1
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Sani MA, Rajput S, Keizer DW, Separovic F. NMR techniques for investigating antimicrobial peptides in model membranes and bacterial cells. Methods 2024; 224:10-20. [PMID: 38295893 DOI: 10.1016/j.ymeth.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/05/2024] Open
Abstract
AMPs are short, mainly cationic membrane-active peptides found in all living organism. They perform diverse roles including signaling and acting as a line of defense against bacterial infections. AMPs have been extensively investigated as templates to facilitate the development of novel antimicrobial therapeutics. Understanding the interplay between these membrane-active peptides and the lipid membranes is considered to be a significant step in elucidating the specific mechanism of action of AMPs against prokaryotic and eukaryotic cells to aid the development of new therapeutics. In this review, we have provided a brief overview of various NMR techniques commonly used for studying AMP structure and AMP-membrane interactions in model membranes and whole cells.
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Affiliation(s)
- Marc-Antoine Sani
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Sunnia Rajput
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - David W Keizer
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Frances Separovic
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia; School of Chemistry, University of Melbourne, Melbourne, VIC 3010, Australia
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2
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Clayton AHA. Spectroscopic and Microscopic Approaches for Investigating the Dynamic Interactions of Anti-microbial Peptides With Membranes and Cells. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 2:628552. [PMID: 35047900 PMCID: PMC8757865 DOI: 10.3389/fmedt.2020.628552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/30/2020] [Indexed: 11/13/2022] Open
Abstract
The emergence of microbes resistant to conventional antibiotics is a burgeoning threat to humanity with significant impacts on the health of people and on the health system itself. Antimicrobial peptides (AMPs) hold promise as potential future alternatives to conventional drugs because they form an integral part of the defense systems of other species in the animal, plant, and fungal kingdoms. To aid the design of the next generation of AMPs optimized for human use, we must first understand the mechanism of action of existing AMPs with their targets, ideally in the context of the complex landscape of the living (microbial) cell. Advances in lasers, optics, detectors, fluid dynamics and various probes has enabled the experimentalist to measure the kinetics of molecule–membrane, molecule–molecule, and molecule–cell interactions with increasing spatial and temporal resolution. The purpose of this review is to highlight studies into these dynamic interactions with a view to improving our understanding of AMP mechanisms.
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Affiliation(s)
- Andrew H A Clayton
- Cell Biophysics Laboratory, Optical Sciences Centre, Department of Physics and Astronomy, School of Science, Swinburne University of Technology, Melbourne, VIC, Australia
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3
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Silk MR, Price JR, Mohanty B, Leiros HKS, Lund BA, Thompson PE, Chalmers DK. Side-Chain Interactions in d/l Peptide Nanotubes: Studies by Crystallography, NMR Spectroscopy and Molecular Dynamics. Chemistry 2021; 27:14489-14500. [PMID: 34415083 DOI: 10.1002/chem.202102106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/07/2022]
Abstract
Our understanding of the factors affecting the stability of cyclic d/l peptide (CP) nanotubes remains underdeveloped. In this work, we investigate the impact of side chain alignment, hydrophobicity and charge on CP nanotube stability through X-ray crystallography, NMR spectroscopy and molecular dynamics (MD) simulations. We characterise the distinct CP-CP alignments that can form and identify stable and unstable dimers by MD simulation. We measure H-bond half-lives of synthesised CPs by 1 H-D exchange experiments and find good correlation with predicted CP-CP stabilities. We find that hydrophobic amino acids improve CP dimer stability but experimentally reduce solubility. Charged amino acids either increase or decrease CP dimer stability depending on the relative orientation and composition of charged groups. X-ray crystal structures are solved for two CPs, revealing non-tubular folded conformations. Ultimately, this work will assist the educated design of stable tubular structures for potential applications in biomedicine.
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Affiliation(s)
- Mitchell R Silk
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Jason R Price
- Australian Synchrotron, The Australian Nuclear Science and Technology Organisation (ANSTO), 800 Blackburn Road, Clayton, VIC, 3168, Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Bjarte A Lund
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
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4
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Solid state NMR of membrane proteins: methods and applications. Biochem Soc Trans 2021; 49:1505-1513. [PMID: 34397082 DOI: 10.1042/bst20200070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/17/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022]
Abstract
Membranes of cells are active barriers, in which membrane proteins perform essential remodelling, transport and recognition functions that are vital to cells. Membrane proteins are key regulatory components of cells and represent essential targets for the modulation of cell function and pharmacological intervention. However, novel folds, low molarity and the need for lipid membrane support present serious challenges to the characterisation of their structure and interactions. We describe the use of solid state NMR as a versatile and informative approach for membrane and membrane protein studies, which uniquely provides information on structure, interactions and dynamics of membrane proteins. High resolution approaches are discussed in conjunction with applications of NMR methods to studies of membrane lipid and protein structure and interactions. Signal enhancement in high resolution NMR spectra through DNP is discussed as a tool for whole cell and interaction studies.
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5
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Weber DK, Veglia G. A theoretical assessment of structure determination of multi-span membrane proteins by oriented sample solid-state NMR spectroscopy. Aust J Chem 2020; 73:246-251. [PMID: 33162560 DOI: 10.1071/ch19307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Oriented sample solid state NMR (OS-ssNMR) spectroscopy allows direct determination of the structure and topology of membrane proteins reconstituted into aligned lipid bilayers. While OS-ssNMR theoretically has no upper size limit, its application to multi-span membrane proteins has not been established since most studies have been restricted to single or dual span proteins and peptides. Here, we present a critical assessment of the application of this method to multi-span membrane proteins. We used molecular dynamics simulations to back-calculate [15N-1H] separated local field (SLF) spectra from a G protein-coupled receptor (GPCR) and show that fully resolved spectra can be obtained theoretically for a multi-span membrane protein with currently achievable resonance linewidths.
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Affiliation(s)
- Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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6
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Liu Y, Shi J, Tong Z, Jia Y, Yang B, Wang Z. The revitalization of antimicrobial peptides in the resistance era. Pharmacol Res 2020; 163:105276. [PMID: 33161137 DOI: 10.1016/j.phrs.2020.105276] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/14/2023]
Abstract
The antibiotic resistance crisis is becoming incredibly thorny due to the indiscriminate employment of antibiotics in agriculture and aquaculture, such as growth promoters, and the emergence of bacteria that are capable of enduring antibiotic treatment in an endless stream. Hence, to reverse this situation, vigorous efforts should be made in the process of identifying other alternative strategies with a lower frequency of resistance. Antimicrobial peptides (AMPs), originated from host defense peptides, are generally produced by a variety of organisms as defensive weapons to protect the host from other pathogenic bacteria. The unique ability of AMPs to control bacterial infections, as well as low propensity to acquire resistance, provides the basis for it to become one of the promising antibacterial substances. Herein, we present new insights into the biological functions, structural properties, distinct mechanisms of action of AMPs and their resistance determinants. Besides, we separately discuss natural and synthetic AMPs, including their source, screening pathway and antibacterial activity. Lastly, challenges and perspectives to identify novel potent AMPs are highlighted, which will expand our understanding of the chemical space of antimicrobials and provide a pipeline for discovering the next-generation of AMPs.
