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Solid-State NMR Approaches to Study Protein Structure and Protein-Lipid Interactions. Methods Mol Biol 2019. [PMID: 31218633 DOI: 10.1007/978-1-4939-9512-7_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Solid-state NMR spectroscopy has been developed for the investigation of membrane-associated polypeptides and remains one of the few techniques to reveal high-resolution structural information in liquid-disordered phospholipid bilayers. In particular, oriented samples have been used to investigate the structure, dynamics and topology of membrane polypeptides. Much of the previous solid-state NMR work has been developed and performed on peptides but the technique is constantly expanding towards larger membrane proteins. Here, a number of protocols are presented describing among other the reconstitution of membrane proteins into oriented membranes, monitoring membrane alignment by 31P solid-state NMR spectroscopy, investigations of the protein by one- and two-dimensional 15N solid-state NMR and measurements of the lipid order parameters using 2H solid-state NMR spectroscopy. Using such methods solid-state NMR spectroscopy has revealed a detailed picture of the ensemble of both lipids and proteins and their mutual interdependence in the bilayer environment.
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Bechinger B. The SMART model: Soft Membranes Adapt and Respond, also Transiently, in the presence of antimicrobial peptides. J Pept Sci 2014; 21:346-55. [PMID: 25522713 DOI: 10.1002/psc.2729] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/21/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022]
Abstract
Biophysical and structural studies of peptide-lipid interactions, peptide topology and dynamics have changed our view on how antimicrobial peptides insert and interact with membranes. Clearly, both the peptides and the lipids are highly dynamic, change and mutually adapt their conformation, membrane penetration and detailed morphology on a local and a global level. As a consequence, the peptides and lipids can form a wide variety of supramolecular assemblies in which the more hydrophobic sequences preferentially, but not exclusively, adopt transmembrane alignments and have the potential to form oligomeric structures similar to those suggested by the transmembrane helical bundle model. In contrast, charged amphipathic sequences tend to stay intercalated at the membrane interface where they cause pronounced disruptions of the phospholipid fatty acyl packing. At increasing local or global concentrations, the peptides result in transient membrane openings, rupture and ultimately lysis. Depending on peptide-to-lipid ratio, lipid composition and environmental factors (temperature, buffer composition, ionic strength, etc.), the same peptide sequence can result in a variety of those responses. Therefore, the SMART model has been introduced to cover the full range of possibilities. With such a view in mind, novel antimicrobial compounds have been designed from amphipathic polymers, peptide mimetics, combinations of ultra-short polypeptides with hydrophobic anchors or small designer molecules.
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Affiliation(s)
- Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070, Strasbourg, France
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Pulagam LP, Steinhoff HJ. Acidic pH-Induced Membrane Insertion of Colicin A into E. coli Natural Lipids Probed by Site-Directed Spin Labeling. J Mol Biol 2013; 425:1782-94. [DOI: 10.1016/j.jmb.2013.01.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 10/27/2022]
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Aisenbrey C, Michalek M, Salnikov ES, Bechinger B. Solid-state NMR approaches to study protein structure and protein-lipid interactions. Methods Mol Biol 2013; 974:357-387. [PMID: 23404284 DOI: 10.1007/978-1-62703-275-9_16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Solid-state NMR spectroscopy has been developed for the investigation of membrane-associated polypeptides and remains one of the few techniques to reveal high-resolution structural information in liquid-disordered phospholipid bilayers. In particular, oriented samples have been used to investigate the structure, dynamics, and topology of membrane polypeptides. Much of the previous solid-state NMR work has been developed and performed on peptides, but the technique is constantly expanding towards larger membrane proteins. Here, a number of protocols are presented describing among other the reconstitution of membrane proteins into oriented membranes, monitoring membrane alignment by (31)P solid-state NMR spectroscopy; investigations of the protein by one- and two-dimensional (15)N solid-state NMR; and measurements of the lipid order parameters using (2)H solid-state NMR spectroscopy. Using such methods solid-state NMR spectroscopy has revealed a detailed picture of the ensemble of both lipids and proteins and their mutual interdependence in the bilayer environment.
