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Alsaker NE, Halskau Ø, Haug BE, Reuter N, Nerdal W. Phospholipid Membrane Interactions of Model Ac-WL-X-LL-OH Peptides Investigated by Solid-State Nuclear Magnetic Resonance. MEMBRANES 2024; 14:105. [PMID: 38786939 PMCID: PMC11123086 DOI: 10.3390/membranes14050105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The role of aromatic amino acids in peripheral protein membrane binding has been reported to involve cation-π interactions with choline lipids. In this study, we have investigated the interactions of the model pentapeptide Ac-WL-X-LL-OH (where X = L, Y, F, or W) with the phospholipid membrane using solid-state NMR. The effect of guest residue X on the peptide-lipid interactome was complementary to the seminal report on the interfacial hydrophobicity scale by Wimley and White. We found that the phospholipids retained a lamellar phase in the presence of each of the peptides with an aromatic X residue, whereas the Leu peptide perturbed the bilayer to an extent where an additional isotropic phase was observed. The solid-state NMR 13C and 31P data provide additional information on the influence of these short peptides on the membrane that has not been previously reported. The magnitude of membrane perturbation was in the order of guest residue X = L > Y~F > W, which is consistent with the relative amino acid interfacial affinity reported by Wimley and White. Further work is, however, required to uncover the behavior of the peptide and localization in the membrane domain due to ambiguity of the 13C NMR data. We have launched efforts in this regard for the objective of better understanding the role of aromatic amino acids in peripheral membrane protein binding.
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Affiliation(s)
- Nicolai Etwin Alsaker
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway; (B.E.H.); (N.R.); (W.N.)
| | - Øyvind Halskau
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53A, N-5006 Bergen, Norway;
| | - Bengt Erik Haug
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway; (B.E.H.); (N.R.); (W.N.)
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway; (B.E.H.); (N.R.); (W.N.)
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Willy Nerdal
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway; (B.E.H.); (N.R.); (W.N.)
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2
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Kariya M, Omoto K, Nomura K, Yonezawa K, Kamikubo H, Nishino T, Inoie T, Rapenne G, Yasuhara K. Lipid cubic phase with an organic-inorganic hybrid structure formed by organoalkoxysilane lipid. Chem Commun (Camb) 2024; 60:2168-2171. [PMID: 38205510 DOI: 10.1039/d3cc05167f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
A lipid cubic phase encompassing a cross-linked siloxane structure was formed by the self-assembly of a synthetic organoalkoxysilane lipid in water. The spontaneous sol-gel reaction of the alkoxysilane moiety on the lipid head group produced an organic-inorganic hybrid material with a double gyroid Ia3d cubic structure.
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Affiliation(s)
- Miki Kariya
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
| | - Kenichiro Omoto
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
| | - Kento Yonezawa
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
- Center for Digital Green-innovation, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan
| | - Hironari Kamikubo
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
- Center for Digital Green-innovation, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan
| | - Toshio Nishino
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
| | - Tomomi Inoie
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
| | - Gwénaël Rapenne
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
- CEMES-CNRS, Université de Toulouse, CNRS, 29 Rue Marvig, F-31055 Toulouse Cedex 4, France
| | - Kazuma Yasuhara
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan.
- Center for Digital Green-innovation, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, 630-0192, Japan
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3
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Radka CD, Grace CR, Hasdemir HS, Li Y, Rodriguez CC, Rodrigues P, Oldham ML, Qayyum MZ, Pitre A, MacCain WJ, Kalathur RC, Tajkhorshid E, Rock CO. The carboxy terminus causes interfacial assembly of oleate hydratase on a membrane bilayer. J Biol Chem 2024; 300:105627. [PMID: 38211817 PMCID: PMC10847778 DOI: 10.1016/j.jbc.2024.105627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
The soluble flavoprotein oleate hydratase (OhyA) hydrates the 9-cis double bond of unsaturated fatty acids. OhyA substrates are embedded in membrane bilayers; OhyA must remove the fatty acid from the bilayer and enclose it in the active site. Here, we show that the positively charged helix-turn-helix motif in the carboxy terminus (CTD) is responsible for interacting with the negatively charged phosphatidylglycerol (PG) bilayer. Super-resolution microscopy of Staphylococcus aureus cells expressing green fluorescent protein fused to OhyA or the CTD sequence shows subcellular localization along the cellular boundary, indicating OhyA is membrane-associated and the CTD sequence is sufficient for membrane recruitment. Using cryo-electron microscopy, we solved the OhyA dimer structure and conducted 3D variability analysis of the reconstructions to assess CTD flexibility. Our surface plasmon resonance experiments corroborated that OhyA binds the PG bilayer with nanomolar affinity and we found the CTD sequence has intrinsic PG binding properties. We determined that the nuclear magnetic resonance structure of a peptide containing the CTD sequence resembles the OhyA crystal structure. We observed intermolecular NOE from PG liposome protons next to the phosphate group to the CTD peptide. The addition of paramagnetic MnCl2 indicated the CTD peptide binds the PG surface but does not insert into the bilayer. Molecular dynamics simulations, supported by site-directed mutagenesis experiments, identify key residues in the helix-turn-helix that drive membrane association. The data show that the OhyA CTD binds the phosphate layer of the PG surface to obtain bilayer-embedded unsaturated fatty acids.
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Affiliation(s)
- Christopher D Radka
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA; Department of Host Microbe Interactions, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
| | - Christy R Grace
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Hale S Hasdemir
- Theoretical and Computational Biophysics Group, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yupeng Li
- Theoretical and Computational Biophysics Group, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Carlos C Rodriguez
- Theoretical and Computational Biophysics Group, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Patrick Rodrigues
- Hartwell Center of Biotechnology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael L Oldham
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - M Zuhaib Qayyum
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Aaron Pitre
- Cell and Tissue Imaging Center, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - William J MacCain
- Department of Host Microbe Interactions, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ravi C Kalathur
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Charles O Rock
- Department of Host Microbe Interactions, St Jude Children's Research Hospital, Memphis, Tennessee, USA
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4
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Zhang Y, Ghosh U, Xie L, Holmes D, Severin KG, Weliky DP. Lipid acyl chain protrusion induced by the influenza virus hemagglutinin fusion peptide detected by NMR paramagnetic relaxation enhancement. Biophys Chem 2023; 299:107028. [PMID: 37247572 DOI: 10.1016/j.bpc.2023.107028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/29/2023] [Accepted: 04/29/2023] [Indexed: 05/31/2023]
Abstract
The glycoprotein spikes of membrane-enveloped viruses include a subunit that catalyzes fusion (joining) of the viral and target cell membranes. For influenza virus, this is subunit 2 of hemagglutinin which has a ∼ 20-residue N-terminal fusion peptide (Fp) region that binds target membrane. An outstanding question is whether there are associated membrane changes important for fusion. Several computational studies have found increased "protrusion" of lipid acyl chains near Fp, i.e. one or more chain carbons are closer to the aqueous region than the headgroup phosphorus. Protrusion may accelerate initial joining of outer leaflets of the two membranes into a stalk intermediate. In this study, higher protrusion probability in membrane with vs. without Fp is convincingly detected by larger Mn2+-associated increases in chain 13C NMR transverse relaxation rates (Γ2's). Data analysis provides a ratio Γ2,neighbor/Γ2,distant for lipids neighboring vs. more distant from the Fp. The calculated ratio depends on the number of Fp-neighboring lipids and the experimentally-derived range of 4 to 24 matches the range of increased protrusion probabilities from different simulations. For samples either with or without Fp, the Γ2 values are well-fitted by an exponential decay as the 13C site moves closer to the chain terminus. The decays correlate with free-energy of protrusion proportional to the number of protruded -CH2 groups, with free energy per -CH2 of ∼0.25 kBT. The NMR data support one major fusion role of the Fp to be much greater protrusion of lipid chains, with highest protrusion probability for chain regions closest to the headgroups.
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Affiliation(s)
- Yijin Zhang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Ujjayini Ghosh
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Li Xie
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Daniel Holmes
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Kathryn G Severin
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - David P Weliky
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.