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Affiliation(s)
- Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009, China.
| | - Jingru Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Ziwen Tong
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Yuqian Jia
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Bingqing Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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7
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Backler F, Wang F. Switching On/Off the Intramolecular Hydrogen Bonding of 2-Methoxyphenol Conformers: An NMR Study. Aust J Chem 2020. [DOI: 10.1071/ch19600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Intramolecular hydrogen bonding of 2-methoxyphenol (2-MP, guaiacol) is studied using NMR spectroscopy combined with quantum mechanical density functional theory (DFT) calculations. The hydrogen bonding of OH⋯O and HO⋯H is switched on in the conformers of anti–syn (AS, 99.64% dominance) and anti–gauche (AG), respectively, with respect to the anti–anti (AA) conformer (without either such hydrogen bonding interactions). It confirms that the 13C and 1H NMR chemical shift of AS dominates the measured NMR spectra, as the AS conformer reproduces the measurements in CDCl3 solvent (RMSD of 1.86ppm for 13C NMR and of 0.27ppm for 1H NMR). The chemical shift of hydroxyl H(1) at 5.66 pm is identified as the fingerprint of the OH(1)⋯OCH3 hydrogen bonding in AS, as it exhibits a significant deshielding from H(1) of AA (4.24ppm) and H(1) of AG (4.38ppm) without such OH(1)⋯OCH3 hydrogen bonding. The AG conformer (C1 point group symmetry) possesses a less strong hydrogen bonding of HO⋯HCH2O, with the methoxyl group out of the aromatic phenol plane. The substituent effect of AG due to the resonance interaction of methoxyl being out of plane in a concentrated solution shifts the ortho- and para-aromatic carbons, C(3)/C(5), of the AG to ~125.05/125.44ppm from the corresponding carbons in AS at 108.81/121.60ppm. The hydrogen bonding exhibits inwards reduction of IR frequency regions of AS and AG from AA. Finally, energy decomposition analysis (EDA) indicates that there is a steric energy of 45.01kcal mol−1 between the AS and AG when different intramolecular hydrogen bonding is switched on.
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Meikle TG, Zabara A, Waddington LJ, Separovic F, Drummond CJ, Conn CE. Incorporation of antimicrobial peptides in nanostructured lipid membrane mimetic bilayer cubosomes. Colloids Surf B Biointerfaces 2017; 152:143-151. [DOI: 10.1016/j.colsurfb.2017.01.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/27/2016] [Accepted: 01/03/2017] [Indexed: 11/28/2022]
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9
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Grau-Campistany A, Strandberg E, Wadhwani P, Rabanal F, Ulrich AS. Extending the Hydrophobic Mismatch Concept to Amphiphilic Membranolytic Peptides. J Phys Chem Lett 2016; 7:1116-1120. [PMID: 26963560 DOI: 10.1021/acs.jpclett.6b00136] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A series of nine amphiphilic, pore-forming α-helical KIA peptides (KIAGKIA repeats) with lengths between 14 and 28 residues were studied by solid-state (15)N NMR to determine their alignment in oriented lipid bilayers. In a 2:1 mixture of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) with its corresponding 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine (lyso-MPC), which has a highly positive spontaneous curvature, the helix tilt angle was found to vary steadily with peptide length. The shortest peptide was aligned transmembrane and upright, while the longer ones successively became tilted away from the membrane normal. This behavior is in agreement with the hydrophobic matching concept, conceived so far only for hydrophobic helices. In 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine, with a negative spontaneous curvature, all KIA peptides remained flat on the bilayer surface, while the cylindrical DMPC lipids permitted a slight tilt. Peptide insertion thus depends critically on the intrinsic lipid curvature, and helix orientation is then fine-tuned by membrane thickness. A refined toroidal pore model is proposed.
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Affiliation(s)
- Ariadna Grau-Campistany
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona , Barcelona, Spain
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
| | - Francesc Rabanal
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona , Barcelona, Spain
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
- Institute of Organic Chemistry , KIT , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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10
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Meikle TG, Conn CE, Separovic F, Drummond CJ. Exploring the structural relationship between encapsulated antimicrobial peptides and the bilayer membrane mimetic lipidic cubic phase: studies with gramicidin A′. RSC Adv 2016. [DOI: 10.1039/c6ra13658c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Lipid based bicontinuous cubic mesophases provide a low-cost, robust membrane mimetic nanomaterial which allows for the incorporation of membrane peptides and proteins.
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Affiliation(s)
- Thomas G. Meikle
- School of Chemistry
- Bio21 Institute
- University of Melbourne
- Australia
- CSIRO Manufacturing Flagship
| | - Charlotte E. Conn
- School of Science
- College of Science, Engineering and Health
- RMIT University
- Melbourne
- Australia
| | | | - Calum J. Drummond
- CSIRO Manufacturing Flagship
- Clayton
- Australia
- School of Science
- College of Science, Engineering and Health
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11
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Opella SJ. Solid-state NMR and membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:129-37. [PMID: 25681966 PMCID: PMC4372479 DOI: 10.1016/j.jmr.2014.11.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/17/2014] [Accepted: 11/30/2014] [Indexed: 05/15/2023]
Abstract
The native environment for a membrane protein is a phospholipid bilayer. Because the protein is immobilized on NMR timescales by the interactions within a bilayer membrane, solid-state NMR methods are essential to obtain high-resolution spectra. Approaches have been developed for both unoriented and oriented samples, however, they all rest on the foundation of the most fundamental aspects of solid-state NMR, and the chemical shift and homo- and hetero-nuclear dipole-dipole interactions. Solid-state NMR has advanced sufficiently to enable the structures of membrane proteins to be determined under near-native conditions in phospholipid bilayers.
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Affiliation(s)
- Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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12
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Sani MA, Separovic F. Progression of NMR studies of membrane-active peptides from lipid bilayers to live cells. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:138-142. [PMID: 25631783 DOI: 10.1016/j.jmr.2014.11.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 11/24/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
Understanding the structure of membrane-active peptides faces many challenges associated with the development of appropriate model membrane systems as the peptide structure depends strongly on the lipid environment. This perspective provides a brief overview of the approach taken to study antimicrobial and amyloid peptides in phospholipid bilayers using oriented bilayers and magic angle spinning techniques. In particular, Boltzmann statistics REDOR and maximum entropy analysis of spinning side bands are used to analyse systems where multiple states of peptide or lipid molecules may co-exist. We propose that in future, rather than model membranes, structural studies in whole cells are feasible.
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Affiliation(s)
- M-A Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, VIC 3010, Australia
| | - F Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, VIC 3010, Australia.
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13
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Fanghänel S, Wadhwani P, Strandberg E, Verdurmen WPR, Bürck J, Ehni S, Mykhailiuk PK, Afonin S, Gerthsen D, Komarov IV, Brock R, Ulrich AS. Structure analysis and conformational transitions of the cell penetrating peptide transportan 10 in the membrane-bound state. PLoS One 2014; 9:e99653. [PMID: 24937132 PMCID: PMC4061077 DOI: 10.1371/journal.pone.0099653] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/18/2014] [Indexed: 11/18/2022] Open
Abstract
Structure analysis of the cell-penetrating peptide transportan 10 (TP10) revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan) was found to exhibit prominent characteristics of (i) amphiphilic α-helices, (ii) intrinsically disordered peptides, as well as (iii) β-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state (19)F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L- or D-enantiomer of 3-(trifluoromethyl)-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg) as a reporter group for (19)F-NMR. Using the L-epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal α-helix is embedded in the membrane with an oblique tilt angle of ∼ 55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D-CF3-Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile β-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D-CF3-Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the α-helix counteracts the tendency of the unfolded N-terminus to self-assemble into β-pleated fibrils.
