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Kobchikova PP, Efimov SV, Klochkov VV. Binding of Different Cyclosporin Variants to Micelles Evidenced by NMR and MD Simulations. MEMBRANES 2023; 13:196. [PMID: 36837699 PMCID: PMC9965255 DOI: 10.3390/membranes13020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/05/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Peptides play a critical role in the life of organisms, performing completely different functions. The biological activity of some peptides, such as cyclosporins, can be determined by the degree of membrane permeability. Thus, it becomes important to study how the molecule interacts with lipid bilayers. Cyclosporins C, E, H and L were characterised molecular dynamics simulation; NMR spectroscopy studies were also carried out for cyclosporins C and E. The comparison of one- and two-dimensional spectra revealed certain similarities between spatial structures of the studied cyclosporin variants. Upon dissolving in water containing DPC micelles, which serve as model membranes, subtle changes in the NMR spectra appear, but in a different way for different cyclosporins. In order to understand whether observed changes are related to any structural modifications, simulation of the interaction of the peptide with the phospholipid micelle was performed. The onset of the interaction was observed, when the peptide is trapped to the surface of the micelle. Simulations of this kind are also of interest in the light of the well-known membrane permeability of cyclosporin, which is important for its biological action.
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Guseva GB, Antina EV, Berezin MB, Smirnova AS, Pavelyev RS, Gilfanov IR, Shevchenko OG, Pestova SV, Izmest’ev ES, Rubtsova SA, Ostolopovskaya OV, Efimov SV, Klochkov VV, Rakhmatullin IZ, Timerova AF, Khodov IA, Lodochnikova OA, Islamov DR, Dorovatovskii PV, Nikitina LE, Boichuk SV. Design, Spectral Characteristics, Photostability, and Possibilities for Practical Application of BODIPY FL-Labeled Thioterpenoid. Bioengineering (Basel) 2022; 9:bioengineering9050210. [PMID: 35621488 PMCID: PMC9138141 DOI: 10.3390/bioengineering9050210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
This paper presents the design and a comparative analysis of the structural and solvation factors on the spectral and biological properties of the BODIPY biomarker with a thioterpene fragment. Covalent binding of the thioterpene moiety to the butanoic acid residue of meso-substituted BODIPY was carried out to find out the membranotropic effect of conjugate to erythrocytes, and to assess the possibilities of its practical application in bioimaging. The molecular structure of the conjugate was confirmed via X-ray, UV/vis-, NMR-, and MS-spectra. It was found that dye demonstrates high photostability and high fluorescence quantum yield (to ~100%) at 514–519 nm. In addition, the marker was shown to effectively penetrate the erythrocytes membrane in the absence of erythrotoxicity. The conjugation of BODIPY with thioterpenoid is an excellent way to increase affinity dyes to biostructures, including blood components.
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Affiliation(s)
- Galina B. Guseva
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, 153045 Ivanovo, Russia; (G.B.G.); (E.V.A.); (M.B.B.); (A.S.S.); (I.A.K.)
| | - Elena V. Antina
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, 153045 Ivanovo, Russia; (G.B.G.); (E.V.A.); (M.B.B.); (A.S.S.); (I.A.K.)
| | - Mikhail B. Berezin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, 153045 Ivanovo, Russia; (G.B.G.); (E.V.A.); (M.B.B.); (A.S.S.); (I.A.K.)
| | - Anastassia S. Smirnova
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, 153045 Ivanovo, Russia; (G.B.G.); (E.V.A.); (M.B.B.); (A.S.S.); (I.A.K.)
- Faculty of Fundamental and Applied Chemistry, Ivanovo State University of Chemistry and Technology, 7, Sheremetevskiy Avenue, 153000 Ivanovo, Russia
| | - Roman S. Pavelyev
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
| | - Ilmir R. Gilfanov
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
- Varnishes and Paints Department, Kazan National Research Technological University, 68 K. Marksa Street, 420015 Kazan, Russia
| | - Oksana G. Shevchenko
- Center of Collective Usage Molecular Biology, Institute of Biology, Komi Science Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya Street, 167982 Syktyvkar, Russia;
| | - Svetlana V. Pestova
- Medical Chemistry Laboratory, Institute of Chemistry, Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 48 Pervomaiskaya Street, 167000 Syktyvkar, Russia; (S.V.P.); (E.S.I.); (S.A.R.)
| | - Evgeny S. Izmest’ev
- Medical Chemistry Laboratory, Institute of Chemistry, Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 48 Pervomaiskaya Street, 167000 Syktyvkar, Russia; (S.V.P.); (E.S.I.); (S.A.R.)
| | - Svetlana A. Rubtsova
- Medical Chemistry Laboratory, Institute of Chemistry, Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 48 Pervomaiskaya Street, 167000 Syktyvkar, Russia; (S.V.P.); (E.S.I.); (S.A.R.)
| | - Olga V. Ostolopovskaya
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
- General and Organic Chemistry Department, Kazan State Medical University, 49 Butlerova Street, 420012 Kazan, Russia
| | - Sergey V. Efimov
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
| | - Vladimir V. Klochkov
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
| | - Ilfat Z. Rakhmatullin
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
| | - Ayzira F. Timerova
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
| | - Ilya A. Khodov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, 153045 Ivanovo, Russia; (G.B.G.); (E.V.A.); (M.B.B.); (A.S.S.); (I.A.K.)
| | - Olga A. Lodochnikova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzova Street, 420029 Kazan, Russia;
| | - Daut R. Islamov
- Laboratory for Structural Analysis of Biomacromolecules, Kazan Scientific Center, Russian Academy of Sciences, 18 Kremlevskaya Street, 420008 Kazan, Russia;
| | - Pavel V. Dorovatovskii
- National Research Centre “Kurchatov Institute”, 1 Academician Kurchatov Street, 123098 Moscow, Russia;
| | - Liliya E. Nikitina
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
- General and Organic Chemistry Department, Kazan State Medical University, 49 Butlerova Street, 420012 Kazan, Russia
| | - Sergei V. Boichuk
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
- General and Organic Chemistry Department, Kazan State Medical University, 49 Butlerova Street, 420012 Kazan, Russia
- Correspondence:
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3
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Schwarze B, Korn A, Höfling C, Zeitschel U, Krueger M, Roßner S, Huster D. Peptide backbone modifications of amyloid β (1-40) impact fibrillation behavior and neuronal toxicity. Sci Rep 2021; 11:23767. [PMID: 34887476 PMCID: PMC8660793 DOI: 10.1038/s41598-021-03091-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022] Open
Abstract
Fibril formation of amyloid β (Aβ) peptides is one of the key molecular events connected to Alzheimer's disease. The pathway of formation and mechanism of action of Aβ aggregates in biological systems is still object of very active research. To this end, systematic modifications of the Phe19-Leu34 hydrophobic contact, which has been reported in almost all structural studies of Aβ40 fibrils, helps understanding Aβ folding pathways and the underlying free energy landscape of the amyloid formation process. In our approach, a series of Aβ40 peptide variants with two types of backbone modifications, namely incorporation of (i) a methylene or an ethylene spacer group and (ii) a N-methylation at the amide functional group, of the amino acids at positions 19 or 34 was applied. These mutations are expected to challenge the inter-β-strand side chain contacts as well as intermolecular backbone β-sheet hydrogen bridges. Using a multitude of biophysical methods, it is shown that these backbone modifications lead, in most of the cases, to alterations in the fibril formation kinetics, a higher local structural heterogeneity, and a somewhat modified fibril morphology without generally impairing the fibril formation capacity of the peptides. The toxicological profile found for the variants depend on the type and extent of the modification.
