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Gopinath T, Kraft A, Shin K, Wood NA, Marassi FM. Solid state NMR spectral editing of histidine, arginine and lysine using Hadamard encoding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604848. [PMID: 39211063 PMCID: PMC11360888 DOI: 10.1101/2024.07.23.604848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The NMR signals from protein sidechains are rich in information about intra- and inter-molecular interactions, but their detection can be complicated due to spectral overlap as well as conformational and hydrogen exchange. In this work, we demonstrate a protocol for multi-dimensional solid-state NMR spectral editing of signals from basic sidechains based on Hadamard matrix encoding. The Hadamard method acquires multi-dimensional experiments in such a way that both the backbone and under-sampled sidechain signals can be decoded for unambiguous editing in the 15 N spectral frequency dimension. All multi-dimensional 15 N-edited solid-state NMR experiments can be acquired using this strategy, thereby accelerating the acquisition of spectra spanning broad frequency bandwidth. Application of these methods to the ferritin nanocage, reveals signals from N atoms from His, Arg, Lys and Trp sidechains, as well as their tightly bound, ordered water molecules. The Hadamard approach adds to the arsenal of spectroscopic approaches for protein NMR signal detection.
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2
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Liu F, Greenwood AI, Xiong Y, Miceli RT, Fu R, Anderson KW, McCallum SA, Mihailescu M, Gross R, Cotten ML. Host Defense Peptide Piscidin and Yeast-Derived Glycolipid Exhibit Synergistic Antimicrobial Action through Concerted Interactions with Membranes. JACS AU 2023; 3:3345-3365. [PMID: 38155643 PMCID: PMC10751773 DOI: 10.1021/jacsau.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 12/30/2023]
Abstract
Developing new antimicrobials as alternatives to conventional antibiotics has become an urgent race to eradicate drug-resistant bacteria and to save human lives. Conventionally, antimicrobial molecules are studied independently even though they can be cosecreted in vivo. In this research, we investigate two classes of naturally derived antimicrobials: sophorolipid (SL) esters as modified yeast-derived glycolipid biosurfactants that feature high biocompatibility and low production cost; piscidins, which are host defense peptides (HDPs) from fish. While HDPs such as piscidins target the membrane of pathogens, and thus result in low incidence of resistance, SLs are not well understood on a mechanistic level. Here, we demonstrate that combining SL-hexyl ester (SL-HE) with subinhibitory concentration of piscidins 1 (P1) and 3 (P3) stimulates strong antimicrobial synergy, potentiating a promising therapeutic window. Permeabilization assays and biophysical studies employing circular dichroism, NMR, mass spectrometry, and X-ray diffraction are performed to investigate the mechanism underlying this powerful synergy. We reveal four key mechanistic features underlying the synergistic action: (1) P1/3 binds to SL-HE aggregates, becoming α-helical; (2) piscidin-glycolipid assemblies synergistically accumulate on membranes; (3) SL-HE used alone or bound to P1/3 associates with phospholipid bilayers where it induces defects; (4) piscidin-glycolipid complexes disrupt the bilayer structure more dramatically and differently than either compound alone, with phase separation occurring when both agents are present. Overall, dramatic enhancement in antimicrobial activity is associated with the use of two membrane-active agents, with the glycolipid playing the roles of prefolding the peptide, coordinating the delivery of both agents to bacterial surfaces, recruiting the peptide to the pathogenic membranes, and supporting membrane disruption by the peptide. Given that SLs are ubiquitously and safely used in consumer products, the SL/peptide formulation engineered and mechanistically characterized in this study could represent fertile ground to develop novel synergistic agents against drug-resistant bacteria.
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Affiliation(s)
- Fei Liu
- Department
of Chemistry, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Alexander I. Greenwood
- Department
of Applied Science, William & Mary, Williamsburg, Virginia 23185, United States
| | - Yawei Xiong
- Department
of Applied Science, William & Mary, Williamsburg, Virginia 23185, United States
| | - Rebecca T. Miceli
- Department
of Chemistry, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Riqiang Fu
- Center
of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Kyle W. Anderson
- National
Institute of Standards and Technology, Rockville, Maryland 20850, United States
| | - Scott A. McCallum
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Mihaela Mihailescu
- Institute
for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States
| | - Richard Gross
- Department
of Chemistry, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Myriam L. Cotten
- Department
of Applied Science, William & Mary, Williamsburg, Virginia 23185, United States
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Ball HL, Said H, Chapman K, Fu R, Xiong Y, Burk JA, Rosenbaum D, Veneziano R, Cotten ML. Orexin A, an amphipathic α-helical neuropeptide involved in pleiotropic functions in the nervous and immune systems: Synthetic approach and biophysical studies of the membrane-bound state. Biophys Chem 2023; 297:107007. [PMID: 37037119 DOI: 10.1016/j.bpc.2023.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023]
Abstract
This research reports on the membrane interactions of orexin A (OXA), an α-helical and amphipathic neuropeptide that contains 33 residues and two disulfide bonds in the N-terminal region. OXA, which activates the orexins 1 and 2 receptors in neural and immune cell membranes, has essential pleiotropic physiological effects, including at the levels of arousal, sleep/wakefulness, energy balance, neuroprotection, lipid signaling, the inflammatory response, and pain. As a result, the orexin system has become a prominent target to treat diseases such as sleep disorders, drug addiction, and inflammation. While the high-resolution structure of OXA has been investigated in water and bound to micelles, there is a lack of information about its conformation bound to phospholipid membranes and its receptors. NMR is a powerful method to investigate peptide structures in a membrane environment. To facilitate the NMR structural studies of OXA exposed to membranes, we present a novel synthetic scheme, leading to the production of isotopically-labeled material at high purity. A receptor activation assay shows that the 15N-labeled peptide is biologically active. Biophysical studies are performed using surface plasmon resonance, circular dichroism, and NMR to investigate the interactions of OXA with phospholipid bilayers. The results demonstrate a strong interaction between the peptide and phospholipids, an increase in α-helical content upon membrane binding, and an in-plane orientation of the C-terminal region critical to function. This new knowledge about structure-activity relationships in OXA could inspire the design of novel therapeutics that leverage the anti-inflammatory and neuro-protective functions of OXA, and therefore could help address neuroinflammation, a major issue associated with neurological disorders such as Alzheimer's disease.
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Affiliation(s)
- Haydn L Ball
- Department of Chemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hooda Said
- Department of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, VA 22030, USA
| | - Karen Chapman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Yawei Xiong
- Department of Applied Science, William & Mary, Williamsburg, VA 23185, USA
| | - Joshua A Burk
- Department of Psychological Sciences, William & Mary, Williamsburg, VA 23185, USA
| | - Daniel Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Remi Veneziano
- Department of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, VA 22030, USA
| | - Myriam L Cotten
- Department of Applied Science, William & Mary, Williamsburg, VA 23185, USA.