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Affiliation(s)
- Susanne Fanghänel
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
| | - Parvesh Wadhwani
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Erik Strandberg
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Wouter P. R. Verdurmen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jochen Bürck
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Sebastian Ehni
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
| | - Pavel K. Mykhailiuk
- Taras Shevchenko National University of Kyiv, Chemistry Department, Kyiv, Ukraine and Enamine Ltd., Kyiv, Ukraine
| | - Sergii Afonin
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | | | - Igor V. Komarov
- Taras Shevchenko National University of Kyiv, Institute of High Technologies, Kyiv, Ukraine
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
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14
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Hansen SK, Vestergaard M, Thøgersen L, Schiøtt B, Nielsen NC, Vosegaard T. Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations. J Phys Chem B 2014; 118:5119-29. [DOI: 10.1021/jp5000304] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Sara K. Hansen
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mikkel Vestergaard
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Lea Thøgersen
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
- Center
for Membrane Pumps in Cells and Diseases, Bioinformatics Research
Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Birgit Schiøtt
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Niels Chr. Nielsen
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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15
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Opella SJ. The development of solid-state NMR of membrane proteins. BIOMEDICAL SPECTROSCOPY AND IMAGING 2014; 3:81-105. [PMID: 26069880 PMCID: PMC4461144 DOI: 10.3233/bsi-140080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Most biological functions are carried out in supramolecular assemblies. As a result of their slow reorientation in solution, these assemblies have been resistant to the widely employed solution NMR approaches. The development of solid-state NMR to first of all overcome the correlation time problem and then obtain informative high-resolution spectra of proteins in supramolecular assemblies, such as virus particles and membranes, is described here. High resolution solid-state NMR is deeply intertwined with the history of NMR, and the seminal paper was published in 1948. Although the general principles were understood by the end of the 1950s, it has taken more than fifty years for instrumentation and experimental methods to become equal to the technical problems presented by the biological assemblies of greatest interest. It is now possible to obtain atomic resolution structures of viral coat proteins in virus particles and membrane proteins in phospholipid bilayers by oriented sample solid-state NMR methods. The development of this aspect of the field of solid-state NMR is summarized in this review article.
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Affiliation(s)
- Stanley J. Opella
- Address for correspondence: Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive 307,La Jolla, California, 92093-0307 USA.,
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16
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Ion channel stability of Gramicidin A in lipid bilayers: Effect of hydrophobic mismatch. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:328-38. [DOI: 10.1016/j.bbamem.2013.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/20/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022]
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17
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Forman A, Renner M, Fujita E, Barkigia K, Evans M, Smith K, Fajer J. ESR and ENDOR Probes of Skeletal Conformations Implications for Conformations and Orientations of Chlorophylls In Vivo. Isr J Chem 2013. [DOI: 10.1002/ijch.198900009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Vostrikov VV, Mote KR, Verardi R, Veglia G. Structural dynamics and topology of phosphorylated phospholamban homopentamer reveal its role in the regulation of calcium transport. Structure 2013; 21:2119-30. [PMID: 24207128 DOI: 10.1016/j.str.2013.09.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/07/2013] [Accepted: 09/11/2013] [Indexed: 01/25/2023]
Abstract
Phospholamban (PLN) inhibits the sarco(endo)plasmic reticulum Ca²⁺-ATPase (SERCA), thereby regulating cardiac diastole. In membranes, PLN assembles into homopentamers that in both the phosphorylated and nonphosphorylated states have been proposed to form ion-selective channels. Here, we determined the structure of the phosphorylated pentamer using a combination of solution and solid-state nuclear magnetic resonance methods. We found that the pinwheel architecture of the homopentamer is preserved upon phosphorylation, with each monomer having an L-shaped conformation. The TM domains form a hydrophobic pore approximately 24 Å long and 2 Å in diameter, which is inconsistent with canonical Ca²⁺-selective channels. Phosphorylation, however, enhances the conformational dynamics of the cytoplasmic region of PLN, causing partial unwinding of the amphipathic helix. We propose that PLN oligomers act as storage for active monomers, keeping SERCA function within a physiological window.
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Affiliation(s)
- Vitaly V Vostrikov
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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19
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Sanderson JM. Resolving the kinetics of lipid, protein and peptide diffusion in membranes. Mol Membr Biol 2012; 29:118-43. [DOI: 10.3109/09687688.2012.678018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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20
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Grage SL, Strandberg E, Wadhwani P, Esteban-Martín S, Salgado J, Ulrich AS. Comparative analysis of the orientation of transmembrane peptides using solid-state 2H- and 15N-NMR: mobility matters. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:475-82. [DOI: 10.1007/s00249-012-0801-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 02/23/2012] [Accepted: 03/06/2012] [Indexed: 02/01/2023]
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21
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Nomura K, Lintuluoto M, Morigaki K. Hydration and temperature dependence of 13C and 1H NMR spectra of the DMPC phospholipid membrane and complete resonance assignment of its crystalline state. J Phys Chem B 2011; 115:14991-5001. [PMID: 22044314 DOI: 10.1021/jp208958a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inhomogeneous line broadening due to conformational distributions of molecules is one of the troublesome problems in solid-state NMR spectroscopy. The best possible way to avoid it is to crystallize the sample. Here, we present a highly resolved (13)C cross-polarization (CP) magic angle spinning (MAS) NMR spectrum of the highly ordered crystalline 1,2-dimyrystoyl-sn-glycero-3-phosphocholine (DMPC) and completely assigned it using two-dimensional (2D) solid-state NMR spectra, dipolar heteronuclear correlation (HETCOR) spectra, scalar heteronuclear J coupling based chemical shift correlation (MAS-J-HMQC) spectra, and Dipolar Assisted Rotational Resonance (DARR) spectra. A comparison between assigned chemical shift values by solid-state NMR in this study and the calculated chemical shift values for X-ray crystal DMPC structures shows good agreement, indicating that the two isomers in the crystalline DMPC take the same conformation as the X-ray crystal structure. The phase diagram of the low hydration level of DMPC (3 ≤ n(W) ≤ 12) determined by (1)H and (13)C NMR spectra indicates that DMPC takes a crystalline state only in a very narrow region around n(W) = 4 and T < 313 K. These findings provide us with conformational information on crystalline DMPC and the physical properties of DMPC at a low hydration level and can possibly help us obtain a highly resolved solid-state NMR spectrum of microcrystalline membrane-associated protein samples.
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Affiliation(s)
- Kaoru Nomura
- Suntory Foundation for Life Sciences, Bioorganic Research Institute, Mishima-Gun, Osaka, Japan.
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22
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Modeling the membrane environment for membrane proteins. Biophys J 2011; 100:2073-4; author reply 2075. [PMID: 21504744 DOI: 10.1016/j.bpj.2011.02.058] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/01/2011] [Accepted: 02/25/2011] [Indexed: 11/24/2022] Open
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23
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Wang C, Teng Q, Cross TA. Solid-state C NMR spectroscopy of a C carbonyl-labeled polypeptide. Biophys J 2010; 61:1550-6. [PMID: 19431834 DOI: 10.1016/s0006-3495(92)81959-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
High resolution structural elucidation of macromolecular structure by solid-state nuclear magnetic resonance requires the preparation of uniformly aligned samples that are isotopically labeled. In addition, to use the chemical shift interaction as a high resolution constraint requires an in situ tensor characterization for each site of interest. For (13)C in the peptide backbone, this characterization is complicated by the presence of dipolar coupled (14)N from the peptide bond. Here the (13)C(1)-Gly(2) site in gramicidin A is studied both as a dry powder and in a fully hydrated lipid bilayer environment. Linewidths reported for the oriented samples are a factor of five narrower than those reported elsewhere, and previous misinterpretations of the linewidths are corrected. The observed frequency from oriented samples is shown to be consistent with the recently determined structure for this site in the gramicidin backbone. It is also shown that, whereas a dipolar coupling between (13)C and (14)N is apparent in dry preparations of the polypeptide, in a hydrated bilayer the dipolar coupling is absent, presumably due to a ;self-decoupling' mechanism.