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Affiliation(s)
- Benedikt Schwarze
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Alexander Korn
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Corinna Höfling
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Ulrike Zeitschel
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Martin Krueger
- Institute of Anatomy, Leipzig University, Liebigstr. 13, 04103, Leipzig, Germany
| | - Steffen Roßner
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany.
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4
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Shaw WJ, Tarasevich BJ, Buchko GW, Arachchige RMJ, Burton SD. Controls of nature: Secondary, tertiary, and quaternary structure of the enamel protein amelogenin in solution and on hydroxyapatite. J Struct Biol 2020; 212:107630. [PMID: 32979496 PMCID: PMC7744360 DOI: 10.1016/j.jsb.2020.107630] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/12/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
Amelogenin, a protein critical to enamel formation, is presented as a model for understanding how the structure of biomineralization proteins orchestrate biomineral formation. Amelogenin is the predominant biomineralization protein in the early stages of enamel formation and contributes to the controlled formation of hydroxyapatite (HAP) enamel crystals. The resulting enamel mineral is one of the hardest tissues in the human body and one of the hardest biominerals in nature. Structural studies have been hindered by the lack of techniques to evaluate surface adsorbed proteins and by amelogenin's disposition to self-assemble. Recent advancements in solution and solid state nuclear magnetic resonance (NMR) spectroscopy, atomic force microscopy (AFM), and recombinant isotope labeling strategies are now enabling detailed structural studies. These recent studies, coupled with insights from techniques such as CD and IR spectroscopy and computational methodologies, are contributing to important advancements in our structural understanding of amelogenesis. In this review we focus on recent advances in solution and solid state NMR spectroscopy and in situ AFM that reveal new insights into the secondary, tertiary, and quaternary structure of amelogenin by itself and in contact with HAP. These studies have increased our understanding of the interface between amelogenin and HAP and how amelogenin controls enamel formation.
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Affiliation(s)
- Wendy J Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Barbara J Tarasevich
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA; School of Molecular Bioscience, Washington State University, Pullman, WA 99164, USA
| | - Rajith M J Arachchige
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sarah D Burton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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5
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Negative charge of the AC-to-Hly linking segment modulates calcium-dependent membrane activities of Bordetella adenylate cyclase toxin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183310. [PMID: 32333856 DOI: 10.1016/j.bbamem.2020.183310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/31/2020] [Accepted: 04/13/2020] [Indexed: 02/08/2023]
Abstract
Two distinct conformers of the adenylate cyclase toxin (CyaA) appear to accomplish its two parallel activities within target cell membrane. The translocating conformer would deliver the N-terminal adenylyl cyclase (AC) enzyme domain across plasma membrane into cytosol of cells, while the pore precursor conformer would assemble into oligomeric cation-selective pores and permeabilize cellular membrane. Both toxin activities then involve a membrane-interacting 'AC-to-Hly-linking segment' (residues 400 to 500). Here, we report the NMR structure of the corresponding CyaA411-490 polypeptide in dodecylphosphocholine micelles and show that it consists of two α-helices linked by an unrestrained loop. The N-terminal α-helix (Gly418 to His439) remained solvent accessible, while the C-terminal α-helix (His457 to Phe485) was fully enclosed within detergent micelles. CyaA411-490 weakly bound Ca2+ ions (apparent KD 2.6 mM) and permeabilized negatively charged lipid vesicles. At high concentrations (10 μM) the CyaA411-490 polypeptide formed stable conductance units in artificial lipid bilayers with applied voltage, suggesting its possible transmembrane orientation in the membrane-inserted toxin. Mutagenesis revealed that two clusters of negatively charged residues within the 'AC-to-Hly-linking segment' (Glu419 to Glu432 and Asp445 to Glu448) regulate the balance between the AC domain translocating and pore-forming capacities of CyaA in function of calcium concentration.
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6
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Xie SX, Boone K, VanOosten SK, Yuca E, Song L, Ge X, Ye Q, Spencer P, Tamerler C. Peptide Mediated Antimicrobial Dental Adhesive System. APPLIED SCIENCES (BASEL, SWITZERLAND) 2019; 9:557. [PMID: 33542835 PMCID: PMC7857482 DOI: 10.3390/app9030557] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The most common cause for dental composite failures is secondary caries due to invasive bacterial colonization of the adhesive/dentin (a/d) interface. Innate material weakness often lead to an insufficient seal between the adhesive and dentin. Consequently, bacterial by-products invade the porous a/d interface leading to material degradation and dental caries. Current approaches to achieve antibacterial properties in these materials continue to raise concerns regarding hypersensitivity and antibiotic resistance. Herein, we have developed a multi-faceted, bio-functionalized approach to overcome the vulnerability of such interfaces. An antimicrobial adhesive formulation was designed using a combination of antimicrobial peptide and a ε-polylysine resin system. Effector molecules boasting innate immunity are brought together with a biopolymer offering a two-fold biomimetic design approach. The selection of ε-polylysine was inspired due to its non-toxic nature and common use as food preservative. Biomolecular characterization and functional activity of our engineered dental adhesive formulation were assessed and the combinatorial formulation demonstrated significant antimicrobial activity against Streptococcus mutans. Our antimicrobial peptide-hydrophilic adhesive hybrid system design offers advanced, biofunctional properties at the critical a/d interface.
