state. At intermediate concentration, PGLa is in exchange between the S- and T-state in the timescale of the NMR experiment. In both states the peptide molecules undergo fast rotation around the membrane normal in liquid crystalline bilayers; hence, large peptide aggregates do not form. Very likely the obliquely tilted T-state represents an antiparallel dimer of PGLa that is formed in the membrane at increasing concentration.
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Affiliation(s)
- Ralf W Glaser
- Institute of Biochemistry and Biophysics, University of Jena, Jena, Germany
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Abstract
Antimicrobial peptides (AMPs) of innate origin are agents of the most ancient form of defense systems. They can be found in a wide variety of species ranging from bacteria through insects to humans. Through the course of evolution, host organisms developed arsenals of AMPs that protect them against a large variety of invading pathogens including both Gram-negative and Gram-positive bacteria. At a time of increasing bacterial resistance, AMPs have been the focus of investigation in a number of laboratories worldwide. Although recent studies show that some of the peptides are likely to have intracellular targets, the vast majority of AMPs appear to act by permeabilization of the bacterial cell membrane. Their activity and selectivity are governed by the physicochemical parameters of the peptide chains as well as the properties of the membrane system itself. In this review, we will summarize some of the recent developments that provide us with a better understanding of the mode of action of this unique family of antibacterial agents. Particular attention will be given to the determinants of AMP-lipid bilayer interactions as well as to the different pore formation mechanisms. The emphasis will be on linear AMPs but representatives of cysteine-bridged AMPs will also be discussed.
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Affiliation(s)
- Orsolya Toke
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Bernard GM, Miskolzie M, Kotovych G, Wasylishen RE. A solid-state NMR investigation of orexin-B. CAN J CHEM 2004. [DOI: 10.1139/v04-131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Some key aspects of the secondary structure of solid orexin-B, a 28 amino-acid peptide, have been investigated by solid-state NMR spectroscopy. The 13C15N dipolar coupling between the carbonyl carbon of Leu11 and the nitrogen of Leu15, as determined by rotational echo double resonance (REDOR) experiments, is 35 Hz, indicating that these nuclei are separated by approximately 4.5 Å. This distance is consistent with the α-helical structure determined for this segment of orexin-B by solution NMR measurements. REDOR measurements of the dipolar coupling between the carbonyl carbon of Ala17 and the nitrogen of Ala22 support the contention in an earlier solution NMR study that a bend exists between the two α helices of orexin-B. However, in the solid state the internuclear distance (6.4 Å) is significantly greater than that observed for orexin-B in aqueous solution. In addition to the distance measurements, the principal components of the amide carbonyl carbon chemical shift (CS) tensors for Leu11 and Ala17 and of the amide nitrogen CS tensors for Leu15 and Ala22 are reported. There are only minor differences between the amide carbonyl carbon CS tensors for Leu11 and Ala17 and between the nitrogen CS tensors for Leu15 and Ala22.Key words: orexin-B, solid-state NMR, REDOR, chemical shift tensors.
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Glaser RW, Ulrich AS. Susceptibility corrections in solid-state NMR experiments with oriented membrane samples. Part I: applications. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 164:104-114. [PMID: 12932462 DOI: 10.1016/s1090-7807(03)00207-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chemical shift referencing of solid-state NMR experiments on oriented membranes has to compensate for bulk magnetic susceptibility effects that are associated with the non-spherical sample shape, as described in the accompanying paper [J. Magn. Reson. 164 (2003) 115-127]. The resulting frequency deviations can be on the order of 10 ppm, which is serious for nuclei with a narrow chemical shift anisotropy such as 1H or 13C, and in some cases even 19F. Two referencing schemes are proposed here to compensate for these effects: A flat (0.4 mm) glass container with an isotropic reference molecule dissolved in a thin film of liquid is stacked on top of the oriented membrane sample. Alternatively, the intrinsic proton signal of the hydrated lipid can be used for chemical shift referencing. Further aspects related to magnetic susceptibility are discussed, such as air gaps in susceptibility-matched probeheads, the benefits of shimming, and limitations in the accuracy of orientational constraints. A biological application is illustrated by a series of experiments on the antimicrobial peptide PGLa, aimed at understanding its concentration-dependent membranolytic effect. To address a wide range of molar peptide/lipid ratios between 1:3000 and 1:8, multilayers of hydrated DMPC containing a 19F-labeled peptide were oriented between stacked glass plates. Maintaining an approximately constant amount of peptide gives rise to thick samples (18 plates) at low, and thin samples (3 plates) at high peptide/lipid ratio. Accurate referencing was critical to reveal a small but significant change over 5 ppm in the anisotropic chemical shift of the 19F label on the peptide, indicative of a change in the orientation and/or dynamics of PGLa in the membrane.
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Affiliation(s)
- Ralf W Glaser
- Institute of Molecular Biology, Friedrich-Schiller-Universität Jena, Winzerlaer Str. 10, D-07745 Jena, Germany
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