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Bechinger B, Salnikov ES. The membrane interactions of antimicrobial peptides revealed by solid-state NMR spectroscopy. Chem Phys Lipids 2012; 165:282-301. [DOI: 10.1016/j.chemphyslip.2012.01.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 01/25/2012] [Accepted: 01/27/2012] [Indexed: 01/29/2023]
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Solution- and solid-state NMR studies of GPCRs and their ligands. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1462-75. [DOI: 10.1016/j.bbamem.2010.10.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Revised: 10/02/2010] [Accepted: 10/05/2010] [Indexed: 12/29/2022]
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Bechinger B, Resende JM, Aisenbrey C. The structural and topological analysis of membrane-associated polypeptides by oriented solid-state NMR spectroscopy: established concepts and novel developments. Biophys Chem 2010; 153:115-25. [PMID: 21145159 DOI: 10.1016/j.bpc.2010.11.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/05/2010] [Accepted: 11/05/2010] [Indexed: 10/18/2022]
Abstract
Solid-state NMR spectroscopy is a powerful technique for the investigation of membrane-associated peptides and proteins as well as their interactions with lipids, and a variety of conceptually different approaches have been developed for their study. The technique is unique in allowing for the high-resolution investigation of liquid disordered lipid bilayers representing well the characteristics of natural membranes. Whereas magic angle solid-state NMR spectroscopy follows approaches that are related to those developed for solution NMR spectroscopy the use of static uniaxially oriented samples results in angular constraints which also provide information for the detailed analysis of polypeptide structures. This review introduces this latter concept theoretically and provides a number of examples. Furthermore, ongoing developments combining solid-state NMR spectroscopy with information from solution NMR spectroscopy and molecular modelling as well as exploratory studies using dynamic nuclear polarization solid-state NMR will be presented.
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Affiliation(s)
- Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4 Rue Blaise Pascal, 67070 Strasbourg, France.
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Prieto L, Lazaridis T. Computational studies of colicin insertion into membranes: the closed state. Proteins 2010; 79:126-41. [PMID: 20941706 DOI: 10.1002/prot.22866] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 08/02/2010] [Accepted: 08/23/2010] [Indexed: 11/05/2022]
Abstract
Colicins are water-soluble toxins that, upon interaction with membranes, undergo a conformational change, insert, and form pores in them. Pore formation activity is localized in a bundle of 10 α-helices named the pore-forming domain (PFD). There is evidence that colicins attach to the membrane via a hydrophobic hairpin embedded in the core of the PFD. Two main models have been suggested for the membrane-bound state: penknife and umbrella, differing in regard to the orientation of the hydrophobic hairpin with respect to the membrane. The arrangement of the amphipathic helices has been described as either a compact three-dimensional structure or a two-dimensional array of loosely interacting helices on the membrane surface. Using molecular dynamics simulations with an implicit membrane model, we studied the structure and stability of the conformations proposed earlier for four colicins. We find that colicins are initially driven towards the membrane by electrostatic interactions between basic residues and the negatively charged membrane surface. They do not have a unique binding orientation, but in the predominant orientations the central hydrophobic hairpin is parallel to the membrane. In the inserted state, the estimated free energy tends to be lower for the compact arrangements of the amphipathic helix, but the more expanded ones are in better agreement with experimental distance distributions. The difference in energy between penknife and umbrella conformations is small enough for equilibrium to exist between them. Elongation of the hydrophobic hairpin helices and membrane thinning were found unable to produce stabilization of the transmembrane configuration of the hydrophobic hairpin.
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Affiliation(s)
- Lidia Prieto
- Department of Chemistry, The City College of CUNY, New York, New York 10031, USA
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Affiliation(s)
- Shi Bai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Salnikov E, Aisenbrey C, Vidovic V, Bechinger B. Solid-state NMR approaches to measure topological equilibria and dynamics of membrane polypeptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:258-65. [DOI: 10.1016/j.bbamem.2009.06.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Revised: 06/12/2009] [Accepted: 06/29/2009] [Indexed: 01/20/2023]
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Membrane association and pore formation by alpha-helical peptides. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 677:24-30. [PMID: 20687478 DOI: 10.1007/978-1-4419-6327-7_3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Membrane-active peptides exhibit antimicrobial, channel-forming and transport activities and have therefore early on been interesting targets for biophysical investigations. When the peptide-lipid interactions are studied a dynamic view emerges in which the peptides change conformation upon membrane insertion, can adopt a variety of topologies and change the macroscopic phase properties of the membrane locally or globally. Interestingly several proteins have been identified that also interact with the membrane in a dynamic fashion and where the lessons learned from peptides may add to our understanding of the ways these proteins function.