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Affiliation(s)
- Sheng-Xue Xie
- Institute for Bioengineering Research, University of Kansas, 1530 W. 15th St., Lawrence, KS 66045, USA
| | - Kyle Boone
- Institute for Bioengineering Research, University of Kansas, 1530 W. 15th St., Lawrence, KS 66045, USA
- Bioengineering Program, 1530 W. 15th St., University of Kansas, Lawrence, KS 66045, USA
| | - Sarah Kay VanOosten
- Institute for Bioengineering Research, University of Kansas, 1530 W. 15th St., Lawrence, KS 66045, USA
- Bioengineering Program, 1530 W. 15th St., University of Kansas, Lawrence, KS 66045, USA
| | - Esra Yuca
- Institute for Bioengineering Research, University of Kansas, 1530 W. 15th St., Lawrence, KS 66045, USA
- Department of Molecular Biology and Genetics, Yildiz Technical University, 34210 Istanbul, Turkey
| | - Linyong Song
- Institute for Bioengineering Research, University of Kansas, 1530 W. 15th St., Lawrence, KS 66045, USA
| | - Xueping Ge
- Institute for Bioengineering Research, University of Kansas, 1530 W. 15th St., Lawrence, KS 66045, USA
| | - Qiang Ye
- Institute for Bioengineering Research, University of Kansas, 1530 W. 15th St., Lawrence, KS 66045, USA
| | - Paulette Spencer
- Institute for Bioengineering Research, University of Kansas, 1530 W. 15th St., Lawrence, KS 66045, USA
- Bioengineering Program, 1530 W. 15th St., University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, 1530 W. 15th St., University of Kansas, Lawrence, KS 66045, USA
| | - Candan Tamerler
- Institute for Bioengineering Research, University of Kansas, 1530 W. 15th St., Lawrence, KS 66045, USA
- Bioengineering Program, 1530 W. 15th St., University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, 1530 W. 15th St., University of Kansas, Lawrence, KS 66045, USA
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7
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Mukhija A, Kishore N. Prevention and Disintegration of Human Serum Albumin Fibrils under Physiological Conditions: Biophysical Aspects. J Phys Chem B 2018; 122:9896-9906. [DOI: 10.1021/acs.jpcb.8b07140] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Achal Mukhija
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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8
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Adler J, Scheidt HA, Lemmnitzer K, Krueger M, Huster D. N-terminal lipid conjugation of amyloid β(1-40) leads to the formation of highly ordered N-terminally extended fibrils. Phys Chem Chem Phys 2018; 19:1839-1846. [PMID: 28000812 DOI: 10.1039/c6cp05982a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fibril formation of amyloid β(1-40) (Aβ(1-40)) peptides N-terminally lipid modified with saturated octanoyl or palmitoyl lipid chains was investigated. Lipid modification of Aβ(1-40) significantly accelerates the fibrillation kinetics of the Aβ peptides as revealed by ThT fluorescence. Electron microscopy and X-ray diffraction results indicate a heterogeneous cross-β structure of the fibrils formed by the lipid-conjugated peptides. Solid-state NMR was used to investigate structural features of these fibrils. The lipid moieties form dynamic and loosely structured heterogeneous lipid assemblies as inferred from 2H NMR of the deuterated lipid chains. 13C NMR studies of selected isotopic labels reveals that in addition to Phe19 and Val39, which are part of the canonical cross-β structure, also N-terminal residues (Ala2, Phe4, Val12) are found in β-strand conformation. This suggests that the increased hydrophobicity induced by the lipid modification, alters the energy landscape rendering an N-terminal extension of the β-sheet structure favorable. Furthermore, the fibrils formed by the Aβ-lipid hybrids are much more rigid than wildtype Aβ fibrils as inferred from NMR order parameter measurements. Taken together, increasing the local hydrophobicity of the Aβ N-terminus results in highly ordered but heterogeneous amyloid fibrils with extended N-terminal β-sheet structure.
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Affiliation(s)
- Juliane Adler
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany.
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany.
| | - Katharina Lemmnitzer
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany.
| | - Martin Krueger
- Institute for Anatomy, Leipzig University, D-04103 Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany.
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9
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Nikitina LE, Kiselev SV, Startseva VA, Bodrov AV, Azizova ZR, Shipina OT, Fedyunina IV, Boichuk SV, Lodochnikova OA, Klochkov VV, Galiullina LF, Khaliullina AV. Sulfur-Containing Monoterpenoids as Potential Antithrombotic Drugs: Research in the Molecular Mechanism of Coagulation Activity Using Pinanyl Sulfoxide as an Example. Front Pharmacol 2018. [PMID: 29515444 PMCID: PMC5825891 DOI: 10.3389/fphar.2018.00116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In this article we present the synthesis of enantiomerically pure sulfoxide and study the influence of this compound on hemostasis. Detailed NMR studies and molecular dynamics simulations using sodium dodecyl sulfate (SDS) membrane models indicated that the bicyclic fragment of sulfoxide was embedded into the SDS micelle whereas the -SO(CH2)2OH fragment remained on the surface of the micelle and was in contact with the solvent. We also found that the pro-coagulative activity of sulfoxide was due to its ability to inhibit platelet activation and inhibited the catalytic activity of phospholipid surface which was involved in formation of coagulation clotting factor complexes.
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Affiliation(s)
- Liliya E Nikitina
- Department of General and Organic Chemistry, Kazan State Medical University, Kazan, Russia.,Medical Physics Department, Institute of Physics, Kazan Federal University, Kazan, Russia
| | - Sergei V Kiselev
- Department of General and Organic Chemistry, Kazan State Medical University, Kazan, Russia
| | - Valeriya A Startseva
- Department of General and Organic Chemistry, Kazan State Medical University, Kazan, Russia
| | - Andrei V Bodrov
- Department of General and Organic Chemistry, Kazan State Medical University, Kazan, Russia
| | - Zulfiya R Azizova
- Department of General and Organic Chemistry, Kazan State Medical University, Kazan, Russia
| | - Olga T Shipina
- Department of Chemistry and Technology of Macromolecular Compounds, Kazan National Research Technological University, Kazan, Russia
| | - Inna V Fedyunina
- Department of General and Organic Chemistry, Kazan State Medical University, Kazan, Russia
| | - Sergei V Boichuk
- Department of General and Organic Chemistry, Kazan State Medical University, Kazan, Russia
| | - Olga A Lodochnikova
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | - Vladimir V Klochkov
- Medical Physics Department, Institute of Physics, Kazan Federal University, Kazan, Russia
| | - Leisan F Galiullina
- Medical Physics Department, Institute of Physics, Kazan Federal University, Kazan, Russia
| | - Aliya V Khaliullina
- Department of General and Organic Chemistry, Kazan State Medical University, Kazan, Russia.,Medical Physics Department, Institute of Physics, Kazan Federal University, Kazan, Russia
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10
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Zerfaß C, Buchko GW, Shaw WJ, Hobe S, Paulsen H. Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P 5 S 3 during silicic acid condensation and silica decondensation. Proteins 2017; 85:2111-2126. [PMID: 28799215 PMCID: PMC5760248 DOI: 10.1002/prot.25366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/08/2022]
Abstract
The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5 S3 , a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains 5 protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5 S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2 ) at globally undersaturated concentrations. The secondary structure of P5 S3 during these 2 processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in the absence of silicate. The NMR studies of dual-labeled (13 C, 15 N) P5 S3 revealed a disordered structure at pH 2.8 and 4.5. Within the pH range of 4.5-9.5 in the absence of silicic acid, the CD data showed a disordered structure with the suggestion of some polyproline II character. Upon silicic acid polymerization and during dissolution of preformed silica, the CD spectrum of P5 S3 indicated partial transition into an α-helical conformation which was transient during silica-dissolution. The secondary structural changes observed for P5 S3 correlate with the presence of oligomeric/polymeric silicic acid, presumably due to P5 S3 -silica interactions. These P5 S3 -silica interactions appear, at least in part, ionic in nature since negatively charged dodecylsulfate caused similar perturbations to the P5 S3 CD spectrum as observed with silica, while uncharged ß-d-dodecyl maltoside did not affect the CD spectrum of P5 S3 . Thus, with an associated increase in α-helical character, P5 S3 influences both the condensation of silicic acid into silica and its decondensation back to silicic acid.