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5
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Phyo P, Zhao X, Templeton AC, Xu W, Cheung JK, Su Y. Understanding molecular mechanisms of biologics drug delivery and stability from NMR spectroscopy. Adv Drug Deliv Rev 2021; 174:1-29. [PMID: 33609600 DOI: 10.1016/j.addr.2021.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/20/2021] [Accepted: 02/07/2021] [Indexed: 02/06/2023]
Abstract
Protein therapeutics carry inherent limitations of membrane impermeability and structural instability, despite their predominant role in the modern pharmaceutical market. Effective formulations are needed to overcome physiological and physicochemical barriers, respectively, for improving bioavailability and stability. Knowledge of membrane affinity, cellular internalization, encapsulation, and release of drug-loaded carrier vehicles uncover the structural basis for designing and optimizing biopharmaceuticals with enhanced delivery efficiency and therapeutic efficacy. Understanding stabilizing and destabilizing interactions between protein drugs and formulation excipients provide fundamental mechanisms for ensuring the stability and quality of biological products. This article reviews the molecular studies of biologics using solution and solid-state NMR spectroscopy on structural attributes pivotal to drug delivery and stability. In-depth investigation of the structure-function relationship of drug delivery systems based on cell-penetrating peptides, lipid nanoparticles and polymeric colloidal, and biophysical and biochemical stability of peptide, protein, monoclonal antibody, and vaccine, as the integrative efforts on drug product design, will be elaborated.
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Affiliation(s)
- Pyae Phyo
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Xi Zhao
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Allen C Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Jason K Cheung
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States.
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6
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Reif B, Ashbrook SE, Emsley L, Hong M. Solid-state NMR spectroscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:2. [PMID: 34368784 PMCID: PMC8341432 DOI: 10.1038/s43586-020-00002-1] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.
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Affiliation(s)
- Bernd Reif
- Technische Universität München, Department Chemie, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sharon E. Ashbrook
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie chimiques, CH-1015 Lausanne, Switzerland
| | - Mei Hong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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7
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Miao Y, Lam D, Zhuang J, Zhu J, Poget SF, Tang M. Membrane Topology of an Ion Channel Detected by Solid-State Nuclear Magnetic Resonance and Paramagnetic Effects. J Phys Chem Lett 2020; 11:9795-9801. [PMID: 33151058 DOI: 10.1021/acs.jpclett.0c02014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ion channels are often targeted by toxins or other ligands to modify their channel activities and alter ion conductance. Interactions between toxins and ion channels could result in changes in membrane insertion depth for residues close to the binding site. Paramagnetic solid-state nuclear magnetic resonance (SSNMR) has shown great potential in providing structural information on membrane samples. We used KcsA as a model ion channel to investigate how the paramagnetic effects of Mn2+ and Dy3+ ions with headgroup-modified chelator lipids would influence the SSNMR signals of membrane proteins in proteoliposomes. Spectral comparisons have shown significant changes of peak intensities for the residues in the loop or terminal regions due to paramagnetic effects corresponding to the close proximity to the membrane surface. Hence, these results demonstrate that paramagnetic SSNMR can be used to detect surface residues based on the topology and membrane insertion properties for integral membrane proteins.
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Affiliation(s)
- Yimin Miao
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Dennis Lam
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Jianqin Zhuang
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Jing Zhu
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Sebastien F Poget
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Ming Tang
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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8
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Yamamoto T, Umegawa Y, Tsuchikawa H, Hanashima S, Matsumori N, Funahashi K, Seo S, Shinoda W, Murata M. The Amphotericin B-Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly. Biochemistry 2019; 58:5188-5196. [PMID: 31793296 DOI: 10.1021/acs.biochem.9b00835] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amphotericin B (AmB) is a polyene macrolide antibiotic clinically used as an antifungal drug. Its preferential complexation with ergosterol (Erg), the major sterol of fungal membranes, leads to the formation of a barrel-stave-like ion channel across a lipid bilayer. To gain a better understanding of the mechanism of action, the mode of lipid bilayer spanning provides essential information. However, because of the lack of methodologies to observe it directly, it has not been revealed for the Erg-containing channel assembly for many years. In this study, we disclosed that the AmB-Erg complex spans a lipid bilayer with a single-molecule length, using solid-state nuclear magnetic resonance (NMR) experiments. Paramagnetic relaxation enhancement by Mn2+ residing near the surface of lipid bilayers induced the depth-dependent decay of 13C NMR signals for individual carbon atoms of AmB. We found that both terminal segments, the 41-COOH group and C38-C40 methyl groups, come close to the lipid bilayer surfaces, suggesting that the AmB-Erg complex spans a palmitoyloleoylphosphatidylcholine (POPC) bilayer with a single-molecule length. Molecular dynamics simulation experiments further confirmed the stabilization of the AmB-Erg complex as a single-length spanning complex. These results provide experimental evidence of the single-length complex incorporated in the membrane by making thinner a POPC-Erg bilayer that mimics fungal membranes.
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Affiliation(s)
- Tomoya Yamamoto
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Project Research Center for Fundamental Sciences, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Project Research Center for Fundamental Sciences, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Department of Chemistry, Graduate School of Science , Kyushu University , Fukuoka 819-0395 , Japan
| | - Kosuke Funahashi
- Department of Materials Chemistry , Nagoya University , Nagoya 464-8603 , Japan
| | - Sangjae Seo
- Department of Materials Chemistry , Nagoya University , Nagoya 464-8603 , Japan
| | - Wataru Shinoda
- Department of Materials Chemistry , Nagoya University , Nagoya 464-8603 , Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
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10
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Beyond electrostatics: Antimicrobial peptide selectivity and the influence of cholesterol-mediated fluidity and lipid chain length on protegrin-1 activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:182977. [DOI: 10.1016/j.bbamem.2019.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/11/2019] [Accepted: 04/28/2019] [Indexed: 12/31/2022]
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11
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Roos M, Mandala VS, Hong M. Determination of Long-Range Distances by Fast Magic-Angle-Spinning Radiofrequency-Driven 19F- 19F Dipolar Recoupling NMR. J Phys Chem B 2018; 122:9302-9313. [PMID: 30211552 DOI: 10.1021/acs.jpcb.8b06878] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanometer-range distances are important for restraining the three-dimensional structure and oligomeric assembly of proteins and other biological molecules. Solid-state NMR determination of protein structures typically utilizes 13C-13C and 13C-15N distance restraints, which can only be measured up to ∼7 Å because of the low gyromagnetic ratios of these nuclear spins. To extend the distance reach of NMR, one can harvest the power of 19F, whose large gyromagnetic ratio in principle allows distances up to 2 nm to be measured. However, 19F possesses large chemical shift anisotropies (CSAs) as well as large isotropic chemical shift dispersions, which pose challenges to dipolar coupling measurements. Here, we demonstrate 19F-19F distance measurements at high magnetic fields under fast magic-angle spinning (MAS) using radiofrequency-driven dipolar recoupling (RFDR). We show that 19F-19F cross-peaks for distances up to 1 nm can be readily observed in two-dimensional 19F-19F correlation spectra using less than 5 ms of RFDR mixing. This efficient 19F-19F dipolar recoupling is achieved using practically accessible MAS frequencies of 15-55 kHz, moderate 19F radio frequency field strengths, and no 1H decoupling. Experiments and simulations show that the fastest polarization transfer for aromatic fluorines with the highest distance accuracy is achieved using either fast MAS (e.g., 60 kHz) with large pulse duty cycles (>50%) or slow MAS with strong 19F pulses. Fast MAS considerably reduces relaxation losses during the RFDR π-pulse train, making finite-pulse RFDR under fast-MAS the method of choice. Under intermediate MAS frequencies (25-40 kHz) and intermediate pulse duty cycles (15-30%), the 19F CSA tensor orientation has a quantifiable effect on the polarization transfer rate; thus, the RFDR buildup curves encode both distance and orientation information. At fast MAS, the impact of CSA orientation is minimized, allowing pure distance restraints to be extracted. We further investigate how relayed transfer and dipolar truncation in multifluorine environments affect polarization transfer. This fast-MAS 19F RFDR approach is complementary to 19F spin diffusion for distance measurements and will be the method of choice under high-field fast-MAS conditions that are increasingly important for protein structure determination by solid-state NMR.