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Ma Y, Wang Z, Wang Y, Zhang S. Molecular insight into the interactions between starch and cuminaldehyde using relaxation and 2D solid-state NMR spectroscopy. Carbohydr Polym 2022; 278:118932. [PMID: 34973750 DOI: 10.1016/j.carbpol.2021.118932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/07/2021] [Accepted: 11/21/2021] [Indexed: 11/19/2022]
Abstract
The interaction between cuminaldehyde and starch mainly governed the effect of further handling on food applications of cuminaldehyde. However, little information is available about the interactions of these components. We utilized relaxation and heteronuclear correlation (HETCOR) solid-state NMR spectroscopy to investigate the interaction between cuminaldehyde and porous starch at molecular level. We found that the interactions occurred mainly through hydrogen bonds. Cuminaldehyde molecules were restricted by starch, which resulted in the limitation of their movements and the longer 1H T1 relaxation time. Furthermore, the well resolved correlated peaks in 2D 1H-13C HETCOR spectrum confirmed the formation of hydrogen bonds. The oxygen atoms at hydroxyl-2,3 of starch were the binding sites, which combined with hydrogens of cuminaldehyde. This present work not only afford a new approach to obtain a molecular understanding of interactions, but also expanded the application of solid-state NMR to investigation of the interaction on functional components.
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Affiliation(s)
- Yunxiang Ma
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, Gansu, China; Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China.
| | - Zhipeng Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Yuxia Wang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, Gansu, China
| | - Shenggui Zhang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, Gansu, China; Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
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Fu R, Rooney MT, Zhang R, Cotten ML. Coordination of Redox Ions within a Membrane-Binding Peptide: A Tale of Aromatic Rings. J Phys Chem Lett 2021; 12:4392-4399. [PMID: 33939920 DOI: 10.1021/acs.jpclett.1c00636] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The amino-terminal-copper-and-nickel-binding (ATCUN) motif, a tripeptide sequence ending with a histidine, confers important functions to proteins and peptides. Few high-resolution studies have been performed on the ATCUN motifs of membrane-associated proteins and peptides, limiting our understanding of how they stabilize Cu2+/Ni2+ in membranes. Here, we leverage solid-state NMR to investigate metal-binding to piscidin-1 (P1), a host-defense peptide featuring F1F2H3 as its ATCUN motif. Bound to redox ions, P1 chemically and physically damages pathogenic cell membranes. We design 13C/15N correlation experiments to detect and assign the deprotonated nitrogens produced and/or shifted by Ni2+-binding. Occupying multiple chemical states in P1-apo, H3 and the neighboring H4 respond to metalation by populating only the τ-tautomer. H3, as a proximal histidine, directly coordinates the metal, compared to the distal H4. Density functional theory calculations reflect this noncanonical arrangement and point toward cation-π interactions between the F1/F2/H4 aromatic rings and metal. These structural findings, which are relevant to other ATCUN-containing membrane peptides, could help design new therapeutics and materials for use in the areas of drug-resistant bacteria, neurological disorders, and biomedical imaging.
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Affiliation(s)
- Riqiang Fu
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Mary T Rooney
- Department of Applied Science, William & Mary, Williamsburg, Virginia 23185, United States
| | - Rongfu Zhang
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Myriam L Cotten
- Department of Applied Science, William & Mary, Williamsburg, Virginia 23185, United States
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Sandhu G, Morrow MR, Booth V. Roles of histidine charge and cardiolipin in membrane disruption by antimicrobial peptides Gaduscidin-1 and Gaduscidin-2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183444. [PMID: 32822647 DOI: 10.1016/j.bbamem.2020.183444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/23/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022]
Abstract
Gad-1 and Gad-2 are helical, histidine-rich antimicrobial peptides (AMPs) from paralogous genes in cod. 15N and 2H solid state nuclear magnetic resonance (NMR) were used to characterize their lipid-bound structures and lipid interactions. Gad-1 was found to position in-plane in POPC: POPG bilayers. Gad-1 displayed greater effects than Gad-2 on lipid acyl chain order of POPE: POPG and POPE: POPG: CL bilayers, in keeping with its greater activity against E. coli. The effect of Gad-1 and Gad-2 on lipid bilayer order was only weakly affected by changes in pH, and hence changes in histidine charge. This was somewhat surprising for Gad-2 as this peptide's biological activity has been shown to be greater at low pH and thus the finding may point to the existence of functional interactions with non-lipid components of bacteria. The incorporation of cardiolipin into POPE: POPG bilayers in such a way as to preserve the overall charge of the bilayers did not alter Gad-1's effects on lipid acyl chain order parameters, which report on motions on the 10-5 s timescale. When cardiolipin and Gad-1 were both present, there were subtle changes on membrane dynamics at other timescales.
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Affiliation(s)
- Gagandeep Sandhu
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Michael R Morrow
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Valerie Booth
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL, Canada; Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada.
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7
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Paredes SD, Kim S, Rooney MT, Greenwood AI, Hristova K, Cotten ML. Enhancing the membrane activity of Piscidin 1 through peptide metallation and the presence of oxidized lipid species: Implications for the unification of host defense mechanisms at lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183236. [DOI: 10.1016/j.bbamem.2020.183236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
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Comert F, Greenwood A, Maramba J, Acevedo R, Lucas L, Kulasinghe T, Cairns LS, Wen Y, Fu R, Hammer J, Blazyk J, Sukharev S, Cotten ML, Mihailescu M. The host-defense peptide piscidin P1 reorganizes lipid domains in membranes and decreases activation energies in mechanosensitive ion channels. J Biol Chem 2019; 294:18557-18570. [PMID: 31619519 PMCID: PMC6901303 DOI: 10.1074/jbc.ra119.010232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/01/2019] [Indexed: 11/06/2022] Open
Abstract
The host-defense peptide (HDP) piscidin 1 (P1), isolated from the mast cells of striped bass, has potent activities against bacteria, viruses, fungi, and cancer cells and can also modulate the activity of membrane receptors. Given its broad pharmacological potential, here we used several approaches to better understand its interactions with multicomponent bilayers representing models of bacterial (phosphatidylethanolamine (PE)/phosphatidylglycerol) and mammalian (phosphatidylcholine/cholesterol (PC/Chol)) membranes. Using solid-state NMR, we solved the structure of P1 bound to PC/Chol and compared it with that of P3, a less potent homolog. The comparison disclosed that although both peptides are interfacially bound and α-helical, they differ in bilayer orientations and depths of insertion, and these differences depend on bilayer composition. Although Chol is thought to make mammalian membranes less susceptible to HDP-mediated destabilization, we found that Chol does not affect the permeabilization effects of P1. X-ray diffraction experiments revealed that both piscidins produce a demixing effect in PC/Chol membranes by increasing the fraction of the Chol-depleted phase. Furthermore, P1 increased the temperature required for the lamellar-to-hexagonal phase transition in PE bilayers, suggesting that it imposes positive membrane curvature. Patch-clamp measurements on the inner Escherichia coli membrane showed that P1 and P3, at concentrations sufficient for antimicrobial activity, substantially decrease the activating tension for bacterial mechanosensitive channels. This indicated that piscidins can cause lipid redistribution and restructuring in the microenvironment near proteins. We conclude that the mechanism of piscidin's antimicrobial activity extends beyond simple membrane destabilization, helping to rationalize its broader spectrum of pharmacological effects.