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Affiliation(s)
- Christian Zerfaß
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
- Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Garry W. Buchko
- Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Wendy J. Shaw
- Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Stephan Hobe
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Harald Paulsen
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
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11
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Khan MV, Zaman M, Chandel TI, Siddiqui MK, Ajmal MR, Abdelhameed AS, Khan RH. Cationic surfactant mediated fibrillogenesis in bovine liver catalase: a biophysical approach. J Biomol Struct Dyn 2017; 36:2543-2557. [DOI: 10.1080/07391102.2017.1363085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mohsin Vahid Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Masihuz Zaman
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Tajalli Ilm Chandel
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Khursheed Siddiqui
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohd. Rehan Ajmal
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Rizwan Hasan Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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12
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Nikitina LE, Kiselev SV, Bodrov AV, Startseva VA, Artemova NP, Klochkov VV, Galiullina LF, Aganova OV, Khaliullina AV, Lodochnikova OA, Azizova ZR, Rakhmatullina AA. Development of Approaches to the Study of the Interaction of Biologically Active Thioterpenoids with Model Membranes. BIONANOSCIENCE 2017. [DOI: 10.1007/s12668-017-0432-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Interaction of the amyloid β peptide with sodium dodecyl sulfate as a membrane-mimicking detergent. J Biol Phys 2016; 42:299-315. [PMID: 26984615 PMCID: PMC4942415 DOI: 10.1007/s10867-016-9408-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 01/04/2016] [Indexed: 12/11/2022] Open
Abstract
The amyloid β (A β) peptide is important in the context of Alzheimer’s disease, since it is one of the major components of the fibrils that constitute amyloid plaques. Agents that can influence fibril formation are important, and of those, membrane mimics are particularly relevant, because the hydrophobic part of A β suggests a possible membrane activity of the peptide. We employed spin-label EPR to investigate the aggregation process of A β1–40 in the presence of the sodium dodecyl sulfate (SDS) detergent as a membrane-mimicking agent. In this work, the effect of SDS on A β is studied using two positions of spin label, the N-terminus and position 26. By comparing the two label positions, the effect of local mobility of the spin label is eliminated, revealing A β aggregation in the SDS concentration regime below the critical micelle concentration (CMC). We demonstrate that, at low SDS concentrations, the N-terminus of A β participates in the solubilization, most likely by being located at the particle–water interface. At higher SDS concentrations, an SDS-solubilized state that is a precursor to the one A β/micelle state above the CMC of SDS prevails. We propose that A β is membrane active and that aggregates include SDS. This study reveals the unique potential of EPR in studying A β aggregation in the presence of detergent.
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14
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Structural studies of pravastatin and simvastatin and their complexes with SDS micelles by NMR spectroscopy. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Lhor M, Méthot M, Horchani H, Salesse C. Structure of the N-terminal segment of human retinol dehydrogenase 11 and its preferential lipid binding using model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:878-85. [DOI: 10.1016/j.bbamem.2014.12.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 12/09/2014] [Accepted: 12/15/2014] [Indexed: 11/25/2022]
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16
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Galiullina LF, Rakhmatullin IZ, Klochkova EA, Aganov AV, Klochkov VV. Structure of pravastatin and its complex with sodium dodecyl sulfate micelles studied by NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:110-114. [PMID: 25264019 DOI: 10.1002/mrc.4146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/13/2014] [Accepted: 08/20/2014] [Indexed: 06/03/2023]
Abstract
The aim of this work was to study the mechanisms of interaction between pravastatin and cell membranes using model membranes (sodium dodecyl sulfate micelles) by nuclear magnetic resonance spectroscopy methods. On the basis of the nuclear magnetic resonance experiments, it was established that pravastatin can form intermolecular complexes with sodium dodecyl sulfate micelles by the interaction of its hydrophilic groups with the polar surface of the micelle. Conformational features of pravastatin molecule were also studied.
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Affiliation(s)
- L F Galiullina
- Institute of Physics, Kazan Federal University, 420008, Kazan, Russia
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17
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Yaseen Z, Rehman SU, Tabish M, Shalla AH, Kabir-ud-Din KUD. Modulation of bovine serum albumin fibrillation by ester bonded and conventional gemini surfactants. RSC Adv 2015. [DOI: 10.1039/c5ra08923a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Modulation of bovine serum albumin fibrillation by gemini surfactants.