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Esteban-Martín S, Giménez D, Fuertes G, Salgado J. Orientational Landscapes of Peptides in Membranes: Prediction of 2H NMR Couplings in a Dynamic Context. Biochemistry 2009; 48:11441-8. [DOI: 10.1021/bi901017y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Santi Esteban-Martín
- Instituto de Ciencia Molecular, Universitat de València, Polígono La Coma s/n, 46980 Paterna, Valencia, Spain
| | - Diana Giménez
- Instituto de Ciencia Molecular, Universitat de València, Polígono La Coma s/n, 46980 Paterna, Valencia, Spain
| | - Gustavo Fuertes
- Instituto de Ciencia Molecular, Universitat de València, Polígono La Coma s/n, 46980 Paterna, Valencia, Spain
| | - Jesús Salgado
- Instituto de Ciencia Molecular, Universitat de València, Polígono La Coma s/n, 46980 Paterna, Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de València, C/Dr. Moliner, 50, 46100 Burjassot, Valencia, Spain
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Aisenbrey C, Prongidi-Fix L, Chenal A, Gillet D, Bechinger B. Side chain resonances in static oriented proton-decoupled 15N solid-state NMR spectra of membrane proteins. J Am Chem Soc 2009; 131:6340-1. [PMID: 19374351 DOI: 10.1021/ja900677b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-decoupled (15)N solid-state NMR spectra are used to analyze the structure, dynamics, and membrane topology of proteins uniformly labeled with (15)N. Preparation of the proteins by bacterial overexpression results in the labeling not only of the backbone amides but also of nitrogens localized within the side chains of arginine, glutamine, tryptophan, asparagines, lysines, and histidines. Most of these side chain resonances appear in the spectral region of the anisotropic backbone amides, and residual intensities have been observed also in cross-polarization spectra. In the past this issue has received little attention although it can cause ambiguities during assignment. Here we show that by combining cross-polarization and Hahn echo solid-state NMR experiments, it is possible to differentiate between side chain and backbone resonances. This is demonstrated using experimental and simulated (15)N spectra of oriented purple membranes, diphtheria toxin T domain and Bcl-x(L).
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Affiliation(s)
- Christopher Aisenbrey
- Insitut de Chimie, Universite de Strasbourg, CNRS UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg, France
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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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Lee DK, Kwon BS, Ramamoorthy A. Freezing point depression of water in phospholipid membranes: a solid-state NMR study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:13598-13604. [PMID: 18991419 PMCID: PMC2649677 DOI: 10.1021/la8023698] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Lipid-water interaction plays an important role in the properties of lipid bilayers, cryoprotectants, and membrane-associated peptides and proteins. The temperature at which water bound to lipid bilayers freezes is lower than that of free water. Here, we report a solid-state NMR investigation on the freezing point depression of water in phospholipid bilayers in the presence and absence of cholesterol. Deuterium NMR spectra at different temperatures ranging from -75 to + 10 degrees C were obtained from fully (2)H2O-hydrated POPC (1-palmitoyl-2-oleoylphosphatidylcholine) multilamellar vesicles (MLVs), prepared with and without cholesterol, to determine the freezing temperature of water and the effect of cholesterol on the freezing temperature of water in POPC bilayers. Our 2H NMR experiments reveal the motional behavior of unfrozen water molecules in POPC bilayers even at temperatures significantly below 0 degrees C and show that the presence of cholesterol further lowered the freezing temperature of water in POPC bilayers. These results suggest that in the presence of cholesterol the fluidity and dynamics of lipid bilayers can be retained even at very low temperatures as exist in the liquid crystalline phase of the lipid. Therefore, bilayer samples prepared with a cryoprotectant like cholesterol should enable the performance of multidimensional solid-state NMR experiments to investigate the structure, dynamics, and topology of membrane proteins at a very low temperature with enhanced sample stability and possibly a better sensitivity. Phosphorus-31 NMR data suggest that lipid bilayers can be aligned at low temperatures, while 15N NMR experiments demonstrate that such aligned samples can be used to enhance the signal-to-noise ratio of is 15N chemical shift spectra of a 37-residue human antimicrobial peptide, LL-37.
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Affiliation(s)
- Dong-Kuk Lee
- Department of Fine Chemistry, Seoul National University of Technology, Seoul 139-743, Korea.
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