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Affiliation(s)
- Fatih Comert
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
| | - Alexander Greenwood
- Department of Applied Science, William and Mary, Williamsburg, Virginia 23185
| | - Joseph Maramba
- Biology Department, University of Maryland, College Park, Maryland 20742
| | - Roderico Acevedo
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
| | - Laura Lucas
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
| | - Thulasi Kulasinghe
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
| | - Leah S Cairns
- Department of Biochemistry and Molecular Biology, The Johns Hopkins University, Baltimore, Maryland 21205
| | - Yi Wen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310
| | - Janet Hammer
- Department of Biomedical Sciences, Ohio University, Athens, Ohio 45701
| | - Jack Blazyk
- Department of Biomedical Sciences, Ohio University, Athens, Ohio 45701
| | - Sergei Sukharev
- Biology Department, University of Maryland, College Park, Maryland 20742
| | - Myriam L Cotten
- Department of Applied Science, William and Mary, Williamsburg, Virginia 23185.
| | - Mihaela Mihailescu
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850.
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9
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Mihailescu M, Sorci M, Seckute J, Silin VI, Hammer J, Perrin BS, Hernandez JI, Smajic N, Shrestha A, Bogardus KA, Greenwood AI, Fu R, Blazyk J, Pastor RW, Nicholson LK, Belfort G, Cotten ML. Structure and Function in Antimicrobial Piscidins: Histidine Position, Directionality of Membrane Insertion, and pH-Dependent Permeabilization. J Am Chem Soc 2019; 141:9837-9853. [PMID: 31144503 DOI: 10.1021/jacs.9b00440] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Piscidins are histidine-enriched antimicrobial peptides that interact with lipid bilayers as amphipathic α-helices. Their activity at acidic and basic pH in vivo makes them promising templates for biomedical applications. This study focuses on p1 and p3, both 22-residue-long piscidins with 68% sequence identity. They share three histidines (H3, H4, and H11), but p1, which is significantly more permeabilizing, has a fourth histidine (H17). This study investigates how variations in amphipathic character associated with histidines affect the permeabilization properties of p1 and p3. First, we show that the permeabilization ability of p3, but not p1, is strongly inhibited at pH 6.0 when the conserved histidines are partially charged and H17 is predominantly neutral. Second, our neutron diffraction measurements performed at low water content and neutral pH indicate that the average conformation of p1 is highly tilted, with its C-terminus extending into the opposite leaflet. In contrast, p3 is surface bound with its N-terminal end tilted toward the bilayer interior. The deeper membrane insertion of p1 correlates with its behavior at full hydration: an enhanced ability to tilt, bury its histidines and C-terminus, induce membrane thinning and defects, and alter membrane conductance and viscoelastic properties. Furthermore, its pH-resiliency relates to the neutral state favored by H17. Overall, these results provide mechanistic insights into how differences in the histidine content and amphipathicity of peptides can elicit different directionality of membrane insertion and pH-dependent permeabilization. This work features complementary methods, including dye leakage assays, NMR-monitored titrations, X-ray and neutron diffraction, oriented CD, molecular dynamics, electrochemical impedance spectroscopy, surface plasmon resonance, and quartz crystal microbalance with dissipation.
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Affiliation(s)
- Mihaela Mihailescu
- Institute for Bioscience and Biotechnology Research , University of Maryland , Rockville , Maryland 20850 , United States
| | - Mirco Sorci
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Jolita Seckute
- Department of Molecular Biology and Genetics , Cornell University , Ithaca , New York 14853 , United States
| | - Vitalii I Silin
- Institute for Bioscience and Biotechnology Research , University of Maryland , Rockville , Maryland 20850 , United States
| | - Janet Hammer
- Department of Biomedical Sciences , Ohio University , Athens , Ohio 45701 , United States
| | - B Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Jorge I Hernandez
- Department of Bioengineering , Clemson University , Clemson , South Carolina 29634 , United States
| | - Nedzada Smajic
- Department of Chemistry , Hamilton College , Clinton , New York 13323 , United States
| | - Akritee Shrestha
- Department of Chemistry , Hamilton College , Clinton , New York 13323 , United States
| | - Kimberly A Bogardus
- Department of Chemistry , Hamilton College , Clinton , New York 13323 , United States
| | - Alexander I Greenwood
- Department of Applied Science , College of William and Mary , Williamsburg , Virginia 23185 , United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory , Tallahassee , Florida 32310 , United States
| | - Jack Blazyk
- Department of Biomedical Sciences , Ohio University , Athens , Ohio 45701 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Linda K Nicholson
- Department of Molecular Biology and Genetics , Cornell University , Ithaca , New York 14853 , United States
| | - Georges Belfort
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Myriam L Cotten
- Department of Applied Science , College of William and Mary , Williamsburg , Virginia 23185 , United States
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10
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Bielytskyi P, Gräsing D, Zahn S, Mote KR, Alia A, Madhu PK, Matysik J. Assignment of NMR resonances of protons covalently bound to photochemically active cofactors in photosynthetic reaction centers by 13C- 1H photo-CIDNP MAS-J-HMQC experiment. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 298:64-76. [PMID: 30529893 DOI: 10.1016/j.jmr.2018.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 06/09/2023]
Abstract
Modified versions of through-bond heteronuclear correlation (HETCOR) experiments are presented to take advantage of the light-induced hyperpolarization that occurs on 13C nuclei due to the solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP) effect. Such 13C-1H photo-CIDNP MAS-J-HMQC and photo-CIDNP MAS-J-HSQC experiments are applied to acquire the 2D 13C-1H correlation spectra of selectively 13C-labeled photochemically active cofactors in the frozen quinone-blocked photosynthetic reaction center (RC) of the purple bacterium Rhodobacter (R.) sphaeroides wild-type (WT). Resulting spectra contain no correlation peaks arising from the protein backbone, which greatly simplifies the assignment of aliphatic region. Based on the photo-CIDNP MAS-J-HMQC NMR experiment, we obtained assignment of selective 1H NMR resonances of the cofactors involved in the electron transfer process in the RC and compared them with values theoretically predicted by density functional theory (DFT) calculation as well as with the chemical shifts obtained from monomeric cofactors in the solution. We also compared proton chemical shifts obtained by photo-CIDNP MAS-J-HMQC experiment under continuous illumination with the ones obtained in dark by classical cross-polarization (CP) HETCOR. We expect that the proposed approach will become a method of choice for obtaining 1H chemical shift maps of the active cofactors in photosynthetic RCs and will aid the interpretation of heteronuclear spin-torch experiments.