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Affiliation(s)
- Zahid Yaseen
- Department of Chemistry
- Islamic University of Science and Technology
- Pulwama 192122
- India
| | - Sayeed Ur Rehman
- Department of Biochemistry
- Faculty of Life Sciences
- Aligarh Muslim University
- Aligarh-202002
- India
| | - Mohammad Tabish
- Department of Biochemistry
- Faculty of Life Sciences
- Aligarh Muslim University
- Aligarh-202002
- India
| | - Aabid H. Shalla
- Department of Chemistry
- Islamic University of Science and Technology
- Pulwama 192122
- India
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18
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Arias M, Nguyen LT, Kuczynski AM, Lejon T, Vogel HJ. Position-Dependent Influence of the Three Trp Residues on the Membrane Activity of the Antimicrobial Peptide, Tritrpticin. Antibiotics (Basel) 2014; 3:595-616. [PMID: 27025758 PMCID: PMC4790384 DOI: 10.3390/antibiotics3040595] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/23/2014] [Accepted: 10/23/2014] [Indexed: 01/30/2023] Open
Abstract
Antimicrobial peptides (AMPs) constitute promising candidates for the development of new antibiotics. Among the ever-expanding family of AMPs, tritrpticin has strong antimicrobial activity against a broad range of pathogens. This 13-residue peptide has an unusual amino acid sequence that is almost symmetrical and features three central Trp residues with two Arg residues near each end of the peptide. In this work, the role of the three sequential Trp residues in tritrpticin was studied in a systematic fashion by making a series of synthetic peptides with single-, double- and triple-Trp substitutions to Tyr or Ala. 1H NMR and fluorescence spectroscopy demonstrated the ability of all of the tritrpticin-analog peptides to interact with negatively-charged membranes. Consequently, most tritrpticin analogs exhibited the ability to permeabilize synthetic ePC:ePG (egg-yolk phosphatidylcholine (ePC), egg-yolk phosphatidylglycerol (ePG)) vesicles and live Escherichia coli bacteria. The membrane perturbation characteristics were highly dependent on the location of the Trp residue substitution, with Trp6 being the most important residue and Trp8 the least. The membrane permeabilization activity of the peptides in synthetic and biological membranes was directly correlated with the antimicrobial potency of the peptides against E. coli. These results contribute to the understanding of the role of each of the three Trp residues to the antimicrobial activity of tritrpticin.
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Affiliation(s)
- Mauricio Arias
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada.
| | - Leonard T Nguyen
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada.
| | - Andrea M Kuczynski
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada.
| | - Tore Lejon
- Department of Chemistry, Faculty of Science, UiT-The Artic University of Norway, Tromsø N-9037, Norway.
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada.
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19
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Pandey NK, Ghosh S, Dasgupta S. Effect of surfactants on preformed fibrils of human serum albumin. Int J Biol Macromol 2013; 59:39-45. [DOI: 10.1016/j.ijbiomac.2013.04.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/08/2013] [Accepted: 04/08/2013] [Indexed: 11/25/2022]
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20
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Efimov S, Karataeva F, Aganov A, Berger S, Klochkov V. Spatial structure of cyclosporin A and insight into its flexibility. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Spatial structure of heptapeptide Glu-Ile-Leu-Asn-His-Met-Lys, a fragment of the HIV enhancer prostatic acid phosphatase, in aqueous and SDS micelle solutions. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Usachev KS, Efimov SV, Yulmetov AR, Filippov AV, Antzutkin ON, Afonin S, Klochkov VV. Spatial structure of heptapeptide Aβ(16-22) (beta-amyloid Aβ(1-40) active fragment) in solution and in complex with a biological membrane model. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:784-792. [PMID: 23034896 DOI: 10.1002/mrc.3880] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 06/29/2012] [Accepted: 09/04/2012] [Indexed: 06/01/2023]
Abstract
The spatial structure of an active fragment of beta-amyloid Aβ(1-40) heptapeptide Aβ(16-22) (Lys-Leu-Val-Phe-Phe-Ala-Glu) in aqueous buffer solution and in complex with sodium dodecyl sulfate micelles as a model membrane system was investigated by (1)H NMR spectroscopy and two-dimensional NMR (TOCSY, HSQC-HECADE (Heteronuclear Couplings from ASSCI-domain experiments with E.COSY-type crosspeaks), NOESY) spectroscopy. Complex formation was confirmed by the chemical shift changes of the heptapeptide's (1)H NMR spectra, as well as by the signs and values of the NOE effects in different environments. We compared the spatial structure of the heptapeptide in borate buffer solution and in complex with a model of the cell surface membrane.
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Affiliation(s)
- Konstantin S Usachev
- Kazan (Volga Region) Federal University, 18 Kremlevskaya St., 420008, Kazan, Russian Federation
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23
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Pedersen SL, Bhatia VK, Jurt S, Paulsson JF, Pedersen MH, Jorgensen R, Holst B, Stamou D, Vrang N, Zerbe O, Jensen KJ. Improving membrane binding as a design strategy for amphipathic peptide hormones: 2-helix variants of PYY3-36. J Pept Sci 2012; 18:579-87. [DOI: 10.1002/psc.2436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/06/2012] [Indexed: 12/20/2022]
Affiliation(s)
- Søren L. Pedersen
- Department of Chemistry, Faculty of Science; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
- The Lundbeck Foundation Center for Biomembranes in Nanomedicine; Unversity of Copenhagen; Denmark
| | - Vikram K. Bhatia
- Faculty of Health Sciences; University of Copenhagen; Blegdamsvej 3B 2200 Copenhagen N Denmark
- Novozymes A/S; Bagsvaerd Denmark
| | - Simon Jurt
- Institute of Organic Chemistry; University of Zurich; Winterthurerstrasse 190 CH 8057 Zurich Switzerland
| | | | - Maria H. Pedersen
- Department of Chemistry, Faculty of Science; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | | | - Birgitte Holst
- Faculty of Health Sciences; University of Copenhagen; Blegdamsvej 3B 2200 Copenhagen N Denmark
| | - Dimitrios Stamou
- Department of Chemistry, Faculty of Science; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
- The Lundbeck Foundation Center for Biomembranes in Nanomedicine; Unversity of Copenhagen; Denmark
| | - Niels Vrang
- gubra Aps; Agern Allé 1 2970 Hørsholm Denmark
| | - Oliver Zerbe
- Institute of Organic Chemistry; University of Zurich; Winterthurerstrasse 190 CH 8057 Zurich Switzerland
| | - Knud J. Jensen
- Department of Chemistry, Faculty of Science; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
- The Lundbeck Foundation Center for Biomembranes in Nanomedicine; Unversity of Copenhagen; Denmark
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24
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Rekdal Ø, Haug BE, Kalaaji M, Hunter HN, Lindin I, Israelsson I, Solstad T, Yang N, Brandl M, Mantzilas D, Vogel HJ. Relative spatial positions of tryptophan and cationic residues in helical membrane-active peptides determine their cytotoxicity. J Biol Chem 2012; 287:233-244. [PMID: 22057278 PMCID: PMC3249074 DOI: 10.1074/jbc.m111.279281] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 11/03/2011] [Indexed: 11/06/2022] Open
Abstract
The cytotoxic activity of 10 analogs of the idealized amphipathic helical 21-mer peptide (KAAKKAA)3, where three of the Ala residues at different positions have been replaced with Trp residues, has been investigated. The peptide's cytotoxic activity was found to be markedly dependent upon the position of the Trp residues within the hydrophobic sector of an idealized α-helix. The peptides with Trp residues located opposite the cationic sector displayed no antitumor activity, whereas those peptides with two or three Trp residues located adjacent to the cationic sector exhibited high cytotoxic activity when tested against three different cancer cell lines. Dye release experiments revealed that in contrast to the peptides with Trp residues located opposite the cationic sector, the peptides with Trp residues located adjacent to the cationic sector induced a strong permeabilizing activity from liposomes composed of a mixture of zwitterionic phosphatidylcholine and negatively charged phosphatidylserine (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS)) (2:1) but not from liposomes composed of zwitterionic phosphatidylcholine, POPC. Fluorescence blue shift and quenching experiments revealed that Trp residues inserted deeper into the hydrophobic environment of POPC/POPS liposomes for peptides with high cytotoxic activity. Through circular dichroism studies, a correlation between the cytotoxic activity and the α-helical propensity was established. Structural studies of one inactive and two active peptides in the presence of micelles using NMR spectroscopy showed that only the active peptides adopted highly coiled to helical structures when bound to a membrane surface.