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Affiliation(s)
- Matthias Roos
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Venkata S Mandala
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Mei Hong
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
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12
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Roos M, Wang T, Shcherbakov AA, Hong M. Fast Magic-Angle-Spinning 19F Spin Exchange NMR for Determining Nanometer 19F- 19F Distances in Proteins and Pharmaceutical Compounds. J Phys Chem B 2018; 122:2900-2911. [PMID: 29486126 PMCID: PMC6312665 DOI: 10.1021/acs.jpcb.8b00310] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Internuclear distances measured using NMR provide crucial constraints of three-dimensional structures but are often restricted to about 5 Å due to the weakness of nuclear-spin dipolar couplings. For studying macromolecular assemblies in biology and materials science, distance constraints beyond 1 nm will be extremely valuable. Here we present an extensive and quantitative analysis of the feasibility of 19F spin exchange NMR for precise and robust measurements of interatomic distances up to 1.6 nm at a magnetic field of 14.1 T, under 20-40 kHz magic-angle spinning (MAS). The measured distances are comparable to those achievable from paramagnetic relaxation enhancement but have higher precision, which is better than ±1 Å for short distances and ±2 Å for long distances. For 19F spins with the same isotropic chemical shift but different anisotropic chemical shifts, intermediate MAS frequencies of 15-25 kHz without 1H irradiation accelerate spin exchange. For spectrally resolved 19F-19F spin exchange, 1H-19F dipolar recoupling significantly speeds up 19F-19F spin exchange. On the basis of data from five fluorinated synthetic, pharmaceutical, and biological compounds, we obtained two general curves for spin exchange between CF groups and between CF3 and CF groups. These curves allow 19F-19F distances to be extracted from the measured spin exchange rates after taking into account 19F chemical shifts. These results demonstrate the robustness of 19F spin exchange NMR for distance measurements in a wide range of biological and chemical systems.
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Affiliation(s)
- Matthias Roos
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Tuo Wang
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Alexander A Shcherbakov
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Mei Hong
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
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13
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Wang S, Gopinath T, Veglia G. Application of paramagnetic relaxation enhancements to accelerate the acquisition of 2D and 3D solid-state NMR spectra of oriented membrane proteins. Methods 2017; 138-139:54-61. [PMID: 29274874 DOI: 10.1016/j.ymeth.2017.12.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 12/21/2022] Open
Abstract
Oriented sample solid-state NMR (OS-ssNMR) spectroscopy is uniquely suited to determine membrane protein topology at the atomic resolution in liquid crystalline bilayers under physiological temperature. However, the inherent low sensitivity of this technique has hindered the throughput of multidimensional experiments necessary for resonance assignments and structure determination. In this work, we show that doping membrane protein bicelle preparations with paramagnetic ion chelated lipids and exploiting paramagnetic relaxation effects it is possible to accelerate the acquisition of both 2D and 3D multidimensional experiments with significant saving in time. We demonstrate the efficacy of this method for a small membrane protein, sarcolipin, reconstituted in DMPC/POPC/DHPC oriented bicelles. In particular, using Cu2+-DMPE-DTPA as a dopant, we observed a decrease of 1H T1 of sarcolipin by 2/3, allowing us to reduce the recycle delay up to 3 times. We anticipate that these new developments will enable the routine acquisition of multidimensional OS-ssNMR experiments.
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Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
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14
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Molugu TR, Lee S, Brown MF. Concepts and Methods of Solid-State NMR Spectroscopy Applied to Biomembranes. Chem Rev 2017; 117:12087-12132. [PMID: 28906107 DOI: 10.1021/acs.chemrev.6b00619] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Concepts of solid-state NMR spectroscopy and applications to fluid membranes are reviewed in this paper. Membrane lipids with 2H-labeled acyl chains or polar head groups are studied using 2H NMR to yield knowledge of their atomistic structures in relation to equilibrium properties. This review demonstrates the principles and applications of solid-state NMR by unifying dipolar and quadrupolar interactions and highlights the unique features offered by solid-state 2H NMR with experimental illustrations. For randomly oriented multilamellar lipids or aligned membranes, solid-state 2H NMR enables direct measurement of residual quadrupolar couplings (RQCs) due to individual C-2H-labeled segments. The distribution of RQC values gives nearly complete profiles of the segmental order parameters SCD(i) as a function of acyl segment position (i). Alternatively, one can measure residual dipolar couplings (RDCs) for natural abundance lipid samples to obtain segmental SCH order parameters. A theoretical mean-torque model provides acyl-packing profiles representing the cumulative chain extension along the normal to the aqueous interface. Equilibrium structural properties of fluid bilayers and various thermodynamic quantities can then be calculated, which describe the interactions with cholesterol, detergents, peptides, and integral membrane proteins and formation of lipid rafts. One can also obtain direct information for membrane-bound peptides or proteins by measuring RDCs using magic-angle spinning (MAS) in combination with dipolar recoupling methods. Solid-state NMR methods have been extensively applied to characterize model membranes and membrane-bound peptides and proteins, giving unique information on their conformations, orientations, and interactions in the natural liquid-crystalline state.
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Affiliation(s)
- Trivikram R Molugu
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Soohyun Lee
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Michael F Brown
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
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15
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Yan S, Shaw DE, Yang L, Sandham DA, Healy MP, Reilly J, Wang B. Interactions between β2-Adrenoceptor Ligands and Membrane: Atomic-Level Insights from Magic-Angle Spinning NMR. J Med Chem 2017; 60:6867-6879. [PMID: 28703592 DOI: 10.1021/acs.jmedchem.7b00205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To understand the relationship between structural properties of the β2-adrenoceptor ligands and their interactions with membranes, we have investigated the location and distribution of five β2 agonists with distinct clinical durations and onsets of action (indacaterol, two indacaterol analogues, salmeterol and formoterol) in monounsaturated model membranes using magic angle spinning NMR to measure these interactions through both 1H nuclear Overhauser enhancement (NOE) and paramagnetic relaxation enhancement (PRE) techniques. The hydrophilic aromatic groups of all five β2 agonists show maximum distribution in the lipid/water interface, but distinct location and dynamic behavior were observed for the lipophilic aromatic rings. Our study elucidates at atomic level that the hydrophobicity and substitution geometry of lipophilic groups play important roles in compound-lipid interactions.
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Affiliation(s)
- Si Yan
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - Duncan E Shaw
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - Linhong Yang
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - David A Sandham
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - Mark P Healy
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - John Reilly
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - Bing Wang
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
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16
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Liebau J, Mäler L. Immersion Depths of Lipid Carbons in Bicelles Measured by Paramagnetic Relaxation Enhancement. J Phys Chem B 2017; 121:7660-7670. [DOI: 10.1021/acs.jpcb.7b05822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jobst Liebau
- Department of Biochemistry
and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry
and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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17
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Koroloff SN, Tesch DM, Awosanya EO, Nevzorov AA. Sensitivity enhancement for membrane proteins reconstituted in parallel and perpendicular oriented bicelles obtained by using repetitive cross-polarization and membrane-incorporated free radicals. JOURNAL OF BIOMOLECULAR NMR 2017; 67:135-144. [PMID: 28205016 DOI: 10.1007/s10858-017-0090-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
Multidimensional separated local-field and spin-exchange experiments employed by oriented-sample solid-state NMR are essential for structure determination and spectroscopic assignment of membrane proteins reconstituted in macroscopically aligned lipid bilayers. However, these experiments typically require a large number of scans in order to establish interspin correlations. Here we have shown that a combination of optimized repetitive cross polarization (REP-CP) and membrane-embedded free radicals allows one to enhance the signal-to-noise ratio by factors 2.4-3.0 in the case of Pf1 coat protein reconstituted in magnetically aligned bicelles with their normals being either parallel or perpendicular to the main magnetic field. Notably, spectral resolution is not affected at the 2:1 radical-to-protein ratio. Spectroscopic assignment of Pf1 coat protein in the parallel bicelles has been established as an illustration of the method. The proposed methodology will advance applications of oriented-sample NMR technique when applied to samples containing smaller quantities of proteins and three-dimensional experiments.