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Affiliation(s)
- C Wang
- Department of Chemistry and the Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-3006
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24
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Maisch D, Wadhwani P, Afonin S, Böttcher C, Koksch B, Ulrich AS. Chemical labeling strategy with (R)- and (S)-trifluoromethylalanine for solid state 19F NMR analysis of peptaibols in membranes. J Am Chem Soc 2010; 131:15596-7. [PMID: 19827760 DOI: 10.1021/ja9067595] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Substitution of a single Aib-residue in a peptaibol with (R)- and (S)-trifluoromethylalanine yields two local orientational constraints theta by solid state (19)F NMR. The structure of the membrane-perturbing antibiotic alamethicin in DMPC bilayers was analyzed in terms of two angles tau and rho from six such constraints, showing that the N-terminus (up to a kink at Pro14) is folded as an alpha-helix, tilted away from the membrane normal by 8 degrees, and assembled as an oligomer. The new (19)F NMR label CF(3)-Ala has thus been demonstrated to be highly sensitive, virtually unperturbing, and ideally suited to characterize peptaibols in membranes.
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Affiliation(s)
- Daniel Maisch
- Karlsruhe Institute of Technology, Institut für Organische Chemie, Fritz-Haber-Weg 6, 76133 Karlsruhe, Germany
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25
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Can antimicrobial peptides scavenge around a cell in less than a second? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:228-34. [DOI: 10.1016/j.bbamem.2009.08.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 08/19/2009] [Accepted: 08/31/2009] [Indexed: 11/20/2022]
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26
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Sherman PJ, Jackway RJ, Gehman JD, Praporski S, McCubbin GA, Mechler A, Martin LL, Separovic F, Bowie JH. Solution Structure and Membrane Interactions of the Antimicrobial Peptide Fallaxidin 4.1a: An NMR and QCM Study. Biochemistry 2009; 48:11892-901. [DOI: 10.1021/bi901668y] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Patrick J. Sherman
- Department of Chemistry, The University of Adelaide, South Australia 5005, Australia
| | - Rebecca J. Jackway
- Department of Chemistry, The University of Adelaide, South Australia 5005, Australia
| | - John D. Gehman
- School of Chemistry, Bio21 Institute, University of Melbourne, Victoria 3010, Australia
| | | | | | - Adam Mechler
- School of Chemistry, Monash University, Victoria 3800, Australia
| | | | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Victoria 3010, Australia
| | - John H. Bowie
- Department of Chemistry, The University of Adelaide, South Australia 5005, Australia
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27
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Esteban-Martín S, Strandberg E, Salgado J, Ulrich AS. Solid state NMR analysis of peptides in membranes: Influence of dynamics and labeling scheme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:252-7. [PMID: 19715662 DOI: 10.1016/j.bbamem.2009.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/28/2009] [Accepted: 08/12/2009] [Indexed: 11/17/2022]
Abstract
The functional state of a membrane-active peptide is often defined by its conformation, molecular orientation, and its oligomeric state in the lipid bilayer. These "static" structural properties can be routinely studied by solid state NMR using isotope-labeled peptides. In the highly dynamic environment of a liquid crystalline biomembrane, however, the whole-body fluctuations of a peptide are also of paramount importance, although difficult to address and most often ignored. Yet it turns out that disregarding such motional averaging in calculating the molecular alignment from orientational NMR-constraints may give a misleading, if not false picture of the system. Here, we demonstrate that the reliability of a simplified static or an advanced dynamic data analysis depends critically on the choice of isotope labeling scheme used. Two distinctly different scenarios have to be considered. When the labels are placed on the side chains of a helical peptide (such as a CD(3)- or CF(3)-group attached to the C(alpha)C(beta) bond), their nuclear spin interaction tensors are very sensitive to motional averaging. If this effect is not properly accounted for, the helix tilt angle tends to be severely underestimated. At the same time, the analysis of labels in the side chains allows to extract valuable dynamical information about whole-body fluctuations of the peptide helix in the membrane. On the other hand, the alternative labeling scheme where (15)N-labels are accommodated within the peptide backbone, will yield nearly correct helix tilt angles, irrespective as to whether dynamics are taken into account or not.
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Williamson PTF, Zandomeneghi G, Barrantes FJ, Watts A, Meier BH. Structural and dynamic studies of the γ-M4 trans-membrane domain of the nicotinic acetylcholine receptor. Mol Membr Biol 2009; 22:485-96. [PMID: 16373320 DOI: 10.1080/09687860500370653] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A structural characterization of a synthetic peptide corresponding to the fourth transmembrane domain (M4-TMD) of the gamma-subunit of the nicotinic acetylcholine receptor from Torpedo californica has been undertaken. Solid-state NMR and CD spectroscopy studies indicate that upon reconstitution into lipid vesicles or magnetically aligned lipid bilayers, the synthetic M4-TMD adopts a linear alpha-helical conformation with the helix aligned within 15 degrees of the membrane normal. Furthermore, analysis of the motional averaging of anisotropic interactions present in the solid-state NMR spectra of the reconstituted peptide, indicate that the dynamics of the peptide within the bilayer are highly sensitive to the phase adopted by the lipid bilayer, providing an insight into how the interaction of lipids with this domain may play a important role in the modulation of this receptor by its lipid environment.
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29
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Kim C, Spano J, Park EK, Wi S. Evidence of pores and thinned lipid bilayers induced in oriented lipid membranes interacting with the antimicrobial peptides, magainin-2 and aurein-3.3. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1482-96. [PMID: 19409370 DOI: 10.1016/j.bbamem.2009.04.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2009] [Revised: 04/22/2009] [Accepted: 04/22/2009] [Indexed: 11/29/2022]
Abstract
Dynamic structures of supramolecular lipid assemblies, such as toroidal pores and thinned bilayers induced in oriented lipid membranes, which are interacting with membrane-acting antimicrobial peptides (AMPs), magainin-2 and aurein-3.3, were explored by 31P and 2H solid-state NMR (ssNMR) spectroscopy. Various types of phospholipid systems, such as POPC-d31, POPC-d31/POPG, and POPC-d31/cholesterol, were investigated to understand the membrane disruption mechanisms of magainin-2 and aurein-3.3 peptides at various peptide-to-lipid (P:L) ratios. The experimental lineshapes of anisotropic 31P and 2H ssNMR spectra measured on these peptide-lipid systems were simulated reasonably well by assuming the presence of supramolecular lipid assemblies, such as toroidal pores and thinned bilayers, in membranes. Furthermore, the observed decrease in the anisotropic frequency span of either 31P or 2H ssNMR spectra of oriented lipid bilayers, particularly when anionic POPG lipids are interacting with AMPs at high P:L ratios, can directly be explained by a thinned membrane surface model with fast lateral diffusive motions of lipids. The spectral analysis protocol we developed enables extraction of the lateral diffusion coefficients of lipids distributed on the curved surfaces of pores and thinned bilayers on a few nanometers scale.