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Affiliation(s)
- Øystein Rekdal
- Institute of Medical Biology, Faculty of Medicine; Lytix Biopharma AS, NO-9294 Tromsø, Norway.
| | - Bengt Erik Haug
- Centre for Pharmacy and Department of Chemistry, University of Bergen, NO-5007 Bergen, Norway
| | | | - Howard N Hunter
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Inger Lindin
- Institute of Medical Biology, Faculty of Medicine
| | | | | | - Nannan Yang
- Institute of Medical Biology, Faculty of Medicine
| | - Martin Brandl
- Drug Transport and Delivery Group, Department of Pharmacy, University of Tromsø, NO-9037 Tromsø, Norway; Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Dimitrios Mantzilas
- Department of Molecular Bioscience, University of Oslo, NO-0316 Oslo, Norway
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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25
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Park TJ, Kim JS, Ahn HC, Kim Y. Solution and solid-state NMR structural studies of antimicrobial peptides LPcin-I and LPcin-II. Biophys J 2011; 101:1193-201. [PMID: 21889457 DOI: 10.1016/j.bpj.2011.06.067] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 06/07/2011] [Accepted: 06/23/2011] [Indexed: 11/26/2022] Open
Abstract
Lactophoricin (LPcin-I) is an antimicrobial, amphiphatic, cationic peptide with 23-amino acid residues isolated from bovine milk. Its analogous peptide, LPcin-II, lacks six N-terminal amino acids compared to LPcin-I. Interestingly, LPcin-II does not display any antimicrobial activity, whereas LPcin-I inhibits the growth of both Gram-negative and Gram-positive bacteria without exhibiting any hemolytic activity. Uniformly (15)N-labeled LPcin peptides were prepared by the recombinant expression of fusion proteins in Escherichia coli, and their properties were characterized by electrospray ionization mass spectrometry, circular dichroism spectroscopy, and antimicrobial activity tests. To understand the structure-activity relationship of these two peptides, they were studied in model membrane environments by a combination of solution and solid-state NMR spectroscopy. We determined the tertiary structure of LPcin-I and LPcin-II in the presence of dodecylphosphorylcholine micelles by solution NMR spectroscopy. Magnetically aligned unflipped bicelle samples were used to investigate the structure and topology of LPcin-I and LPcin-II by solid-state NMR spectroscopy.
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Affiliation(s)
- Tae-Joon Park
- Department of Chemistry and Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yong-In, Korea
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26
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Arsequell G, Rosa M, Mayato C, Dorta RL, Gonzalez-Nunez V, Barreto-Valer K, Marcelo F, Calle LP, Vázquez JT, Rodríguez RE, Jiménez-Barbero J, Valencia G. Synthesis, biological evaluation and structural characterization of novel glycopeptide analogues of nociceptin N/OFQ. Org Biomol Chem 2011; 9:6133-42. [PMID: 21773621 DOI: 10.1039/c1ob05197k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
To examine if the biological activity of the N/OFQ peptide, which is the native ligand of the pain-related and viable drug target NOP receptor, could be modulated by glycosylation and if such effects could be conformationally related, we have synthesized three N/OFQ glycopeptide analogues, namely: [Thr(5)-O-α-D-GalNAc-N/OFQ] (glycopeptide 1), [Ser(10)-O-α-D-GalNAc]-N/OFQ (glycopeptide 2) and [Ser(10)-O-β-D-GlcNAc]-N/OFQ] (glycopeptide 3). They were tested for biological activity in competition binding assays using the zebrafish animal model in which glycopeptide 2 exhibited a slightly improved binding affinity, whereas glycopeptide 1 showed a remarkably reduced binding affinity compared to the parent compound and glycopeptide 3. The structural analysis of these glycopeptides and the parent N/OFQ peptide by NMR and circular dichroism indicated that their aqueous solutions are mainly populated by random coil conformers. However, in membrane mimic environments a certain proportion of the molecules of all these peptides exist as α-helix structures. Interestingly, under these experimental conditions, glycopeptide 1 (glycosylated at Thr-5) exhibited a population of folded hairpin-like geometries. From these facts it is tempting to speculate that nociceptin analogues showing linear helical structures are more complementary and thus interact more efficiently with the native NOP receptor than folded structures, since glycopeptide 1 showed a significantly reduced binding affinity for the NOP receptor.
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Affiliation(s)
- Gemma Arsequell
- Instituto de Química Avanzada de Cataluña (IQAC-CSIC), Barcelona, Spain
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27
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Conformational and membrane interaction studies of the antimicrobial peptide alyteserin-1c and its analogue [E4K]alyteserin-1c. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1975-84. [DOI: 10.1016/j.bbamem.2011.04.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 04/21/2011] [Accepted: 04/22/2011] [Indexed: 11/22/2022]
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28
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Dorovkov MV, Kostyukova AS, Ryazanov AG. Phosphorylation of annexin A1 by TRPM7 kinase: a switch regulating the induction of an α-helix. Biochemistry 2011; 50:2187-93. [PMID: 21280599 PMCID: PMC3062375 DOI: 10.1021/bi101963h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
TRPM7 is an unusual bifunctional protein consisting of an α-kinase domain fused to a TRP ion channel. Previously, we have identified annexin A1 as a substrate for TRPM7 kinase and found that TRPM7 phosphorylates annexin A1 at Ser5 within the N-terminal α-helix. Annexin A1 is a Ca(2+)-dependent membrane binding protein, which has been implicated in membrane trafficking and reorganization. The N-terminal tail of annexin A1 can interact with either membranes or S100A11 protein, and it adopts the conformation of an amphipathic α-helix upon these interactions. Moreover, the existing evidence indicates that the formation of an α-helix is essential for these interactions. Here we show that phosphorylation at Ser5 prevents the N-terminal peptide of annexin A1 from adopting an α-helical conformation in the presence of membrane-mimetic micelles as well as phospholipid vesicles. We also show that phosphorylation at Ser5 dramatically weakens the binding of the peptide to S100A11. Our data suggest that phosphorylation at Ser5 regulates the interaction of annexin A1 with membranes as well as S100A11 protein.