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Affiliation(s)
- Pavlo Bielytskyi
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany
| | - Daniel Gräsing
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany
| | - Stefan Zahn
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, D-04318 Leipzig, Germany
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500107, India
| | - A Alia
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2301 RA Leiden, the Netherlands; Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500107, India
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany.
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11
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Huang Y, Yang Y, Cai S, Chen Z, Zhan H, Li C, Tan C, Chen Z. General Two-Dimensional Absorption-Mode J-Resolved NMR Spectroscopy. Anal Chem 2017; 89:12646-12651. [DOI: 10.1021/acs.analchem.7b02740] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yuqing Huang
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Yu Yang
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Shuhui Cai
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhiwei Chen
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Haolin Zhan
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Chen Li
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Chunhua Tan
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhong Chen
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
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12
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Qin H, Miao Y, Cross TA, Fu R. Beyond Structural Biology to Functional Biology: Solid-State NMR Experiments and Strategies for Understanding the M2 Proton Channel Conductance. J Phys Chem B 2017; 121:4799-4809. [PMID: 28425709 DOI: 10.1021/acs.jpcb.7b02468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In terms of structural biology, solid-state NMR experiments and strategies have been well established for resonance assignments, leading to the determination of three-dimensional structures of insoluble membrane proteins in their native-like environment. It is also known that NMR has the unique capabilities to characterize structure-function relationships of membrane-bound biological systems beyond structural biology. Here, we report on solid-state NMR experiments and strategies for extracting functional activities on a sub-millisecond time scale. Specifically, we use the His37-labeled full length M2 (M2FL) protein of the Influenza A virus embedded in synthetic lipid bilayers as an example to characterize the proton conduction mechanism and kinetics. The integral membrane M2 protein assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH and is essential for the viral lifecycle. Our results present convincing evidence for the formation of imidazolium-imidazole hydrogen bonds in the His37 tetrad at low pH and that these hydrogen bonds have a low barrier that facilitates the proton conduction mechanism in the M2FL protein. Moreover, it has been possible to measure hydronium ion exchange between water and the protons in the His37 NH bonds based on chemical exchange spectroscopy with minimized spin diffusion. The results identify an exchange rate constant of ∼4000 s-1 for pH 5.8 at -10 °C.
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Affiliation(s)
- Huajun Qin
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Yimin Miao
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Timothy A Cross
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States.,National High Magnet Field Lab , 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Riqiang Fu
- National High Magnet Field Lab , 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
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13
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Fu R, Miao Y, Qin H, Cross TA. Probing Hydronium Ion Histidine NH Exchange Rate Constants in the M2 Channel via Indirect Observation of Dipolar-Dephased 15N Signals in Magic-Angle-Spinning NMR. J Am Chem Soc 2016; 138:15801-15804. [PMID: 27960325 PMCID: PMC5368641 DOI: 10.1021/jacs.6b08376] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Water-protein chemical exchange in membrane-bound proteins is an important parameter for understanding how proteins interact with their aqueous environment, but has been difficult to observe in membrane-bound biological systems. Here, we demonstrate the feasibility of probing specific water-protein chemical exchange in membrane-bound proteins in solid-state MAS NMR. By spin-locking the 1H magnetization along the magic angle, the 1H spin diffusion is suppressed such that a water-protein chemical exchange process can be monitored indirectly by dipolar-dephased 15N signals through polarization transfer from 1H. In the example of the Influenza A full length M2 protein, the buildup of dipolar-dephased 15N signals from the tetrad of His37 side chains have been observed as a function of spin-lock time. This confirms that hydronium ions are in exchange with protons in the His37 NH bonds at the heart of the M2 proton conduction mechanism, with an exchange rate constant of ∼1750 s-1 for pH 6.2 at -10 °C.
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Affiliation(s)
- Riqiang Fu
- National High Magnet Field Lab, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Yimin Miao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Huajun Qin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Timothy A. Cross
- National High Magnet Field Lab, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
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14
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Huang Y, Lin YY, Cai S, Yang Y, Sun H, Lin Y, Chen Z. High-resolution nuclear magnetic resonance measurements in inhomogeneous magnetic fields: A fast two-dimensional J-resolved experiment. J Chem Phys 2016; 144:104202. [DOI: 10.1063/1.4943575] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Yuqing Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Yung-Ya Lin
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Shuhui Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Yu Yang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Huijun Sun
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Yanqin Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
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15
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Singh MK, Shweta H, Khan MF, Sen S. New insight into probe-location dependent polarity and hydration at lipid/water interfaces: comparison between gel- and fluid-phases of lipid bilayers. Phys Chem Chem Phys 2016; 18:24185-97. [DOI: 10.1039/c6cp01201a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Location dependent polarity and hydration probed by a new series of 4-aminophthalimide-based fluorescent molecules (4AP-Cn;n= 2–10, 12) show different behaviour at gel- and fluid-phase lipid/water interfaces.
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Affiliation(s)
- Moirangthem Kiran Singh
- Spectroscopy Laboratory
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
| | - Him Shweta
- Spectroscopy Laboratory
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
| | - Mohammad Firoz Khan
- Spectroscopy Laboratory
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
| | - Sobhan Sen
- Spectroscopy Laboratory
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
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16
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Vugmeyster L, Ostrovsky D, Fu R. (15)N CSA tensors and (15)N-(1)H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 259:225-31. [PMID: 26367322 PMCID: PMC4600402 DOI: 10.1016/j.jmr.2015.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/24/2015] [Accepted: 08/28/2015] [Indexed: 06/01/2023]
Abstract
In this work, we assess the usefulness of static (15)N NMR techniques for the determination of the (15)N chemical shift anisotropy (CSA) tensor parameters and (15)N-(1)H dipolar splittings in powder protein samples. By using five single labeled samples of the villin headpiece subdomain protein in a hydrated lyophilized powder state, we determine the backbone (15)N CSA tensors at two temperatures, 22 and -35 °C, in order to get a snapshot of the variability across the residues and as a function of temperature. All sites probed belonged to the hydrophobic core and most of them were part of α-helical regions. The values of the anisotropy (which include the effect of the dynamics) varied between 130 and 156 ppm at 22 °C, while the values of the asymmetry were in the 0.32-0.082 range. The Leu-75 and Leu-61 backbone sites exhibited high mobility based on the values of their temperature-dependent anisotropy parameters. Under the assumption that most differences stem from dynamics, we obtained the values of the motional order parameters for the (15)N backbone sites. While a simple one-dimensional line shape experiment was used for the determination of the (15)N CSA parameters, a more advanced approach based on the "magic sandwich" SAMMY pulse sequence (Nevzorov and Opella, 2003) was employed for the determination of the (15)N-(1)H dipolar patterns, which yielded estimates of the dipolar couplings. Accordingly, the motional order parameters for the dipolar interaction were obtained. It was found that the order parameters from the CSA and dipolar measurements are highly correlated, validating that the variability between the residues is governed by the differences in dynamics. The values of the parameters obtained in this work can serve as reference values for developing more advanced magic-angle spinning recoupling techniques for multiple labeled samples.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, 1201 Larimer St, Denver, CO 80204, United States.