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Affiliation(s)
- Chul Kim
- Department of Chemistry, Virginia Tech, Blacksburg, VA 24061, USA
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30
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Tiburu EK, Bowman AL, Struppe JO, Janero DR, Avraham HK, Makriyannis A. Solid-state NMR and molecular dynamics characterization of cannabinoid receptor-1 (CB1) helix 7 conformational plasticity in model membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1788:1159-67. [PMID: 19366584 PMCID: PMC3712639 DOI: 10.1016/j.bbamem.2009.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 01/30/2009] [Accepted: 02/02/2009] [Indexed: 11/30/2022]
Abstract
Little direct information is available regarding the influence of membrane environment on transmembrane (TM) G-protein-coupled receptor (GPCR) conformation and dynamics. The human CB1 cannabinoid receptor (hCB1) is a prominent GPCR pharmacotherapeutic target in which helix 7 appears critical to ligand recognition. We have chemically synthesized a hCB1 peptide corresponding to a segment of TM helix 7 and the entire contiguous helix 8 domain (fourth cytoplasmic loop) and reconstituted it in defined phospholipid-bilayer model membranes. Using an NMR-based strategy combined with molecular dynamics simulations, we provide the first direct experimental description of the orientation of hCB1 helix 7 in phospholipid membranes of varying thickness and the mechanism by which helix-7 conformation adjusts to avoid hydrophobic mismatch. Solid-state (15)N NMR data show that hCB1 helices 7 and 8 reconstituted into phospholipid bilayers are oriented in a TM and in-plane (i.e., parallel to the phospholipid membrane surface) fashion, respectively. TM helix orientation is influenced by the thickness of the hydrophobic membrane bilayer as well as the interaction of helix 8 with phospholipid polar headgroups. Molecular dynamics simulations show that a decrease in phospholipid chain-length induces a kink at P394 in TM helix 7 to avoid hydrophobic mismatch. Thus, the NP(X)nY motif found in hCB1 and highly conserved throughout the GPCR superfamily is important for flexing helix 7 to accommodate bilayer thickness. Dynamic modulation of hCB1-receptor TM helix conformation by its membrane environment may have general relevance to GPCR structure and function.
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Affiliation(s)
- Elvis K. Tiburu
- Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
| | - Anna L. Bowman
- Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
| | | | - David R. Janero
- Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
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31
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Kandasamy SK, Lee DK, Nanga RP, Xu J, Santos JS, Larson RG, Ramamoorthy A. Solid-state NMR and molecular dynamics simulations reveal the oligomeric ion-channels of TM2-GABAA stabilized by intermolecular hydrogen bonding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:686-95. [DOI: 10.1016/j.bbamem.2008.11.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 10/31/2008] [Accepted: 11/03/2008] [Indexed: 11/16/2022]
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Dynamics and Cleavability at the alpha-cleavage site of APP(684-726) in different lipid environments. Biophys J 2008; 95:1460-73. [PMID: 18390599 DOI: 10.1529/biophysj.108.129726] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The occurrence of late-onset Alzheimer's disease has been related to the lipid homeostasis. We tested whether the membrane lipid environment affects the dynamics and cleavability of a model peptide corresponding to the amino acid sequence 684-726 of the amyloid precursor protein APP reconstituted in liposomes. Solid-state NMR with (2)H-Ala(713), which is located within the putative transmembrane domain, suggested that the peptide observes less rotational motion in egg phosphatidylcholine (PhC) membranes than in dimyristoyl-phosphatidylcholine (DMPC) bilayers above the main phase transition temperature T(c). The residue (15)N-Ala(692), which is in the vicinity of the alpha-cleavage site, i.e., Lys(687), showed less motion after reconstitution in distearoyl-phosphatidylcholine liposomes <T(c) than in PhC, DMPC, or sphingomyelin vesicles. In all tested liposomal systems the alpha-cleavage site was accessible for hydrolysis by trypsin. However, the catalytic rate constant was higher in the PhC and DMPC than in the sphingomyelin and distearoyl-phosphatidylcholine systems. In conclusion, the dynamics of APP(684-726) on the transmembrane level as well as the motion of the alpha-cleavage site and its hydrolysis by a model enzyme are dependent on the bilayer characteristics. This could be relevant for the processing of APP in vivo.
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Vosegaard T, Bertelsen K, Pedersen JM, Thøgersen L, Schiøtt B, Tajkhorshid E, Skrydstrup T, Nielsen NC. Resolution enhancement in solid-state NMR of oriented membrane proteins by anisotropic differential linebroadening. J Am Chem Soc 2008; 130:5028-9. [PMID: 18341279 DOI: 10.1021/ja8000612] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate that a significant improvement in the spectral resolution may be achieved in solid-state NMR experiments of proteins in inhomogeneously disordered oriented lipid bilayers. Using 1H homonuclear decoupling instead of standard 1H heteronuclear decoupling, the 15N line widths may be reduced by up to seven times for such samples. For large oriented membrane proteins, such resolution enhancements may be crucial for assignment and structural interpretation.
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Affiliation(s)
- Thomas Vosegaard
- Center for Insoluble Protein Structures and Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark.
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34
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Karp ES, Tiburu EK, Abu-Baker S, Lorigan GA. The structural properties of the transmembrane segment of the integral membrane protein phospholamban utilizing 13C CPMAS, 2H, and REDOR solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:772-80. [PMID: 16839519 DOI: 10.1016/j.bbamem.2006.04.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 03/22/2006] [Accepted: 04/04/2006] [Indexed: 11/18/2022]
Abstract
Solid-state NMR spectroscopic techniques were used to investigate the secondary structure of the transmembrane peptide phospholamban (TM-PLB), a sarcoplasmic Ca(2+) regulator. (13)C cross-polarization magic angle spinning spectra of (13)C carbonyl-labeled Leu39 of TM-PLB exhibited two peaks in a pure 1-palmitoyl-2-oleoyl-phosphocholine (POPC) bilayer, each due to a different structural conformation of phospholamban as characterized by the corresponding (13)C chemical shift. The addition of a negatively charged phospholipid (1-palmitoyl-2-oleoylphosphatidylglycerol (POPG)) to the POPC bilayer stabilized TM-PLB to an alpha-helical conformation as monitored by an enhancement of the alpha-helical carbonyl (13)C resonance in the corresponding NMR spectrum. (13)C-(15)N REDOR solid-state NMR spectroscopic experiments revealed the distance between the (13)C carbonyl carbon of Leu39 and the (15)N amide nitrogen of Leu42 to be 4.2+/-0.2A indicating an alpha-helical conformation of TM-PLB with a slight deviation from an ideal 3.6 amino acid per turn helix. Finally, the quadrupolar splittings of three (2)H labeled leucines (Leu28, Leu39, and Leu51) incorporated in mechanically aligned DOPE/DOPC bilayers yielded an 11 degrees +/-5 degrees tilt of TM-PLB with respect to the bilayer normal. In addition to elucidating valuable TM-PLB secondary structure information, the solid-state NMR spectroscopic data indicates that the type of phospholipids and the water content play a crucial role in the secondary structure and folding of TM-PLB in a phospholipid bilayer.