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Affiliation(s)
- Maxim V Dorovkov
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey 08854, United States.
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29
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Qureshi T, Goto NK. Contemporary methods in structure determination of membrane proteins by solution NMR. Top Curr Chem (Cham) 2011; 326:123-85. [PMID: 22160391 DOI: 10.1007/128_2011_306] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Integral membrane proteins are vital to life, being responsible for information and material exchange between a cell and its environment. Although high-resolution structural information is needed to understand how these functions are achieved, membrane proteins remain an under-represented subset of the protein structure databank. Solution NMR is increasingly demonstrating its ability to help address this knowledge shortfall, with the development of a diverse array of techniques to counter the challenges presented by membrane proteins. Here we document the advances that are helping to define solution NMR as an effective tool for membrane protein structure determination. Developments introduced over the last decade in the production of isotope-labeled samples, reconstitution of these samples into the growing selection of NMR-compatible membrane-mimetic systems, and the approaches used for the acquisition and application of structural restraints from these complexes are reviewed.
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Affiliation(s)
- Tabussom Qureshi
- Department of Chemistry, University of Ottawa, Ottawa, ON, Canada
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30
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Koch K, Afonin S, Ieronimo M, Berditsch M, Ulrich AS. Solid-State 19F-NMR of Peptides in Native Membranes. Top Curr Chem (Cham) 2011; 306:89-118. [DOI: 10.1007/128_2011_162] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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31
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Tzeng J, Lee BL, Sykes BD, Fliegel L. Structural and functional analysis of transmembrane segment VI of the NHE1 isoform of the Na+/H+ exchanger. J Biol Chem 2010; 285:36656-65. [PMID: 20843797 PMCID: PMC2978594 DOI: 10.1074/jbc.m110.161471] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 08/23/2010] [Indexed: 01/17/2023] Open
Abstract
The Na(+)/H(+) exchanger isoform 1 is a ubiquitously expressed integral membrane protein. It resides on the plasma membrane of cells and regulates intracellular pH in mammals by extruding an intracellular H(+) in exchange for one extracellular Na(+). We characterized structural and functional aspects of the transmembrane segment (TM) VI (residues 227-249) by using cysteine scanning mutagenesis and high resolution NMR. Each residue of TM VI was mutated to cysteine in the background of the cysteineless NHE1 protein, and the sensitivity to water-soluble sulfhydryl-reactive compounds (2-(trimethylammonium)ethyl)methanethiosulfonate (MTSET) and (2-sulfonatoethyl)methanethiosulfonate (MTSES) was determined for those residues with significant activity remaining. Three residues were essentially inactive when mutated to Cys: Asp(238), Pro(239), and Glu(247). Of the remaining residues, proteins with the mutations N227C, I233C, and L243C were strongly inhibited by MTSET, whereas amino acids Phe(230), Gly(231), Ala(236), Val(237), Ala(244), Val(245), and Glu(248) were partially inhibited by MTSET. MTSES did not affect the activity of the mutant NHE1 proteins. The structure of a peptide representing TM VI was determined using high resolution NMR spectroscopy in dodecylphosphocholine micelles. TM VI contains two helical regions oriented at an approximate right angle to each other (residues 229-236 and 239-250) surrounding a central unwound region. This structure bears a resemblance to TM IV of the Escherichia coli protein NhaA. The results demonstrate that TM VI of NHE1 is a discontinuous pore-lining helix with residues Asn(227), Ile(233), and Leu(243) lining the translocation pore.
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Affiliation(s)
- Jennifer Tzeng
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Brian L. Lee
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Brian D. Sykes
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Larry Fliegel
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Syncytial phenotype of C-terminally truncated herpes simplex virus type 1 gB is associated with diminished membrane interactions. J Virol 2010; 84:4923-35. [PMID: 20200237 DOI: 10.1128/jvi.00206-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cytoplasmic domain of glycoprotein B (gB) from herpes simplex virus type 1 (HSV-1) is an important regulator of membrane fusion. C-terminal truncations of the cytoplasmic domain lead to either hyperfusion or fusion-null phenotypes. Currently, neither the structure of the cytoplasmic domain nor its mechanism of fusion regulation is known. Here we show, for the first time, that the full-length cytoplasmic domain of HSV-1 gB associates stably with lipid membranes, preferentially binding to membranes containing anionic head groups. This interaction involves a large increase in helical content. However, the truncated cytoplasmic domains associated with the hyperfusion phenotype show a small increase in helical structure and a diminished association with lipid membranes, whereas the one associated with the fusion-null phenotype shows no increase in helical structure and only a minimal association with lipid membranes. We hypothesize that stable binding to lipid membranes is an important part of the mechanism by which the cytoplasmic domain negatively regulates membrane fusion. Moreover, our experiments with truncated cytoplasmic domains point to two specific regions that are critical for membrane interactions. Taken together, our work provides several important new insights into the architecture of the cytoplasmic domain of HSV-1 gB and its interaction with lipid membranes.