| | - Dmitry Ostrovsky
- Department of Mathematics and Department of Physics, University of Colorado at Denver, 1201 Larimer Street, Denver, CO 80204, United States
| | - Riqiang Fu
- National High Field Magnetic Laboratory, 1800 E Paul Dirac Drive, Tallahassee, FL 32310, United States
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17
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Hansen SK, Bertelsen K, Paaske B, Nielsen NC, Vosegaard T. Solid-state NMR methods for oriented membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:48-85. [PMID: 26282196 DOI: 10.1016/j.pnmrs.2015.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Oriented-sample solid-state NMR represents one of few experimental methods capable of characterising the membrane-bound conformation of proteins in the cell membrane. Since the technique was developed 25 years ago, the technique has been applied to study the structure of helix bundle membrane proteins and antimicrobial peptides, characterise protein-lipid interactions, and derive information on dynamics of the membrane anchoring of membrane proteins. We will review the major developments in various aspects of oriented-sample solid-state NMR, including sample-preparation methods, pulse sequences, theory required to interpret the experiments, perspectives for and guidelines to new experiments, and a number of representative applications.
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Affiliation(s)
- Sara K Hansen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Berit Paaske
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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18
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Structure and membrane interactions of chionodracine, a piscidin-like antimicrobial peptide from the icefish Chionodraco hamatus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1285-93. [DOI: 10.1016/j.bbamem.2015.02.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/23/2015] [Accepted: 02/27/2015] [Indexed: 12/24/2022]
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19
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Lin L, Wei Z, Lin Y, Chen Z. A single-scan method for NMR 2D J-resolved spectroscopy. Chem Commun (Camb) 2015; 51:1234-6. [DOI: 10.1039/c4cc07751b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A single-scan NMR 2D J-resolved method is proposed for obtaining decoupled proton spectra and fine scalar-coupling splitting patterns.
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Affiliation(s)
- Liangjie Lin
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Xiamen University
- Xiamen
| | - Zhiliang Wei
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Xiamen University
- Xiamen
| | - Yanqin Lin
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Xiamen University
- Xiamen
| | - Zhong Chen
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Xiamen University
- Xiamen
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20
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Khatami MH, Bromberek M, Saika-Voivod I, Booth V. Molecular dynamics simulations of histidine-containing cod antimicrobial peptide paralogs in self-assembled bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2778-87. [DOI: 10.1016/j.bbamem.2014.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 07/10/2014] [Accepted: 07/14/2014] [Indexed: 01/24/2023]
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21
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Chen W, Cotten ML. Expression, purification, and micelle reconstitution of antimicrobial piscidin 1 and piscidin 3 for NMR studies. Protein Expr Purif 2014; 102:63-8. [PMID: 25131859 DOI: 10.1016/j.pep.2014.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 07/31/2014] [Accepted: 08/01/2014] [Indexed: 12/28/2022]
Abstract
Piscidin 1 and piscidin 3, which were discovered in the mast cells of hybrid striped sea bass, are homologous antimicrobial peptides that are active against drug-resistant bacteria. Piscidin 1, the more antimicrobial and hemolytic peptide, also has anti-HIV-1 and anti-cancer properties. To understand the reasons underlying the different biological activities of the two peptides and identify principles to design antimicrobial drugs with improved efficacy and lower toxicity, their atomic-level structures must be obtained under physiologically-relevant conditions. High-resolution backbone structures of both piscidins exist in the presence of hydrated phospholipid bilayers but full structures that include the side chains are missing. Here, the piscidins 1 and 3 genes were cloned into the TrpLE vector. The corresponding TrpLE-piscidin fusion partners were expressed in Escherichiacoli and recovered from inclusion bodies. Following steps that included Ni-NTA chromatography, cyanogen bromide cleavage of the fusion proteins, and reverse-phase HPLC, purified piscidins 1 and 3 were recovered in very good yield and characterized by NMR. High quality (15)N-(1)H HSQC spectra of piscidins 1 and 3 bound to SDS micelles were collected, demonstrating the feasibility of producing and purifying the isotopically-labeled piscidin peptides required to determine their full structures by multidimensional NMR spectroscopy.
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Affiliation(s)
- Wen Chen
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States
| | - Myriam L Cotten
- Department of Chemistry, Hamilton College, 198 College Hill Road, Clinton, NY 13323, United States.
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22
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Perrin BS, Tian Y, Fu R, Grant CV, Chekmenev EY, Wieczorek W, Dao AE, Hayden RM, Burzynski CM, Venable RM, Sharma M, Opella SJ, Pastor RW, Cotten ML. High-resolution structures and orientations of antimicrobial peptides piscidin 1 and piscidin 3 in fluid bilayers reveal tilting, kinking, and bilayer immersion. J Am Chem Soc 2014; 136:3491-504. [PMID: 24410116 PMCID: PMC3985945 DOI: 10.1021/ja411119m] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Indexed: 01/16/2023]
Abstract
While antimicrobial peptides (AMPs) have been widely investigated as potential therapeutics, high-resolution structures obtained under biologically relevant conditions are lacking. Here, the high-resolution structures of the homologous 22-residue long AMPs piscidin 1 (p1) and piscidin 3 (p3) are determined in fluid-phase 3:1 phosphatidylcholine/phosphatidylglycerol (PC/PG) and 1:1 phosphatidylethanolamine/phosphatidylglycerol (PE/PG) bilayers to identify molecular features important for membrane destabilization in bacterial cell membrane mimics. Structural refinement of (1)H-(15)N dipolar couplings and (15)N chemical shifts measured by oriented sample solid-state NMR and all-atom molecular dynamics (MD) simulations provide structural and orientational information of high precision and accuracy about these interfacially bound α-helical peptides. The tilt of the helical axis, τ, is between 83° and 93° with respect to the bilayer normal for all systems and analysis methods. The average azimuthal rotation, ρ, is 235°, which results in burial of hydrophobic residues in the bilayer. The refined NMR and MD structures reveal a slight kink at G13 that delineates two helical segments characterized by a small difference in their τ angles (<10°) and significant difference in their ρ angles (~25°). Remarkably, the kink, at the end of a G(X)4G motif highly conserved among members of the piscidin family, allows p1 and p3 to adopt ρ angles that maximize their hydrophobic moments. Two structural features differentiate the more potent p1 from p3: p1 has a larger ρ angle and less N-terminal fraying. The peptides have comparable depths of insertion in PC/PG, but p3 is 1.2 Å more deeply inserted than p1 in PE/PG. In contrast to the ideal α-helical structures typically assumed in mechanistic models of AMPs, p1 and p3 adopt disrupted α-helical backbones that correct for differences in the amphipathicity of their N- and C-ends, and their centers of mass lie ~1.2-3.6 Å below the plane defined by the C2 atoms of the lipid acyl chains.