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Affiliation(s)
- Ethan S Karp
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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35
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36
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Boland MP, Separovic F. Membrane interactions of antimicrobial peptides from Australian tree frogs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:1178-83. [PMID: 16580625 DOI: 10.1016/j.bbamem.2006.02.010] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 02/04/2006] [Accepted: 02/11/2006] [Indexed: 12/25/2022]
Abstract
The skin secretions of amphibians are rich in host defence peptides. The membrane interactions of the antimicrobial peptides, aurein 1.2, citropin 1.1 and maculatin 1.1, isolated from Australian tree frogs, are reviewed. Although all three peptides are amphipathic alpha-helices, the mode of action of these membrane-active peptides is not defined. The peptides have a net positive charge and range in length from 13 to 21 residues, with the longest, maculatin 1.1, having a proline at position 15. Interestingly, alanine substitution at Pro-15 leads to loss of activity. The effects of these peptides on phospholipid bilayers indicate different mechanisms for pore formation and lysis of model membranes, with the shorter peptides exhibiting a carpet-like mechanism and the longest peptide forming pores in phospholipid bilayer membranes.
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Affiliation(s)
- Martin P Boland
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne VIC 3010, Australia
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37
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Pulay P, Scherer EM, van der Wel PCA, Koeppe RE. Importance of tensor asymmetry for the analysis of 2H NMR spectra from deuterated aromatic rings. J Am Chem Soc 2006; 127:17488-93. [PMID: 16332101 PMCID: PMC2532822 DOI: 10.1021/ja054935x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used ab initio calculations to compute all of the tensor elements of the electric field gradient for each carbon-deuterium bond in the ring of deuterated 3-methyl-indole. Previous analyses have ignored the smaller tensor elements perpendicular to principal component Vzz which is aligned with the C-2H bond (local bond z-axis). At each ring position, the smallest element Vxx is in the molecular plane and Vyy is normal to the plane of the ring. The asymmetry parameter = (Vyy - Vxx)/Vzz ranges from 0.07 at C4 to 0.11 at C2. We used the perpendicular (off-bond) tensor elements, in concert with an improved understanding of the indole ring geometry, to analyze prototype 2H NMR spectra from well-oriented, hydrated peptide/lipid samples. For each of the four tryptophans of membrane-spanning gramicidin A (gA) channels, the inclusion of the perpendicular elements changes the deduced ring tilt by nearly 10 and increases the ring principal order parameter Szz for overall "wobble" with respect to the membrane normal (molecular z-axis). With the improved analysis, the magnitude of Szz for the outermost indole rings of Trp13 and Trp15 is indistinguishable from that observed previously for backbone atoms (0.93 +/- 0.03). For the Trp9 and Trp11 rings, which are slightly more buried within the membrane, Szz is slightly lower (0.86 +/- 0.03). The results show that the perpendicular elements are important for the detailed analysis of 2H NMR spectra from aromatic ring systems.
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Affiliation(s)
- Peter Pulay
- To whom correspondence should be addressed: Phone: 479−575−4601. Fax: 479−575−4049. E-mail: or
| | | | | | - Roger E. Koeppe
- To whom correspondence should be addressed: Phone: 479−575−4601. Fax: 479−575−4049. E-mail: or
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38
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Marcotte I, Bélanger A, Auger M. The orientation effect of gramicidin A on bicelles and Eu3+-doped bicelles as studied by solid-state NMR and FT-IR spectroscopy. Chem Phys Lipids 2006; 139:137-49. [PMID: 16413519 DOI: 10.1016/j.chemphyslip.2005.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Revised: 12/06/2005] [Accepted: 12/08/2005] [Indexed: 10/25/2022]
Abstract
We have explored the effect of gramicidin A (gA) on bicelle (Bic) orientation in the absence and presence of Eu(3+) by (31)P and (2)H NMR at different DMPC/gA ratios. FT-IR spectroscopy was used to assess the lipid chain ordering and verify the transmembrane peptide conformation. Our results show a time-dependent flipping of the bilayer normal alignment at high temperatures and high proportion of gA. The results are explained by both the diamagnetic susceptibility anisotropy of the beta(6.3) helical peptides and viscosity of the lipid mixture. The concentration effect of gramicidin on Bic/Eu(3+) is compared to that on Eu(3+)-doped DMPC liposomes. The Bic/Eu(3+) system is no longer oriented in the presence of gA and adopts a vesicular morphology while the peptide incorporation induces the formation of ellipsoidal DMPC/Eu(3+) assemblies aligned with their normal parallel to the magnetic field. The difference is explained in terms of lipid chain disorder and size of the bilayers.
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Affiliation(s)
- Isabelle Marcotte
- Département de Chimie, Centre de Recherche en Sciences et Ingénierie des Macromolécules, Université Laval, Québec, Qué., Canada G1K 7P4
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Abstract
Gramicidin channels are mini-proteins composed of two tryptophan-rich subunits. The conducting channels are formed by the transbilayer dimerization of nonconducting subunits, which are tied to the bilayer/solution interface through hydrogen bonds between the indole NH groups and the phospholipid backbone and water. The channel structure is known at atomic resolution and the channel's permeability characteristics are particularly well defined: gramicidin channels are selective for monovalent cations, with no measurable permeability to anions or polyvalent cations; ions and water move through a pore whose wall is formed by the peptide backbone; and the single-channel conductance and cation selectivity vary when the amino acid sequence is varied, even though the permeating ions make no contact with the amino acid side chains. Given the amount of experimental information that is available--for both the wild-type channels and for channels formed by amino acid-substituted gramicidin analogues--gramicidin channels provide important insights into the microphysics of ion permeation through bilayer-spanning channels. For the same reason, gramicidin channels constitute the system of choice for evaluating computational strategies for obtaining mechanistic insights into ion permeation through the complex channels formed by integral membrane proteins.
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Affiliation(s)
- Olaf S Andersen
- Weill Medical College of Cornell University, New York, NY 10021, USA.
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40
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Orädd G, Lindblom G. NMR Studies of lipid lateral diffusion in the DMPC/gramicidin D/water system: peptide aggregation and obstruction effects. Biophys J 2005; 87:980-7. [PMID: 15298904 PMCID: PMC1304505 DOI: 10.1529/biophysj.103.038828] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The PFG-NMR method has been used in macroscopically oriented bilayers to investigate the effect of the peptide gramicidin D on the lateral diffusion of dimyristoylphosphatidylcholine. By varying both the temperature (21-35 degrees C) and the gramicidin content (0-5 mol %) we have introduced solid obstacles into the lipid liquid crystalline bilayer. It was shown that the obstruction effect exerted by the peptide can be described with several different theoretical models, each based on different premises, and that the fit of the models to experimental data gave reasonable results. We found that each gramicidin molecule was surrounded by approximately one layer of bound lipids and that the obstruction from gel phase patches can be described as small solid obstacles. No evidence of linear aggregates of gramicidin, such as those reported by atomic force microscopy in the gel phase, was found.
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Affiliation(s)
- Greger Orädd
- Department of Biophysical Chemistry, Umeå University, Umeå, Sweden.