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Affiliation(s)
- Sophie N Koroloff
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Deanna M Tesch
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
- Shaw University, 118 E. South Street, Raleigh, NC, 27601, USA
| | - Emmanuel O Awosanya
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA.
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18
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Combining NMR Spectroscopy and Molecular Dynamics Simulation to Investigate the Structure and Dynamics of Membrane-Associated Proteins. SPRINGER SERIES IN BIOPHYSICS 2017. [DOI: 10.1007/978-3-319-66601-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Wang T, Chen Y, Tabuchi A, Cosgrove DJ, Hong M. The Target of β-Expansin EXPB1 in Maize Cell Walls from Binding and Solid-State NMR Studies. PLANT PHYSIOLOGY 2016; 172:2107-2119. [PMID: 27729469 PMCID: PMC5129719 DOI: 10.1104/pp.16.01311] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/07/2016] [Indexed: 05/18/2023]
Abstract
The wall-loosening actions of β-expansins are known primarily from studies of EXPB1 extracted from maize (Zea mays) pollen. EXPB1 selectively loosens cell walls (CWs) of grasses, but its specific binding target is unknown. We characterized EXPB1 binding to sequentially extracted maize CWs, finding that the protein primarily binds glucuronoarabinoxylan (GAX), the major matrix polysaccharide in grass CWs. This binding is strongly reduced by salts, indicating that it is predominantly electrostatic in nature. For direct molecular evidence of EXPB1 binding, we conducted solid-state nuclear magnetic resonance experiments using paramagnetic relaxation enhancement (PRE), which is sensitive to distances between unpaired electrons and nuclei. By mixing 13C-enriched maize CWs with EXPB1 functionalized with a Mn2+ tag, we measured Mn2+-induced PRE Strong 1H and 13C PREs were observed for the carboxyls of GAX, followed by more moderate PREs for carboxyl groups in homogalacturonan and rhamnogalacturonan-I, indicating that EXPB1 preferentially binds GAX In contrast, no PRE was observed for cellulose, indicating very weak interaction of EXPB1 with cellulose. Dynamics experiments show that EXPB1 changes GAX mobility in a complex manner: the rigid fraction of GAX became more rigid upon EXPB1 binding while the dynamic fraction became more mobile. Combining these data with previous results, we propose that EXPB1 loosens grass CWs by disrupting noncovalent junctions between highly substituted GAX and GAX of low substitution, which binds cellulose. This study provides molecular evidence of β-expansin's target in grass CWs and demonstrates a new strategy for investigating ligand binding for proteins that are difficult to express heterologously.
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Affiliation(s)
- Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Yuning Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Akira Tabuchi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Daniel J Cosgrove
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
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20
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Yao H, Lee M, Liao SY, Hong M. Solid-State Nuclear Magnetic Resonance Investigation of the Structural Topology and Lipid Interactions of a Viral Fusion Protein Chimera Containing the Fusion Peptide and Transmembrane Domain. Biochemistry 2016; 55:6787-6800. [DOI: 10.1021/acs.biochem.6b00568] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hongwei Yao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Myungwoon Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shu-Yu Liao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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21
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Liao SY, Lee M, Wang T, Sergeyev IV, Hong M. Efficient DNP NMR of membrane proteins: sample preparation protocols, sensitivity, and radical location. JOURNAL OF BIOMOLECULAR NMR 2016; 64:223-37. [PMID: 26873390 PMCID: PMC4826309 DOI: 10.1007/s10858-016-0023-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 02/07/2016] [Indexed: 05/04/2023]
Abstract
Although dynamic nuclear polarization (DNP) has dramatically enhanced solid-state NMR spectral sensitivities of many synthetic materials and some biological macromolecules, recent studies of membrane-protein DNP using exogenously doped paramagnetic radicals as polarizing agents have reported varied and sometimes surprisingly limited enhancement factors. This motivated us to carry out a systematic evaluation of sample preparation protocols for optimizing the sensitivity of DNP NMR spectra of membrane-bound peptides and proteins at cryogenic temperatures of ~110 K. We show that mixing the radical with the membrane by direct titration instead of centrifugation gives a significant boost to DNP enhancement. We quantify the relative sensitivity enhancement between AMUPol and TOTAPOL, two commonly used radicals, and between deuterated and protonated lipid membranes. AMUPol shows ~fourfold higher sensitivity enhancement than TOTAPOL, while deuterated lipid membrane does not give net higher sensitivity for the membrane peptides than protonated membrane. Overall, a ~100 fold enhancement between the microwave-on and microwave-off spectra can be achieved on lipid-rich membranes containing conformationally disordered peptides, and absolute sensitivity gains of 105-160 can be obtained between low-temperature DNP spectra and high-temperature non-DNP spectra. We also measured the paramagnetic relaxation enhancement of lipid signals by TOTAPOL and AMUPol, to determine the depths of these two radicals in the lipid bilayer. Our data indicate a bimodal distribution of both radicals, a surface-bound fraction and a membrane-bound fraction where the nitroxides lie at ~10 Å from the membrane surface. TOTAPOL appears to have a higher membrane-embedded fraction than AMUPol. These results should be useful for membrane-protein solid-state NMR studies under DNP conditions and provide insights into how biradicals interact with phospholipid membranes.
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Affiliation(s)
- Shu Y Liao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Myungwoon Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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22
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Guo JJ, Yang DP, Tian X, Vemuri VK, Yin D, Li C, Duclos RI, Shen L, Ma X, Janero DR, Makriyannis A. 17β-estradiol (E2) in membranes: Orientation and dynamic properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:344-53. [PMID: 26607010 DOI: 10.1016/j.bbamem.2015.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 11/27/2022]
Abstract
Non-genomic membrane effects of estrogens are of great interest because of the diverse biological activities they may elicit. To further our understanding of the molecular features of the interaction between estrogenic hormones and membrane bilayers, we have determined the preferred orientation, location, and dynamic properties of 17β-estradiol (E2) in two different phospholipid membrane environments using (2)H-NMR and 2D (1)H-(13)C HSQC in conjunction with molecular dynamics simulations. Unequivocal spectral assignments to specific (2)H labels were made possible by synthesizing six selectively deuterated E2 molecules. The data allow us to conclude that the E2 molecule adopts a nearly "horizontal" orientation in the membrane bilayer with its long axis essentially perpendicular to the lipid acyl-chains. All four rings of the E2 molecule are located near the membrane interface, allowing both the E2 3-OH and the 17β-OH groups to engage in hydrogen bonding and electrostatic interactions with polar phospholipid groups. The findings augment our knowledge of the molecular interactions between E2 and membrane bilayer and highlight the asymmetric nature of the dynamic motions of the rigid E2 molecule in a membrane environment.
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Affiliation(s)
- Jason J Guo
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA.
| | - De-Ping Yang
- Physics Department, College of the Holy Cross, 1 College Street, Worcester, MA 01610, USA
| | - Xiaoyu Tian
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - V Kiran Vemuri
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - Dali Yin
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - Chen Li
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - Richard I Duclos
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - Lingling Shen
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - Xiaoyu Ma
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - David R Janero
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - Alexandros Makriyannis
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA.
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23
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Schlagnitweit J, Tang M, Baias M, Richardson S, Schantz S, Emsley L. Nanostructure of Materials Determined by Relayed Paramagnetic Relaxation Enhancement. J Am Chem Soc 2015; 137:12482-5. [PMID: 26397956 PMCID: PMC4598824 DOI: 10.1021/jacs.5b08249] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 11/29/2022]
Abstract
Particle and domain sizes strongly influence the properties of materials. Here we present an NMR approach based on paramagnetic relaxation enhancement (PRE) relayed by spin diffusion (SD), which allows us to determine lengths in the nm-μm range. We demonstrate the method on multicomponent organic polymer mixtures by selectively doping one component with a paramagnetic center in order to measure the domain size in a second component. Using this approach we determine domain sizes in ethyl cellulose/hydroxypropyl cellulose film coatings in pharmaceutical controlled release formulations. Here we measure particle sizes ranging from around 50 to 200 nm.