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Affiliation(s)
- B. Scott Perrin
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ye Tian
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093-0307, United States
| | - Riqiang Fu
- National High Magnetic
Field Laboratory, Tallahassee, Florida 32310, United
States
| | - Christopher V. Grant
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093-0307, United States
| | - Eduard Y. Chekmenev
- National High Magnetic
Field Laboratory, Tallahassee, Florida 32310, United
States
| | - William
E. Wieczorek
- Department
of Chemistry, Hamilton College, Clinton, New York 13323, United States
| | - Alexander E. Dao
- Department
of Chemistry, Hamilton College, Clinton, New York 13323, United States
| | - Robert M. Hayden
- Department
of Chemistry, Hamilton College, Clinton, New York 13323, United States
| | - Caitlin M. Burzynski
- Department
of Chemistry, Hamilton College, Clinton, New York 13323, United States
| | - Richard M. Venable
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Mukesh Sharma
- Department
of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Stanley J. Opella
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093-0307, United States
| | - Richard W. Pastor
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Myriam L. Cotten
- Department
of Chemistry, Hamilton College, Clinton, New York 13323, United States
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23
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Gopinath T, Mote KR, Veglia G. Sensitivity and resolution enhancement of oriented solid-state NMR: application to membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 75:50-68. [PMID: 24160761 PMCID: PMC3850070 DOI: 10.1016/j.pnmrs.2013.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/16/2013] [Indexed: 05/19/2023]
Abstract
Oriented solid-state NMR (O-ssNMR) spectroscopy is a major technique for the high-resolution analysis of the structure and topology of transmembrane proteins in native-like environments. Unlike magic angle spinning (MAS) techniques, O-ssNMR spectroscopy requires membrane protein preparations that are uniformly oriented (mechanically or magnetically) so that anisotropic NMR parameters, such as dipolar and chemical shift interactions, can be measured to determine structure and orientation of membrane proteins in lipid bilayers. Traditional sample preparations involving mechanically aligned lipids often result in short relaxation times which broaden the (15)N resonances and encumber the manipulation of nuclear spin coherences. The introduction of lipid bicelles as membrane mimicking systems has changed this scenario, and the more favorable relaxation properties of membrane protein (15)N and (13)C resonances make it possible to develop new, more elaborate pulse sequences for higher spectral resolution and sensitivity. Here, we describe our recent progress in the optimization of O-ssNMR pulse sequences. We explain the theory behind these experiments, demonstrate their application to small and medium size proteins, and describe the technical details for setting up these new experiments on the new generation of NMR spectrometers.
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Affiliation(s)
- T. Gopinath
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Kaustubh R. Mote
- Department of Chemistry, 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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24
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Li PX, Li ZX, Shen HH, Thomas RK, Penfold J, Lu JR. Application of the Gibbs equation to the adsorption of nonionic surfactants and polymers at the air-water interface: comparison with surface excesses determined directly using neutron reflectivity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:9324-9334. [PMID: 23758191 DOI: 10.1021/la4018344] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Four recent papers by Menger et al. have questioned methods of analysis of surface tension (ST) data that use the Gibbs equation to obtain the surface excess (Γ) of a surfactant at the air-water interface. There have been two responses which challenge the assertions of Menger et al. and a response from Menger et al. We use directly determined values of Γ from a range of neutron reflectometry (NR) data to examine some of the issues that are relevant to these seven papers. We show that there is excellent agreement between NR measurements and careful ST analyses for a wide range of nonionic adsorbents, including surfactants and polymers. The reason it is possible to obtain good agreement near the critical micelle concentration (CMC) is that nonionic surfactants generally seem to saturate the surface before the CMC is reached and this makes it relatively easy to determine the limiting slope (and hence Γ) of the ST-log(concentration) plot at the CMC. Furthermore, there is also generally good agreement between ST and NR over the whole range of concentrations below the CMC until depletion effects become important. Depletion effects are shown to become important at higher concentrations than expected, which brings them into the range of many experiments, including techniques other than ST and NR. This is illustrated with new measurements on the biosurfactant surfactin. The agreement between ST and NR outside the depletion range can be regarded as a mutual validation of the two methods, especially as it is demonstrated independently of any model adsorption isotherms. In the normal experimental situation NR is less vulnerable to depletion than ST and we show how NR and a single ST measurement can be used to determine the hitherto undetermined CMC of the nonionic surfactant C18E12, which is found to be 1.3 × 10(-6) M.
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Affiliation(s)
- Pei Xun Li
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
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25
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Xu H, Li PX, Ma K, Thomas RK, Penfold J, Lu JR. Limitations in the application of the Gibbs equation to anionic surfactants at the air/water surface: sodium dodecylsulfate and sodium dodecylmonooxyethylenesulfate above and below the CMC. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:9335-9351. [PMID: 23819862 DOI: 10.1021/la401835d] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This is a second paper responding to recent papers by Menger et al. and the ensuing discussion about the application of the Gibbs equation to surface tension (ST) data. Using new neutron reflection (NR) measurements on sodium dodecylsulfate (SDS) and sodium dodecylmonooxyethylene sulfate (SLES) above and below their CMCs and with and without added NaCl, in conjunction with the previous ST measurements on SDS by Elworthy and Mysels (EM), we conclude that (i) ST measurements are often seriously compromised by traces of divalent ions, (ii) adsorption does not generally reach saturation at the CMC, making it difficult to obtain the limiting Gibbs slope, and (iii) the significant width of micellization may make it impossible to apply the Gibbs equation in a significant range of concentration below the CMC. Menger et al. proposed ii as a reason for the difficulty of applying the Gibbs equation to ST data. Conclusions i and iii now further emphasize the failings of the ST-Gibbs analysis for determining the limiting coverage at the CMC, especially for SDS. For SDS, adsorption increases above the CMC to a value of 10 × CMC, which is about 25% greater than at the CMC and about the same as at the CMC in the presence of 0.1 M NaCl. In contrast, the adsorption of SLES reaches a limit at the CMC with no further increase up to 10 × CMC, but the addition of 0.1 M NaCl increases the surface excess by 20-25%. The results for SDS are combined with earlier NR results to generate an adsorption isotherm from 2 to 100 mM. The NR results for SDS are compared to the definitive surface tension (ST) measurements of EM, and the surface excesses agree over the range where they can safely be compared, from 2 to 6 mM. This confirms that the anomalous decrease in the slope of EM's σ - ln c curve between 6 mM and the CMC at 8.2 mM results from changes in activity associated with a significant width of micellization. This anomaly shows that it is impossible to apply the Gibbs equation usefully from 6 to 8.2 mM (i.e., the lack of knowledge of the activity in this range is the same as above the CMC (8.2 mM)). It was found that a mislabeling of the original data in EM may have prevented the use of this excellent ST data as a standard by other authors. Although NR and ST results for SDS in the absence of added electrolyte show that the discrepancies can be rationalized, ST is generally shown to be less accurate and more vulnerable to impurities, especially divalent ions, than NR. The radiotracer technique is shown to be less accurate than ST-Gibbs in that the four radiotracer measurements of the surface excess are consistent neither with each other nor with ST and NR. It is also shown that radiotracer results on aerosol-OT are likely to be incorrect. Application of the mass action (MA) model of micellization to the ST curves of SDS and SLES through and above the CMC shows that they can be explained by this model and that they depend on the degree of dissociation of the micelle, which leads to a larger change in the mean activity, and hence the adsorption, for the more highly dissociated SDS micelles than for SLES. Previous measurements of the activity of SDS above the CMC were found to be semiquantitatively consistent with the change in mean activity predicted by the MA model but inconsistent with the combined ST, NR, and Gibbs equation results.