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41
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Buffy JJ, McCormick MJ, Wi S, Waring A, Lehrer RI, Hong M. Solid-state NMR investigation of the selective perturbation of lipid bilayers by the cyclic antimicrobial peptide RTD-1. Biochemistry 2004; 43:9800-12. [PMID: 15274634 DOI: 10.1021/bi036243w] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RTD-1 is a cyclic beta-hairpin antimicrobial peptide isolated from rhesus macaque leukocytes. Using (31)P, (2)H, (13)C, and (15)N solid-state NMR, we investigated the interaction of RTD-1 with lipid bilayers of different compositions. (31)P and (2)H NMR of uniaxially oriented membranes provided valuable information about how RTD-1 affects the static and dynamic disorder of the bilayer. Toward phosphatidylcholine (PC) bilayers, RTD-1 causes moderate orientational disorder independent of the bilayer thickness, suggesting that RTD-1 binds to the surface of PC bilayers without perturbing its hydrophobic core. Addition of cholesterol to the POPC membrane does not affect the orientational disorder. In contrast, binding of RTD-1 to anionic bilayers containing PC and phosphatidylglycerol lipids induces much greater orientational disorder without affecting the dynamic disorder of the membrane. These correlate with the selectivity of RTD-1 for anionic bacterial membranes as opposed to cholesterol-rich zwitterionic mammalian membranes. Line shape simulations indicate that RTD-1 induces the formation of micrometer-diameter lipid cylinders in anionic membranes. The curvature stress induced by RTD-1 may underlie the antimicrobial activity of RTD-1. (13)C and (15)N anisotropic chemical shifts of RTD-1 in oriented PC bilayers indicate that the peptide adopts a distribution of orientations relative to the magnetic field. This is most likely due to a small fraction of lipid cylinders that change the RTD-1 orientation with respect to the magnetic field. Membrane-bound RTD-1 exhibits narrow line widths in magic-angle spinning spectra, but the sideband intensities indicate rigid-limit anisotropies. These suggest that RTD-1 has a well-defined secondary structure and is likely aggregated in the membrane. These structural and dynamical features of RTD-1 differ significantly from those of PG-1, a related beta-hairpin antimicrobial peptide.
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Affiliation(s)
- Jarrod J Buffy
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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42
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Rawat SS, Kelkar DA, Chattopadhyay A. Monitoring gramicidin conformations in membranes: a fluorescence approach. Biophys J 2004; 87:831-43. [PMID: 15298892 PMCID: PMC1304493 DOI: 10.1529/biophysj.104.041715] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2004] [Accepted: 04/12/2004] [Indexed: 12/16/2022] Open
Abstract
We have monitored the membrane-bound channel and nonchannel conformations of gramicidin utilizing red-edge excitation shift (REES), and related fluorescence parameters. In particular, we have used fluorescence lifetime, polarization, quenching, chemical modification, and membrane penetration depth analysis in addition to REES measurements to distinguish these two conformations. Our results show that REES of gramicidin tryptophans can be effectively used to distinguish conformations of membrane-bound gramicidin. The interfacially localized tryptophans in the channel conformation display REES of 7 nm whereas the tryptophans in the nonchannel conformation exhibit REES of 2 nm which highlights the difference in their average environments in terms of localization in the membrane. This is supported by tryptophan penetration depth measurements using the parallax method and fluorescence lifetime and polarization measurements. Further differences in the average tryptophan microenvironments in the two conformations are brought out by fluorescence quenching experiments using acrylamide and chemical modification of the tryptophans by N-bromosuccinimide. In summary, we report novel fluorescence-based approaches to monitor conformations of this important ion channel peptide. Our results offer vital information on the organization and dynamics of the functionally important tryptophan residues in gramicidin.
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43
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Abstract
Although most antibiotics do not need metal ions for their biological activities, there are a number of antibiotics that require metal ions to function properly, such as bleomycin (BLM), streptonigrin (SN), and bacitracin. The coordinated metal ions in these antibiotics play an important role in maintaining proper structure and/or function of these antibiotics. Removal of the metal ions from these antibiotics can cause changes in structure and/or function of these antibiotics. Similar to the case of "metalloproteins," these antibiotics are dubbed "metalloantibiotics" which are the title subjects of this review. Metalloantibiotics can interact with several different kinds of biomolecules, including DNA, RNA, proteins, receptors, and lipids, rendering their unique and specific bioactivities. In addition to the microbial-originated metalloantibiotics, many metalloantibiotic derivatives and metal complexes of synthetic ligands also show antibacterial, antiviral, and anti-neoplastic activities which are also briefly discussed to provide a broad sense of the term "metalloantibiotics."
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Affiliation(s)
- Li-June Ming
- Department of Chemistry and Institute for Biomolecular Science, University of South Florida, Tampa, Florida 33620-5250, USA.
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44
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Barnham KJ, Ciccotosto GD, Tickler AK, Ali FE, Smith DG, Williamson NA, Lam YH, Carrington D, Tew D, Kocak G, Volitakis I, Separovic F, Barrow CJ, Wade JD, Masters CL, Cherny RA, Curtain CC, Bush AI, Cappai R. Neurotoxic, redox-competent Alzheimer's beta-amyloid is released from lipid membrane by methionine oxidation. J Biol Chem 2003; 278:42959-65. [PMID: 12925530 DOI: 10.1074/jbc.m305494200] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The amyloid beta peptide is toxic to neurons, and it is believed that this toxicity plays a central role in the progression of Alzheimer's disease. The mechanism of this toxicity is contentious. Here we report that an Abeta peptide with the sulfur atom of Met-35 oxidized to a sulfoxide (Met(O)Abeta) is toxic to neuronal cells, and this toxicity is attenuated by the metal chelator clioquinol and completely rescued by catalase implicating the same toxicity mechanism as reduced Abeta. However, unlike the unoxidized peptide, Met(O)Abeta is unable to penetrate lipid membranes to form ion channel-like structures, and beta-sheet formation is inhibited, phenomena that are central to some theories for Abeta toxicity. Our results show that, like the unoxidized peptide, Met(O)Abeta will coordinate Cu2+ and reduce the oxidation state of the metal and still produce H2O2. We hypothesize that Met(O)Abeta production contributes to the elevation of soluble Abeta seen in the brain in Alzheimer's disease.
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Affiliation(s)
- Kevin J Barnham
- Department of Pathology, The University of Melbourne and The Mental Health Research Institute of Victoria, Victoria 3010, Australia.
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45
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Balla MS, Bowie JH, Separovic F. Solid-state NMR study of antimicrobial peptides from Australian frogs in phospholipid membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2003; 33:109-16. [PMID: 13680211 DOI: 10.1007/s00249-003-0342-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2003] [Revised: 06/29/2003] [Accepted: 06/29/2003] [Indexed: 10/26/2022]
Abstract
Antimicrobial peptides, isolated from the dorsal glands of Australian tree frogs, possess a wide spectrum of biological activity and some are specific to certain pathogens. These peptides have the capability of disrupting bacterial membranes and lysing lipid bilayers. This study focused on the following amphibian peptides: (1) aurein 1.2, a 13-residue peptide; (2) citropin 1.1, with 16 residues; and (3) maculatin 1.1, with 21 residues. The antibiotic activity and structure of these peptides have been studied and compared and possible mechanisms by which the peptides lyse bacterial membrane cells have been proposed. The peptides adopt amphipathic alpha-helical structures in the presence of lipid micelles and vesicles. Specifically 15N-labelled peptides were studied using solid-state NMR to determine their structure and orientation in model lipid bilayers. The effect of these peptides on phospholipid membranes was determined by 2H and 31P solid-state NMR techniques in order to understand the mechanisms by which they exert their biological effects that lead to the disruption of the bacterial cell membrane. Aurein 1.2 and citropin 1.1 are too short to span the membrane bilayer while the longer maculatin 1.1, which may be flexible due to the central proline, would be able to span the bilayer as a transmembrane alpha-helix. All three peptides had a peripheral interaction with phosphatidylcholine bilayers and appear to be located in the aqueous region of the membrane bilayer. It is proposed that these antimicrobial peptides have a "detergent"-like mechanism of membrane lysis.