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Affiliation(s)
- Judith Schlagnitweit
- Institut
de Science Analytiques, Centre de RMN à très hauts champs, Université de Lyon, CNRS/ENS de Lyon/UCB Lyon1, 69100 Villeurbanne, France
| | - Mingxue Tang
- Institut
de Science Analytiques, Centre de RMN à très hauts champs, Université de Lyon, CNRS/ENS de Lyon/UCB Lyon1, 69100 Villeurbanne, France
| | - Maria Baias
- Institut
de Science Analytiques, Centre de RMN à très hauts champs, Université de Lyon, CNRS/ENS de Lyon/UCB Lyon1, 69100 Villeurbanne, France
| | - Sara Richardson
- R&D
Pharmaceutical Development, AstraZeneca, 431 50 Mölndal, Sweden
| | - Staffan Schantz
- R&D
Pharmaceutical Development, AstraZeneca, 431 50 Mölndal, Sweden
| | - Lyndon Emsley
- Institut
de Science Analytiques, Centre de RMN à très hauts champs, Université de Lyon, CNRS/ENS de Lyon/UCB Lyon1, 69100 Villeurbanne, France
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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24
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Usachev KS, Efimov SV, Kolosova OA, Klochkova EA, Aganov AV, Klochkov VV. Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study. JOURNAL OF BIOMOLECULAR NMR 2015; 62:71-79. [PMID: 25786621 DOI: 10.1007/s10858-015-9920-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/14/2015] [Indexed: 06/04/2023]
Abstract
A tendency to dimerize in the presence of lipids was found for the protegrin. The dimer formation by the protegrin-1 (PG-1) is the first step for further oligomeric membrane pore formation. Generally there are two distinct model of PG-1 dimerization in either a parallel or antiparallel β-sheet. But despite the wealth of data available today, protegrin dimer structure and pore formation is still not completely understood. In order to investigate a more detailed dimerization process of PG-1 and if it will be the same for another type of protegrins, in this work we used a high-resolution NMR spectroscopy for structure determination of protegrin-3 (RGGGL-CYCRR-RFCVC-VGR) in the presence of perdeuterated DPC micelles and demonstrate that PG-3 forms an antiparallel NCCN dimer with a possible association of these dimers. This structural study complements previously published solution, solid state and computational studies of PG-1 in various environments and validate the potential of mean force simulations of PG-1 dimers and association of dimers to form octameric or decameric β-barrels.
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Affiliation(s)
- K S Usachev
- NMR Laboratory, Institute of Physics, Kazan Federal University, Kremlevskaya, 18, Kazan, 420008, Russian Federation,
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25
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Kim C. Alignment change of lipid molecules in lipid bilayers by an antimicrobial peptide protegrin-1. ANALYTICAL SCIENCE AND TECHNOLOGY 2015. [DOI: 10.5806/ast.2015.28.2.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Jaroniec CP. Structural studies of proteins by paramagnetic solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:50-9. [PMID: 25797004 PMCID: PMC4371136 DOI: 10.1016/j.jmr.2014.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/17/2014] [Indexed: 05/03/2023]
Abstract
Paramagnetism-based nuclear pseudocontact shifts and spin relaxation enhancements contain a wealth of information in solid-state NMR spectra about electron-nucleus distances on the ∼20 Å length scale, far beyond that normally probed through measurements of nuclear dipolar couplings. Such data are especially vital in the context of structural studies of proteins and other biological molecules that suffer from a sparse number of experimentally-accessible atomic distances constraining their three-dimensional fold or intermolecular interactions. This perspective provides a brief overview of the recent developments and applications of paramagnetic magic-angle spinning NMR to biological systems, with primary focus on the investigations of metalloproteins and natively diamagnetic proteins modified with covalent paramagnetic tags.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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27
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Sengupta I, Gao M, Arachchige RJ, Nadaud PS, Cunningham TF, Saxena S, Schwieters CD, Jaroniec CP. Protein structural studies by paramagnetic solid-state NMR spectroscopy aided by a compact cyclen-type Cu(II) binding tag. JOURNAL OF BIOMOLECULAR NMR 2015; 61:1-6. [PMID: 25432438 PMCID: PMC4304965 DOI: 10.1007/s10858-014-9880-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 11/18/2014] [Indexed: 05/07/2023]
Abstract
Paramagnetic relaxation enhancements (PREs) are a rich source of structural information in protein solid-state NMR spectroscopy. Here we demonstrate that PRE measurements in natively diamagnetic proteins are facilitated by a thiol-reactive compact, cyclen-based, high-affinity Cu(2+) binding tag, 1-[2-(pyridin-2-yldisulfanyl)ethyl]-1,4,7,10-tetraazacyclododecane (TETAC), that overcomes the key shortcomings associated with the use of larger, more flexible metal-binding tags. Using the TETAC-Cu(2+) K28C mutant of B1 immunoglobulin-binding domain of protein G as a model, we find that amino acid residues located within ~10 Å of the Cu(2+) center experience considerable transverse PREs leading to severely attenuated resonances in 2D (15)N-(13)C correlation spectra. For more distant residues, electron-nucleus distances are accessible via quantitative measurements of longitudinal PREs, and we demonstrate such measurements for (15)N-Cu(2+) distances up to ~20 Å.
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Affiliation(s)
- Ishita Sengupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Min Gao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rajith J. Arachchige
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Philippe S. Nadaud
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Timothy F. Cunningham
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Charles D. Schwieters
- Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Corresponding author: Christopher P. Jaroniec,
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Koers EJ, van der Cruijsen EAW, Rosay M, Weingarth M, Prokofyev A, Sauvée C, Ouari O, van der Zwan J, Pongs O, Tordo P, Maas WE, Baldus M. NMR-based structural biology enhanced by dynamic nuclear polarization at high magnetic field. JOURNAL OF BIOMOLECULAR NMR 2014; 60:157-68. [PMID: 25284462 DOI: 10.1007/s10858-014-9865-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/23/2014] [Indexed: 05/04/2023]
Abstract
Dynamic nuclear polarization (DNP) has become a powerful method to enhance spectroscopic sensitivity in the context of magnetic resonance imaging and nuclear magnetic resonance spectroscopy. We show that, compared to DNP at lower field (400 MHz/263 GHz), high field DNP (800 MHz/527 GHz) can significantly enhance spectral resolution and allows exploitation of the paramagnetic relaxation properties of DNP polarizing agents as direct structural probes under magic angle spinning conditions. Applied to a membrane-embedded K(+) channel, this approach allowed us to refine the membrane-embedded channel structure and revealed conformational substates that are present during two different stages of the channel gating cycle. High-field DNP thus offers atomic insight into the role of molecular plasticity during the course of biomolecular function in a complex cellular environment.
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Affiliation(s)
- Eline J Koers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
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29
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Koller D, Lohner K. The role of spontaneous lipid curvature in the interaction of interfacially active peptides with membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2250-9. [PMID: 24853655 DOI: 10.1016/j.bbamem.2014.05.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 01/28/2023]
Abstract
Research on antimicrobial peptides is in part driven by urgent medical needs such as the steady increase in pathogens being resistant to antibiotics. Despite the wealth of information compelling structure-function relationships are still scarce and thus the interfacial activity model has been proposed to bridge this gap. This model also applies to other interfacially active (membrane active) peptides such as cytolytic, cell penetrating or antitumor peptides. One parameter that is strongly linked to interfacial activity is the spontaneous lipid curvature, which is experimentally directly accessible. We discuss different parameters such as H-bonding, electrostatic repulsion, changes in monolayer surface area and lateral pressure that affect induction of membrane curvature, but also vice versa how membrane curvature triggers peptide response. In addition, the impact of membrane lipid composition on the formation of curved membrane structures and its relevance for diverse mode of action of interfacially active peptides and in turn biological activity are described. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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Affiliation(s)
- Daniel Koller
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Schmiedlstraße 6, A-8042 Graz, Austria.
| | - Karl Lohner
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Schmiedlstraße 6, A-8042 Graz, Austria.