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Affiliation(s)
- Hui Xu
- Physical and Theoretical Chemistry Laboratory, South Parks Road, University of Oxford, Oxford OX1 3QZ, UK
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Lu GJ, Park SH, Opella SJ. Improved 1H amide resonance line narrowing in oriented sample solid-state NMR of membrane proteins in phospholipid bilayers. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 220:54-61. [PMID: 22683581 PMCID: PMC3760517 DOI: 10.1016/j.jmr.2012.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 04/14/2012] [Accepted: 04/16/2012] [Indexed: 05/11/2023]
Abstract
We demonstrate (1)H amide resonance line widths <300 Hz in (1)H/(15)N heteronuclear correlation (HETCOR) spectra of membrane proteins in aligned phospholipid bilayers. This represents a substantial improvement over typically observed line widths of ∼1 kHz. Furthermore, in a proton detected local field (PDLF) version of the experiment that measures heteronuclear dipolar couplings, line widths <130 Hz are observed. This dramatic line narrowing of (1)H amide resonances enables many more individual signals to be resolved and assigned from uniformly (15)N labeled membrane proteins in phospholipid bilayers under physiological conditions of temperature and pH. Finding that the decrease in line widths occurs only for membrane proteins that undergo fast rotational diffusion around the bilayer normal, but not immobile molecules, such as peptide single crystals, identifies a potential new direction for pulse sequence development that includes overall molecular dynamics in their design.
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Lin HJ, Huang TC, Muthusamy S, Lee JF, Duann YF, Lin CH. Piscidin-1, an Antimicrobial Peptide from Fish (Hybrid Striped BassMorone saxatilisxM. chrysops), Induces Apoptotic and Necrotic Activity in HT1080 Cells. Zoolog Sci 2012; 29:327-32. [DOI: 10.2108/zsj.29.327] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Wadhwani P, Strandberg E, Heidenreich N, Bürck J, Fanghänel S, Ulrich AS. Self-assembly of flexible β-strands into immobile amyloid-like β-sheets in membranes as revealed by solid-state 19F NMR. J Am Chem Soc 2012; 134:6512-5. [PMID: 22452513 DOI: 10.1021/ja301328f] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cationic peptide [KIGAKI](3) was designed as an amphiphilic β-strand and serves as a model for β-sheet aggregation in membranes. Here, we have characterized its molecular conformation, membrane alignment, and dynamic behavior using solid-state (19)F NMR. A detailed structure analysis of selectively (19)F-labeled peptides was carried out in oriented DMPC bilayers. It showed a concentration-dependent transition from monomeric β-strands to oligomeric β-sheets. In both states, the rigid (19)F-labeled side chains project straight into the lipid bilayer but they experience very different mobilities. At low peptide-to-lipid ratios ≤1:400, monomeric [KIGAKI](3) swims around freely on the membrane surface and undergoes considerable motional averaging, with essentially uncoupled φ/ψ torsion angles. The flexibility of the peptide backbone in this 2D plane is reminiscent of intrinsically unstructured proteins in 3D. At high concentrations, [KIGAKI](3) self-assembles into immobilized β-sheets, which are untwisted and lie flat on the membrane surface as amyloid-like fibrils. This is the first time the transition of monomeric β-strands into oligomeric β-sheets has been characterized by solid-state NMR in lipid bilayers. It promises to be a valuable approach for studying membrane-induced amyloid formation of many other, clinically relevant peptide systems.
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Affiliation(s)
- Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, D-76021 Karlsruhe, Germany
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29
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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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30
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De Angelis AA, Grant CV, Baxter MK, McGavin JA, Opella SJ, Cotten ML. Amphipathic antimicrobial piscidin in magnetically aligned lipid bilayers. Biophys J 2011; 101:1086-94. [PMID: 21889445 DOI: 10.1016/j.bpj.2011.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 06/29/2011] [Accepted: 07/01/2011] [Indexed: 10/17/2022] Open
Abstract
The amphipathic antimicrobial peptide piscidin 1 was studied in magnetically aligned phospholipid bilayers by oriented-sample solid-state NMR spectroscopy. (31)P NMR and double-resonance (1)H/(15)N NMR experiments performed between 25 °C and 61 °C enabled the lipid headgroups as well as the peptide amide sites to be monitored over a range of temperatures. The α-helical peptide dramatically affects the phase behavior and structure of anionic bilayers but not those of zwitterionic bilayers. Piscidin 1 stabilizes anionic bilayers, which remain well aligned up to 61 °C when piscidin 1 is on the membrane surface. Two-dimensional separated-local-field experiments show that the tilt angle of the peptide is 80 ± 5°, in agreement with previous results on mechanically aligned bilayers. The peptide undergoes fast rotational diffusion about the bilayer normal under these conditions, and these studies demonstrate that magnetically aligned bilayers are well suited for structural studies of amphipathic peptides.