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Affiliation(s)
- M S Balla
- School of Chemistry, University of Melbourne, 3010, VIC, Australia
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46
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Curtain CC, Ali FE, Smith DG, Bush AI, Masters CL, Barnham KJ. Metal ions, pH, and cholesterol regulate the interactions of Alzheimer's disease amyloid-beta peptide with membrane lipid. J Biol Chem 2003; 278:2977-82. [PMID: 12435742 DOI: 10.1074/jbc.m205455200] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of A beta peptides with the lipid matrix of neuronal cell membranes plays an important role in the pathogenesis of Alzheimer's disease. By using EPR and CD spectroscopy, we found that in the presence of Cu(2+) or Zn(2+), pH, cholesterol, and the length of the peptide chain influenced the interaction of these peptides with lipid bilayers. In the presence of Zn(2+), A beta 40 and A beta 42 both inserted into the bilayer over the pH range 5.5-7.5, as did A beta 42 in the presence of Cu(2+). However, A beta 40 only penetrated the lipid bilayer in the presence of Cu(2+) at pH 5.5-6.5; at higher pH there was a change in the Cu(2+) coordination sphere that inhibited membrane insertion. In the absence of the metals, insertion of both peptides only occurred at pH < 5.5. Raising cholesterol to 0.2 mol fraction of the total lipid inhibited insertion of both peptides under all conditions investigated. Membrane insertion was accompanied by the formation of alpha-helical structures. The nature of these structures was the same irrespective of the conditions used, indicating a single low energy structure for A beta in membranes. Peptides that did not insert into the membrane formed beta-sheet structures on the surface of the lipid.
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Affiliation(s)
- Cyril C Curtain
- Department of Pathology, University of Melbourne, Victoria 3052, Australia
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47
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Marcotte I, Wegener KL, Lam YH, Chia BCS, de Planque MRR, Bowie JH, Auger M, Separovic F. Interaction of antimicrobial peptides from Australian amphibians with lipid membranes. Chem Phys Lipids 2003; 122:107-20. [PMID: 12598042 DOI: 10.1016/s0009-3084(02)00182-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Solid-state NMR and CD spectroscopy were used to study the effect of antimicrobial peptides (aurein 1.2, citropin 1.1, maculatin 1.1 and caerin 1.1) from Australian tree frogs on phospholipid membranes. 31P NMR results revealed some effect on the phospholipid headgroups when the peptides interact with DMPC/DHPC (dimyristoylphosphatidylcholine/dihexanoylphosphatidylcholine) bicelles and aligned DMPC multilayers. 2H NMR showed a small effect of the peptides on the acyl chains of DMPC in bicelles or aligned multilayers, suggesting interaction with the membrane surface for the shorter peptides and partial insertion for the longer peptides. 15N NMR of selectively labelled peptides in aligned membranes and oriented CD spectra indicated an alpha-helical conformation with helix long axis approximately 50 degrees to the bilayer surface at high peptide concentrations. The peptides did not appear to insert deeply into PC membranes, which may explain why these positively charged peptides preferentially lyse bacterial rather than eucaryotic cells.
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Affiliation(s)
- Isabelle Marcotte
- Département de Chimie, Centre de Recherche en Sciences et en Ingénierie des Macromolécules, Université Laval, Québec, Québec, Canada G1K 7P4
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48
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van der Wel PCA, Strandberg E, Killian JA, Koeppe RE. Geometry and intrinsic tilt of a tryptophan-anchored transmembrane alpha-helix determined by (2)H NMR. Biophys J 2002; 83:1479-88. [PMID: 12202373 PMCID: PMC1302246 DOI: 10.1016/s0006-3495(02)73918-0] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We used solid-state deuterium NMR spectroscopy and an approach involving geometric analysis of labeled alanines (GALA method) to examine the structure and orientation of a designed synthetic hydrophobic, membrane-spanning alpha-helical peptide in phosphatidylcholine (PC) bilayers. The 19-amino-acid peptide consists of an alternating leucine and alanine core, flanked by tryptophans that serve as interfacial anchors: acetyl-GWW(LA)(6)LWWA-ethanolamine (WALP19). A single deuterium-labeled alanine was introduced at different positions within the peptide. Peptides were incorporated in oriented bilayers of dilauroyl- (di-C12:0-), dimyristoyl- (di-C14:0-), or dioleoyl- (di-C18:1(c)-) phosphatidylcholine. The NMR data fit well to a WALP19 orientation characterized by a distinctly nonzero tilt, approximately 4 degrees from the membrane normal, and rapid reorientation about the membrane normal in all three lipids. Although the orientation of WALP19 varies slightly in the different lipids, hydrophobic mismatch does not seem to be the dominant factor causing the tilt. We suggest rather that the peptide itself has an inherently preferred tilted orientation, possibly related to peptide surface characteristics or the disposition of tryptophan indole anchors relative to the lipids, the peptide backbone, and the membrane/water interface. Additionally, the data allow us to define more precisely the local alanine geometry in this membrane-spanning alpha-helix.
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Affiliation(s)
- Patrick C A van der Wel
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701 USA.
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49
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Soto M, Sotomayor C, Lissi E. Effect of gramicidin addition upon the physicochemical properties of dipalmitoyl phosphatidyl choline large unilamellar vesicles. J Photochem Photobiol A Chem 2002. [DOI: 10.1016/s1010-6030(02)00209-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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50
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Fahsel S, Pospiech EM, Zein M, Hazlet TL, Gratton E, Winter R. Modulation of concentration fluctuations in phase-separated lipid membranes by polypeptide insertion. Biophys J 2002; 83:334-44. [PMID: 12080124 PMCID: PMC1302151 DOI: 10.1016/s0006-3495(02)75173-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The lateral membrane organization and phase behavior of the binary lipid mixture DMPC (1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine) - DSPC (1,2-distearoyl-sn-glycero-3-phosphatidylcholine) without and with incorporated gramicidin D (GD) as a model biomembrane polypeptide was studied by small-angle neutron scattering, Fourier-transform infrared spectroscopy, and by two-photon excitation fluorescence microscopy on giant unilamellar vesicles. The small-angle neutron scattering method allows the detection of concentration fluctuations in the range from 1 to 200 nm. Fluorescence microscopy was used for direct visualization of the lateral lipid organization and domain shapes on a micrometer length scale including information of the lipid phase state. In the fluid-gel coexistence region of the pure binary lipid system, large-scale concentration fluctuations appear. Infrared spectral parameters were used to determine the peptide conformation adopted in the different lipid phases. The data show that the structure of the temperature-dependent lipid phases is significantly altered by the insertion of 2 to 5 mol% GD. At temperatures corresponding to the gel-fluid phase coexistence region the concentration fluctuations drastically decrease, and we observe domains in the giant unilamellar vesicles, which mainly disappear by the incorporation of 2 to 5 mol% GD. Further, the lipid matrix has the ability to modulate the conformation of the inserted polypeptide. The balance between double-helical and helical dimer structures of GD depends on the phospholipid chain length and phase state. A large hydrophobic mismatch, such as in gel phase one-component DSPC bilayers, leads to an increase in population of double-helical structures. Using an effective molecular sorting mechanism, a large hydrophobic mismatch can be avoided in the DMPC-DSPC lipid mixture, which leads to significant changes in the heterogeneous lipid structure and in polypeptide conformation.
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Affiliation(s)
- S Fahsel
- University of Dortmund, Department of Chemistry, Physical Chemistry I, D-44221 Dortmund, Germany
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