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30
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Maltsev S, Hudson SM, Sahu ID, Liu L, Lorigan GA. Solid-state NMR (31)P paramagnetic relaxation enhancement membrane protein immersion depth measurements. J Phys Chem B 2014; 118:4370-7. [PMID: 24689497 PMCID: PMC4002136 DOI: 10.1021/jp500267y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 04/01/2014] [Indexed: 11/29/2022]
Abstract
Paramagnetic relaxation enhancement (PRE) is a widely used approach for measuring long-range distance constraints in biomolecular solution NMR spectroscopy. In this paper, we show that (31)P PRE solid-state NMR spectroscopy can be utilized to determine the immersion depth of spin-labeled membrane peptides and proteins. Changes in the (31)P NMR PRE times coupled with modeling studies can be used to describe the spin-label position/amino acid within the lipid bilayer and the corresponding helical tilt. This method provides valuable insight on protein-lipid interactions and membrane protein structural topology. Solid-state (31)P NMR data on the 23 amino acid α-helical nicotinic acetylcholine receptor nAChR M2δ transmembrane domain model peptide followed predicted behavior of (31)P PRE rates of the phospholipid headgroup as the spin-label moves from the membrane surface toward the center of the membrane. Residue 11 showed the smallest changes in (31)P PRE (center of the membrane), while residue 22 shows the largest (31)P PRE change (near the membrane surface), when compared to the diamagnetic control M2δ sample. This PRE SS-NMR technique can be used as a molecular ruler to measure membrane immersion depth.
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Affiliation(s)
- Sergey Maltsev
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Stephen M. Hudson
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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31
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Nomura K, Harada E, Sugase K, Shimamoto K. Solid-state NMR spectra of lipid-anchored proteins under magic angle spinning. J Phys Chem B 2014; 118:2405-13. [PMID: 24517164 DOI: 10.1021/jp4124106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solid-state NMR is a promising tool for elucidating membrane-related biological phenomena. We achieved the measurement of high-resolution solid-state NMR spectra for a lipid-anchored protein embedded in lipid bilayers under magic angle spinning (MAS). To date, solid-state NMR measurements of lipid-anchored proteins have not been accomplished due to the difficulty in supplying sufficient amount of stable isotope labeled samples in the overexpression of lipid-anchored proteins requiring complex posttranslational modification. We designed a pseudo lipid-anchored protein in which the protein component was expressed in E. coli and attached to a chemically synthesized lipid-anchor mimic. Using two types of membranes, liposomes and bicelles, we demonstrated different types of insertion procedures for lipid-anchored protein into membranes. In the liposome sample, we were able to observe the cross-polarization and the (13)C-(13)C chemical shift correlation spectra under MAS, indicating that the liposome sample can be used to analyze molecular interactions using dipolar-based NMR experiments. In contrast, the bicelle sample showed sufficient quality of spectra through scalar-based experiments. The relaxation times and protein-membrane interaction were capable of being analyzed in the bicelle sample. These results demonstrated the applicability of two types of sample system to elucidate the roles of lipid-anchors in regulating diverse biological phenomena.
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Affiliation(s)
- Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences , 1-1-1 Wakayamadai, Shimamoto-Cho, Mishima-Gun, Osaka 618-8503, Japan
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32
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33
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Tesch DM, Nevzorov AA. Sensitivity enhancement and contrasting information provided by free radicals in oriented-sample NMR of bicelle-reconstituted membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 239:9-15. [PMID: 24355622 DOI: 10.1016/j.jmr.2013.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/13/2013] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
Elucidating structure and topology of membrane proteins (MPs) is essential for unveiling functionality of these important biological constituents. Oriented-sample solid-state NMR (OS-NMR) is capable of providing such information on MPs under nearly physiological conditions. However, two dimensional OS-NMR experiments can take several days to complete due to long longitudinal relaxation times combined with the large number of scans to achieve sufficient signal sensitivity in biological samples. Here, free radicals 5-DOXYL stearic acid, TEMPOL, and CAT-1 were added to uniformly (15)N-labeled Pf1 coat protein reconstituted in DMPC/DHPC bicelles, and their effect on the longitudinal relaxation times (T1Z) was investigated. The dramatically shortened T1Z's allowed for the signal gain per unit time to be used for either: (i) up to a threefold reduction of the total experimental time at 99% magnetization recovery or (ii) obtaining up to 74% signal enhancement between the control and radical samples during constant experimental time at "optimal" relaxation delays. In addition, through OS-NMR and high-field EPR studies, free radicals were able to provide positional constraints in the bicelle system, which provide a description of the location of each residue in Pf1 coat protein within the bicellar membranes. This information can be useful in the determination of oligomerization states and immersion depths of larger membrane proteins.
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Affiliation(s)
- Deanna M Tesch
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
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34
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Kim C. A solid-state NMR study on the hydration effect on the lipid phase change in the presence of an antimicrobial peptide. ANALYTICAL SCIENCE AND TECHNOLOGY 2013. [DOI: 10.5806/ast.2013.26.6.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Xin A, Zhao Y, Yu H, Shi H, Liu H, Diao H, Zhang Y. Soluble fusion expression, characterization and localization of human β-defensin 6. Mol Med Rep 2013; 9:149-55. [PMID: 24189797 DOI: 10.3892/mmr.2013.1768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 10/10/2013] [Indexed: 11/06/2022] Open
Abstract
Human β‑defensin 6 (DEFB106) is an antimicrobial peptide expressed in the epididymis, testis and lung, which indicates that DEFB106 may be involved in innate immunity and fertility. However, as a β‑defensin, this protein has not been well characterized. Using an intein‑mediated fusion expression system, the recombinant DEFB106 was expressed and purified (yield, 3‑5 mg/l) under optimized conditions. The purified protein was characterized using mass spectrometry and circular dichroism spectroscopy. The measured molecular weight was consistent with its theoretical value and the predominant secondary structure was β‑sheet, the common structure of β‑defensin family members. The purified DEFB106 showed antimicrobial activity against not only Escherichia coli (E. coli) and Candida albicans (C. albicans) SC5314, but also Staphylococcus aureus (S. aureus) CMCC26003. Furthermore, it exhibited a high affinity for heparin and lipopolysaccharide. In addition, it was determined that native DEFB106 was located in the epididymis, bone marrow and skin. These observations may aid in the determination of the physiological and pathological functions of DEFB106.
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Affiliation(s)
- Aijie Xin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
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36
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Weingarth M, Baldus M. Solid-state NMR-based approaches for supramolecular structure elucidation. Acc Chem Res 2013; 46:2037-46. [PMID: 23586937 DOI: 10.1021/ar300316e] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Supramolecular chemistry provides structural and conformational information about complexes formed from multiple molecules. While the molecule is held together by strong intramolecular contacts like covalent bonds, supramolecular structures can be further stabilized by weaker or transient intermolecular interactions. These interactions can confer a great diversity and sensitivity to exogenous factors like temperature, pressure, or ionic strength to multimolecular arrangements. Solid-state nuclear magnetic resonance (ssNMR) can provide atomic-scale structural and dynamical information in highly disordered or heterogeneous biological systems, even in complex environments such as cellular membranes or whole cells. In these systems, the molecule of interest no longer exists as a separate unit, but it entangles with its surroundings in a dynamic interplay. Researchers have long accounted for the complexity of these intermolecular arrangements through a rather phenomenological description. But now the focus is shifting toward a detailed understanding of supramolecular structure at atomic resolution, constantly expanding our understanding of the stunning influence of the environment. In this Account, we discuss how ssNMR can help to dissect the remarkable interplay between intra- and intermolecular interactions. We describe biochemical and spectroscopic strategies that tailor ssNMR spectroscopic methods to the challenge of supramolecular structure investigation. In particular, we consider protein-protein interactions or the protein-membrane topology, and we review recent applications of these techniques. Furthermore, we summarize methods for integrating ssNMR information with other experimental techniques or computational methods, and we offer perspectives on how this overall information allows us to target increasingly large and intricate supramolecular structures of biomolecules. Advancements in ssNMR methodology and instrumentation, including the incorporation of signal enhancement methods such as dynamic nuclear polarization will further increase the potential of ssNMR spectroscopy, and together with additional developments in the field of NMR-hybrid strategies, ssNMR may become an ideal tool to study the heterogeneous, dynamic, and often transient nature of molecular interactions in complex biological systems.