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Affiliation(s)
- Anna A De Angelis
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA
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31
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Gopinath T, Mote KR, Veglia G. Proton evolved local field solid-state nuclear magnetic resonance using Hadamard encoding: theory and application to membrane proteins. J Chem Phys 2011; 135:074503. [PMID: 21861572 DOI: 10.1063/1.3622604] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
NMR anisotropic parameters such as dipolar couplings and chemical shifts are central to structure and orientation determination of aligned membrane proteins and liquid crystals. Among the separated local field experiments, the proton evolved local field (PELF) scheme is particularly suitable to measure dynamically averaged dipolar couplings and give information on local molecular motions. However, the PELF experiment requires the acquisition of several 2D datasets at different mixing times to optimize the sensitivity for the complete range of dipolar couplings of the resonances in the spectrum. Here, we propose a new PELF experiment that takes the advantage of the Hadamard encoding (HE) to obtain higher sensitivity for a broad range of dipolar couplings using a single 2D experiment. The HE scheme is obtained by selecting the spin operators with phase switching of hard pulses. This approach enables one to detect four spin operators, simultaneously, which can be processed into two 2D spectra covering a broader range of dipolar couplings. The advantages of the new approach are illustrated for a U-(15)N NAL single crystal and the U-(15)N labeled single-pass membrane protein sarcolipin reconstituted in oriented lipid bicelles. The HE-PELF scheme can be implemented in other multidimensional experiments to speed up the characterization of the structure and dynamics of oriented membrane proteins and liquid crystalline samples.
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Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, Minnesota 55455, USA
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32
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Traaseth NJ, Veglia G. Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 211:18-24. [PMID: 21482162 PMCID: PMC3328402 DOI: 10.1016/j.jmr.2011.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/10/2011] [Accepted: 03/14/2011] [Indexed: 05/15/2023]
Abstract
We present a new method that combines carbonyl-selective labeling with frequency-selective heteronuclear recoupling to resolve the spectral overlap of magic angle spinning (MAS) NMR spectra of membrane proteins in fluid lipid membranes with broad lines and high redundancy in the primary sequence. We implemented this approach in both heteronuclear (15)N-(13)C(α) and homonuclear (13)C-(13)C dipolar assisted rotational resonance (DARR) correlation experiments. We demonstrate its efficacy for the membrane protein phospholamban reconstituted in fluid PC/PE/PA lipid bilayers. The main advantage of this method is to discriminate overlapped (13)C(α) resonances by strategically labeling the preceding residue. This method is highly complementary to (13)C(i-1)(')-(15)N(i)-(13)C(i)(α) and (13)C(i-1)(α)-(15)N(i-1)-(13)C(i)(') experiments to distinguish inter-residue spin systems at a minimal cost to signal-to-noise.
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Affiliation(s)
- Nathaniel J. Traaseth
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55445
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55445
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55445
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Traaseth NJ, Gopinath T, Veglia G. On the performance of spin diffusion NMR techniques in oriented solids: prospects for resonance assignments and distance measurements from separated local field experiments. J Phys Chem B 2010; 114:13872-80. [PMID: 20936833 PMCID: PMC3000634 DOI: 10.1021/jp105718r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
NMR spin diffusion experiments have the potential to provide both resonance assignment and internuclear distances for protein structure determination in oriented solid-state NMR. In this paper, we compared the efficiencies of three spin diffusion experiments: proton-driven spin diffusion (PDSD), cross-relaxation-driven spin diffusion (CRDSD), and proton-mediated proton transfer (PMPT). As model systems for oriented proteins, we used single crystals of N-acetyl-L-(15)N-leucine (NAL) and N-acetyl-L-(15)N-valyl-L-(15)N-leucine (NAVL) to probe long and short distances, respectively. We demonstrate that, for short (15)N/(15)N distances such as those found in NAVL (3.3 Å), the PDSD mechanism gives the most intense cross-peaks, while, for longer distances (>6.5 Å), the CRDSD and PMPT experiments are more efficient. The PDSD was highly inefficient for transferring magnetization across distances greater than 6.5 Å (NAL crystal sample), due to small (15)N/(15)N dipolar couplings (<4.5 Hz). Interestingly, the mismatched Hartmann-Hahn condition present in the PMPT experiment gave more intense cross-peaks for lower (1)H and (15)N RF spinlock amplitudes (32 and 17 kHz, respectively) rather than higher values (55 and 50 kHz), suggesting a more complex magnetization transfer mechanism. Numerical simulations are in good agreement with the experimental findings, suggesting a combined PMPT and CRDSD effect. We conclude that, in order to assign SLF spectra and measure short- and long-range distances, the combined use of homonuclear correlation spectra, such as the ones surveyed in this work, are necessary.
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Affiliation(s)
- Nathaniel J Traaseth
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Kim JK, Lee SA, Shin S, Lee JY, Jeong KW, Nan YH, Park YS, Shin SY, Kim Y. Structural flexibility and the positive charges are the key factors in bacterial cell selectivity and membrane penetration of peptoid-substituted analog of Piscidin 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1913-25. [PMID: 20603100 DOI: 10.1016/j.bbamem.2010.06.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 06/11/2010] [Accepted: 06/25/2010] [Indexed: 01/25/2023]
Abstract
Piscidin 1 (Pis-1) is a novel cytotoxic peptide with a cationic alpha-helical structure isolated from the mast cells of hybrid striped bass. In our previous study, we showed that Pis-1[PG] with a substitution of Pro(8) for Gly(8) in Pis-1 had higher bacterial cell selectivity than Pis-1. We designed peptoid residue-substituted peptide, Pis-1[NkG], in which Gly(8) of Pis-1 was replaced with Nlys (Lys peptoid residue). Pis-1[NkG] had higher antibacterial activity and lower cytotoxicity against mammalian cells than Pis-1 and Pis-1[PG]. We determined the tertiary structure of Pis-1[PG] and Pis-1[NkG] in the presence of DPC micelles by NMR spectroscopy. Both peptides had a three-turn helix in the C-terminal region and a bent structure in the center. Pis-1[PG] has a rigid bent structure at Pro(8) whereas Pis-1[NkG] existed as a dynamic equilibrium of two conformers with a flexible hinge structure at Nlys(8). Depolarization of the membrane potential of Staphylococcus aureus and confocal laser-scanning microscopy study revealed that Pis-1[NkG] effectively penetrated the bacterial cell membrane and accumulated in the cytoplasm, whereas Pis-1[PG] did not penetrate the membrane but remained outside or on the cell surface. Introduction of a lysine peptoid at position 8 of Pis-1 provided conformational flexibility and increased the positive charge at the hinge region; both factors facilitated penetration of the bacterial cell membrane and conferred bacterial cell selectivity on Pis-1[NkG].
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Affiliation(s)
- Jin-Kyoung Kim
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Korea
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35
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Affiliation(s)
- Shi Bai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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36
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Can antimicrobial peptides scavenge around a cell in less than a second? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:228-34. [DOI: 10.1016/j.bbamem.2009.08.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 08/19/2009] [Accepted: 08/31/2009] [Indexed: 11/20/2022]
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37
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Efficient heteronuclear dipolar decoupling in NMR of static solid samples using phase-wiggled two-pulse phase modulation. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.10.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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