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Affiliation(s)
- Markus Weingarth
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marc Baldus
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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37
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Chen WW, Yoon YJ, Leong SSJ, Kwak SK. Dimers of human β-defensins and their interactions with the POPG membrane. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.773433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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38
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Lazaridis T, He Y, Prieto L. Membrane interactions and pore formation by the antimicrobial peptide protegrin. Biophys J 2013; 104:633-42. [PMID: 23442914 DOI: 10.1016/j.bpj.2012.12.038] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Revised: 12/06/2012] [Accepted: 12/21/2012] [Indexed: 11/18/2022] Open
Abstract
Protegrin is an antimicrobial peptide with a β-hairpin structure stabilized by a pair of disulfide bonds. It has been extensively studied by solid-state NMR and computational methods. Here we use implicit membrane models to examine the binding of monomers on the surface and in the interior of the membrane, the energetics of dimerization, the binding to membrane pores, and the stability of different membrane barrel structures in pores. Our results challenge a number of conclusions based on previous experimental and theoretical work. The burial of monomers into the membrane interior is found to be unfavorable for any membrane thickness. Because of its imperfect amphipathicity, protegrin binds weakly, at most, on the surface of zwitterionic membranes. However, it binds more favorably onto toroidal pores. Anionic charge on the membrane facilitates the binding due to electrostatic interactions. Solid-state NMR results have suggested a parallel NCCN association of monomers in dimers and association of dimers to form octameric or decameric β-barrels. We find that this structure is not energetically plausible for binding to bilayers, because in this configuration the hydrophobic sides of two monomers point in opposite directions. In contrast, the antiparallel NCCN and especially the parallel NCNC octamers are stable and exhibit a favorable binding energy to the pore. The results of 100-ns simulations in explicit bilayers corroborate the higher stability of the parallel NCNC barrel compared with the parallel NCCN barrel. The ability to form pores in zwitterionic membranes provides a rationalization for the peptide's cytotoxicity. The discrepancies between our results and experiment are discussed, and new experiments are proposed to resolve them and to test the validity of the models.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY, New York, New York, USA.
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39
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Wang T, Yao H, Hong M. Determining the depth of insertion of dynamically invisible membrane peptides by gel-phase ¹H spin diffusion heteronuclear correlation NMR. JOURNAL OF BIOMOLECULAR NMR 2013; 56:139-148. [PMID: 23606274 PMCID: PMC3700645 DOI: 10.1007/s10858-013-9730-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 04/10/2013] [Indexed: 05/28/2023]
Abstract
Solid-state NMR determination of the depth of insertion of membrane peptides and proteins has so far utilized (1)H spin diffusion and paramagnetic relaxation enhancement experiments, which are typically conducted in the liquid-crystalline phase of the lipid bilayer. For membrane proteins or peptide assemblies that undergo intermediate-timescale motion in the liquid-crystalline membrane, these approaches are no longer applicable because the protein signals are broadened beyond detection. Here we show that the rigid-solid HETCOR experiment, with an additional spin diffusion period, can be used to determine the depth of proteins in gel-phase lipid membranes, where the proteins are immobilized to give high-intensity solid-state NMR spectra. Demonstration on two membrane peptides with known insertion depths shows that well-inserted peptides give rise to high lipid cross peak intensities and low water cross peaks within a modest spin diffusion mixing time, while surface-bound peptides have higher water than lipid cross peaks. Furthermore, well-inserted membrane peptides have nearly identical (1)H cross sections as the lipid chains, indicating equilibration of the peptide and lipid magnetization. Using this approach, we measured the membrane topology of the α-helical fusion peptide of the paramyxovirus, PIV5, in the anionic POPC/POPG membrane, in which the peptide undergoes intermediate-timescale motion at physiological temperature. The gel-phase HETCOR spectra indicate that the α-helical fusion peptide is well inserted into the POPC/POPG bilayer, spanning both leaflets. This insertion motif gives insight into the functional role of the α-helical PIV5 fusion peptide in virus-cell membrane fusion.
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Affiliation(s)
| | | | - M. Hong
- Corresponding author: Mei Hong Tel: 515-294-3521, Fax: 515-294-0105,
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40
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Shenkarev ZO, Paramonov AS, Lyukmanova EN, Gizatullina AK, Zhuravleva AV, Tagaev AA, Yakimenko ZA, Telezhinskaya IN, Kirpichnikov MP, Ovchinnikova TV, Arseniev AS. Peptaibol Antiamoebin I: Spatial Structure, Backbone Dynamics, Interaction with Bicelles and Lipid-Protein Nanodiscs, and Pore Formation in Context of Barrel-Stave Model. Chem Biodivers 2013; 10:838-63. [DOI: 10.1002/cbdv.201200421] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Indexed: 11/12/2022]
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41
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Choi HG, Kim C. A 2H solid-state NMR study on the lipid phase change in the presence of an antimicrobial peptide. ANALYTICAL SCIENCE AND TECHNOLOGY 2013. [DOI: 10.5806/ast.2013.26.1.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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42
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Xie L, Ghosh U, Schmick SD, Weliky DP. Residue-specific membrane location of peptides and proteins using specifically and extensively deuterated lipids and ¹³C-²H rotational-echo double-resonance solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2013; 55:11-7. [PMID: 23225071 PMCID: PMC3557618 DOI: 10.1007/s10858-012-9692-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/28/2012] [Indexed: 05/12/2023]
Abstract
Residue-specific location of peptides in the hydrophobic core of membranes was examined using (13)C-(2)H REDOR and samples in which the lipids were selectively deuterated. The transmembrane topology of the KALP peptide was validated with this approach with substantial dephasing observed for deuteration in the bilayer center and reduced or no dephasing for deuteration closer to the headgroups. Insertion of β sheet HIV and helical and β sheet influenza virus fusion peptides into the hydrophobic core of the membrane was validated in samples with extensively deuterated lipids.
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Affiliation(s)
- Li Xie
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Ujjayini Ghosh
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Scott D. Schmick
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - David P. Weliky
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
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43
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Abstract
Antimicrobial peptides (AMPs) provide a primordial source of immunity, conferring upon eukaryotic cells resistance against bacteria, protozoa, and viruses. Despite a few examples of anionic peptides, AMPs are usually relatively short positively charged polypeptides, consisting of a dozen to about a hundred amino acids, and exhibiting amphipathic character. Despite significant differences in their primary and secondary structures, all AMPs discovered to date share the ability to interact with cellular membranes, thereby affecting bilayer stability, disrupting membrane organization, and/or forming well-defined pores. AMPs selectively target infectious agents without being susceptible to any of the common pathways by which these acquire resistance, thereby making AMPs prime candidates to provide therapeutic alternatives to conventional drugs. However, the mechanisms of AMP actions are still a matter of intense debate. The structure-function paradigm suggests that a better understanding of how AMPs elicit their biological functions could result from atomic resolution studies of peptide-lipid interactions. In contrast, more strict thermodynamic views preclude any roles for three-dimensional structures. Indeed, the design of selective AMPs based solely on structural parameters has been challenging. In this chapter, we will focus on selected AMPs for which studies on the corresponding AMP-lipid interactions have helped reach an understanding of how AMP effects are mediated. We will emphasize the roles of both liquid- and solid-state NMR spectroscopy for elucidating the mechanisms of action of AMPs.
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44
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Supramolecular structure of membrane-associated polypeptides by combining solid-state NMR and molecular dynamics simulations. Biophys J 2012; 103:29-37. [PMID: 22828329 DOI: 10.1016/j.bpj.2012.05.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/30/2012] [Accepted: 05/07/2012] [Indexed: 02/02/2023] Open
Abstract
Elemental biological functions such as molecular signal transduction are determined by the dynamic interplay between polypeptides and the membrane environment. Determining such supramolecular arrangements poses a significant challenge for classical structural biology methods. We introduce an iterative approach that combines magic-angle spinning solid-state NMR spectroscopy and atomistic molecular dynamics simulations for the determination of the structure and topology of membrane-bound systems with a resolution and level of accuracy difficult to obtain by either method alone. Our study focuses on the Shaker B ball peptide that is representative for rapid N-type inactivating domains of voltage-gated K(+) channels, associated with negatively charged lipid bilayers.
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45
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Lorin A, Noël M, Provencher MÈ, Turcotte V, Cardinal S, Lagüe P, Voyer N, Auger M. Determining the mode of action involved in the antimicrobial activity of synthetic peptides: a solid-state NMR and FTIR study. Biophys J 2012; 103:1470-9. [PMID: 23062339 DOI: 10.1016/j.bpj.2012.08.055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/20/2012] [Accepted: 08/28/2012] [Indexed: 10/27/2022] Open
Abstract
We have previously shown that leucine to lysine substitution(s) in neutral synthetic crown ether containing 14-mer peptide affect the peptide structure and its ability to permeabilize bilayers. Depending on the substitution position, the peptides adopt mainly either a α-helical structure able to permeabilize dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylglycerol (DMPG) vesicles (nonselective peptides) or an intermolecular β-sheet structure only able to permeabilize DMPG vesicles (selective peptides). In this study, we have used a combination of solid-state NMR and Fourier transform infrared spectroscopy to investigate the effects of nonselective α-helical and selective intermolecular β-sheet peptides on both types of bilayers. (31)P NMR results indicate that both types of peptides interact with the headgroups of DMPC and DMPG bilayers. (2)H NMR and Fourier transform infrared results reveal an ordering of the hydrophobic core of bilayers when leakage is noted, i.e., for DMPG vesicles in the presence of both types of peptides and DMPC vesicles in the presence of nonselective peptides. However, selective peptides have no significant effect on the ordering of DMPC acyl chains. The ability of these 14-mer peptides to permeabilize lipid vesicles therefore appears to be related to their ability to increase the order of the bilayer hydrophobic core.
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Affiliation(s)
- Aurélien Lorin
- Département de chimie, PROTEO (Regroupement Québécois de Recherche sur la Fonction, la Structure et l'Ingénierie des Protéines), CERMA (Centre de Recherche sur les Matériaux Avancés), Université Laval, Québec, Québec, Canada
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46
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Su Y, Hu F, Hong M. Paramagnetic Cu(II) for probing membrane protein structure and function: inhibition mechanism of the influenza M2 proton channel. J Am Chem Soc 2012; 134:8693-702. [PMID: 22519936 DOI: 10.1021/ja3026328] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Paramagnetic Cu(II) ions enhance nuclear spin relaxation in a distance-dependent fashion and can be used as a structural probe of proteins. Cu(II) can also serve as a functionally important ligand in proteins. Here we investigate the structural basis of Cu(II) inhibition of the influenza M2 proton channel through Cu(II)-induced paramagnetic relaxation enhancement (PRE). (13)C T(1) relaxation rates of the central residues of the transmembrane (TM) domain of M2 are significantly enhanced by Cu(II), and pronounced spectral broadening is observed for the proton-selective residue, His37. These data yielded quantitative distances of (13)C spins to the Cu(II) center and identified the Cu(II) binding site to be Nε2 of His37. This binding site is surrounded by four imidazole rings from the top and four indole rings of Trp41 from the bottom, thus explaining the high affinity of Cu(II) binding. Bound at this location, Cu(II) can inhibit proton currents by perturbing histidine-water proton exchange, preventing histidine conformational dynamics, and interfering with His-Trp cation-π interaction. The Cu(II) binding site is distinct from the binding site of the hydrophobic drug amantadine, which is about 10 Å N-terminal to His37. Consistently, Cu(II) and amantadine induce distinct conformational changes at several key residues, suggesting the possibility of designing new drugs that target the His37 site to inhibit amantadine-resistant mutant M2 proteins. In addition to the high-affinity His37 binding site, we also examined the weaker and nonspecific binding of Cu(II) to membrane-surface lipid phosphates and the extent of the resulting PRE to surface-proximal protein residues. This study demonstrates the feasibility of NMR studies of paramagnetic-ion-complexed membrane proteins, where the ion serves as both a functional ligand and a distance probe.
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Affiliation(s)
- Yongchao Su
- Department of Chemistry, Iowa State University, Ames, 50011, United States
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47
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Jaroniec CP. Solid-state nuclear magnetic resonance structural studies of proteins using paramagnetic probes. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2012; 43-44:1-13. [PMID: 22464402 DOI: 10.1016/j.ssnmr.2012.02.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 05/31/2023]
Abstract
Determination of three-dimensional structures of biological macromolecules by magic-angle spinning (MAS) solid-state NMR spectroscopy is hindered by the paucity of nuclear dipolar coupling-based restraints corresponding to distances exceeding 5 Å. Recent MAS NMR studies of uniformly (13)C,(15)N-enriched proteins containing paramagnetic centers have demonstrated the measurements of site-specific nuclear pseudocontact shifts and spin relaxation enhancements, which report on electron-nucleus distances up to ~20 Å. These studies pave the way for the application of such long-distance paramagnetic restraints to protein structure elucidation and analysis of protein-protein and protein-ligand interactions in the solid phase. Paramagnetic species also facilitate the rapid acquisition of high resolution and sensitivity multidimensional solid-state NMR spectra of biomacromolecules using condensed data collection schemes, and characterization of solvent-accessible surfaces of peptides and proteins. In this review we discuss some of the latest applications of magic-angle spinning NMR spectroscopy in conjunction with paramagnetic probes to the structural studies of proteins in the solid state.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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Orientation and depth of surfactant protein B C-terminal helix in lung surfactant bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1165-72. [PMID: 22252270 DOI: 10.1016/j.bbamem.2012.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 12/19/2011] [Accepted: 01/03/2012] [Indexed: 11/22/2022]
Abstract
SP-B(CTERM) is a cationic amphipathic helical peptide and functional fragment composed of residues 63 to 78 of surfactant protein B (SP-B). Static oriented and magic angle spinning solid state NMR, along with molecular dynamics simulation was used to investigate its structure, orientation, and depth in lipid bilayers of several compositions, namely POPC, DPPC, DPPC/POPC/POPG, and bovine lung surfactant extract (BLES). In all lipid environments the peptide was oriented parallel to the membrane surface. While maintaining this approximately planar orientation, SP-B(CTERM) exhibited a flexible topology controlled by subtle variations in lipid composition. SP-B(CTERM)-induced lipid realignment and/or conformational changes at the level of the head group were observed using (31)P solid-state NMR spectroscopy. Measurements of the depth of SP-B(CTERM) indicated the peptide center positions ~8Å more deeply than the phosphate headgroups, a topology that may allow the peptide to promote functional lipid structures without causing micellization upon compression.
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Abstract
We review the current state of membrane protein structure determination using solid-state nuclear magnetic resonance (NMR) spectroscopy. Multidimensional magic-angle-spinning correlation NMR combined with oriented-sample experiments has made it possible to measure a full panel of structural constraints of membrane proteins directly in lipid bilayers. These constraints include torsion angles, interatomic distances, oligomeric structure, protein dynamics, ligand structure and dynamics, and protein orientation and depth of insertion in the lipid bilayer. Using solid-state NMR, researchers have studied potassium channels, proton channels, Ca(2+) pumps, G protein-coupled receptors, bacterial outer membrane proteins, and viral fusion proteins to elucidate their mechanisms of action. Many of these membrane proteins have also been investigated in detergent micelles using solution NMR. Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.
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Affiliation(s)
- Mei Hong
- Department of Chemistry, Iowa State University, Ames, 50011, USA.
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