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33
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Saviello MR, Malfi S, Campiglia P, Cavalli A, Grieco P, Novellino E, Carotenuto A. New Insight into the Mechanism of Action of the Temporin Antimicrobial Peptides. Biochemistry 2010; 49:1477-85. [DOI: 10.1021/bi902166d] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Maria Rosaria Saviello
- Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, I-80131 Naples, Italy
| | - Stefania Malfi
- Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, I-80131 Naples, Italy
| | - Pietro Campiglia
- Department of Pharmaceutical Science, University of Salerno, I-84084 Fisciano, Salerno, Italy
| | - Andrea Cavalli
- Department of Pharmaceutical Science, University of Bologna, I-40126 Bologna, Italy
- Department of Drug Discovery and Development, Italian Institute of Technology, I-16163 Genova, Italy
| | - Paolo Grieco
- Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, I-80131 Naples, Italy
| | - Ettore Novellino
- Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, I-80131 Naples, Italy
| | - Alfonso Carotenuto
- Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, I-80131 Naples, Italy
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34
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Grimaldi M, Scrima M, Esposito C, Vitiello G, Ramunno A, Limongelli V, D'Errico G, Novellino E, D'Ursi AM. Membrane charge dependent states of the beta-amyloid fragment Abeta (16-35) with differently charged micelle aggregates. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:660-71. [PMID: 20045392 DOI: 10.1016/j.bbamem.2009.12.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 12/08/2009] [Accepted: 12/16/2009] [Indexed: 11/24/2022]
Abstract
Abeta (16-35) is the hydrophobic central core of beta-amyloid peptide, the main component of plaques found in the brain tissue of Alzheimer's disease patients. Depending on the conditions present, beta-amyloid peptides undergo a conformational transition from random coil or alpha-helical monomers, to highly toxic beta-sheet oligomers and aggregate fibrils. The behavior of beta-amyloid peptide at plasma membrane level has been extensively investigated, and membrane charge has been proved to be a key factor modulating its conformational properties. In the present work we probed the conformational behavior of Abeta (16-35) in response to negative charge modifications of the micelle surface. CD and NMR conformational analyses were performed in negatively charged pure SDS micelles and in zwitterionic DPC micelles "doped" with small amounts of SDS. To analyze the tendency of Abeta (16-35) to interact with these micellar systems, we performed EPR experiments on three spin-labeled analogues of Abeta (16-35), bearing the methyl 3-(2,2,5,5-tetramethyl-1-oxypyrrolinyl) methanethiolsulfonate spin label at the N-terminus, in the middle of the sequence and at the C-terminus, respectively. Our conformational data show that, by varying the negative charge of the membrane, Abeta (16-35) undergoes a conformational transition from a soluble helical-kink-helical structure, to a U-turn shaped conformation that resembles protofibril models.
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Affiliation(s)
- Manuela Grimaldi
- Department of Pharmaceutical Sciences, University of Salerno, I-84084 Fisciano, Italy
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35
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Zdobinsky T, Scherkenbeck J, Zerbe O, Antonicek H, Chen H. Structures of Micelle-Bound Selected Insect Neuropeptides and Analogues: Implications for Receptor Selection. Chembiochem 2009; 10:2644-53. [DOI: 10.1002/cbic.200900450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Kim HJ, Howell SC, Van Horn WD, Jeon YH, Sanders CR. Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 55:335-360. [PMID: 20161395 PMCID: PMC2782866 DOI: 10.1016/j.pnmrs.2009.07.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Hak Jun Kim
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, 406-840, Korea
| | - Stanley C. Howell
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Wade D. Van Horn
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Young Ho Jeon
- Center for Magnetic Resonance, Korea Basic Research Institute, Daejon, 305-333, Korea
| | - Charles R. Sanders
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
- Corresponding Author: ; phone: 615-936-3756; fax: 615-936-2211
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37
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Duarte AMS, de Jong ER, Koehorst RBM, Hemminga MA. Conformational studies of peptides representing a segment of TM7 from H+-VO-ATPase in SDS micelles. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:639-46. [PMID: 19669749 PMCID: PMC2841257 DOI: 10.1007/s00249-009-0522-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/09/2009] [Accepted: 07/09/2009] [Indexed: 11/25/2022]
Abstract
The conformation of a transmembrane peptide, sMTM7, encompassing the cytoplasmic hemi-channel domain of the seventh transmembrane section of subunit a from V-ATPase from Saccharomyces cerevisiae solubilized in SDS solutions was studied by circular dichroism (CD) spectroscopy and fluorescence spectroscopy of the single tryptophan residue of this peptide. The results show that the peptide adopts an alpha-helical conformation or aggregated beta-sheet depending on the peptide-to-SDS ratio used. The results are compared with published data about a longer version of the peptide (i.e., MTM7). It is concluded that the bulky, positively charged arginine residue located in the center of both peptides has a destabilizing effect on the helical conformation of the SDS-solubilized peptides, leading to beta-sheet formation and subsequent aggregation.
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Affiliation(s)
- Afonso M. S. Duarte
- Laboratory of Biophysics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
- Present Address: Cellular Protein Chemistry Laboratory, Utrecht University, Utrecht, The Netherlands
| | - Edwin R. de Jong
- Laboratory of Biophysics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Rob B. M. Koehorst
- Laboratory of Biophysics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Marcus A. Hemminga
- Laboratory of Biophysics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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38
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Thomas L, Scheidt HA, Bettio A, Beck-Sickinger AG, Huster D, Zschörnig O. The interaction of neuropeptide Y with negatively charged and zwitterionic phospholipid membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:663-77. [PMID: 19319516 DOI: 10.1007/s00249-009-0423-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 01/25/2009] [Accepted: 02/15/2009] [Indexed: 10/21/2022]
Abstract
The interaction of the 36 amino acid neuropeptide Y (NPY) with liposomes was studied using the intrinsic tyrosine fluorescence of NPY and an NPY fragment comprising amino acids 18-36. The vesicular membranes were composed of phosphatidylcholine and phosphatidylserine at varying mixing ratios. From the experimentally measured binding curves, the standard Gibbs free energy for the peptide transfer from aqueous solution to the lipid membrane was calculated to be around -30 kJ/mol for membrane mixtures containing physiological amounts of acidic lipids at pH 5. The effective charge of the peptide depends on the pH of the buffer and is about half of its theoretical net charge. The results were confirmed using the fluorescence of the NPY analogue [Trp(32)]-NPY. Further, the position of NPY's alpha-helix in the membrane was estimated from the intrinsic tyrosine fluorescence of NPY, from quenching experiments with spin-labelled phospholipids using [Trp(32)]-NPY, and from (1)H magic-angle spinning NMR relaxation measurements using spin-labelled [Ala(31), TOAC(32)]-NPY. The results suggest that the immersion depth of NPY into the membrane is triggered by the membrane composition. The alpha-helix of NPY is located in the upper chain region of zwitterionic membranes but its position is shifted to the glycerol region in negatively charged membranes. For membranes composed of phosphatidylcholine and phosphatidylserine, an intermediate position of the alpha-helix is observed.
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Affiliation(s)
- Lars Thomas
- Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
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39
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Lee BL, Li X, Liu Y, Sykes BD, Fliegel L. Structural and functional analysis of transmembrane XI of the NHE1 isoform of the Na+/H+ exchanger. J Biol Chem 2009; 284:11546-56. [PMID: 19176522 DOI: 10.1074/jbc.m809201200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Na(+)/H(+) exchanger isoform 1 is a ubiquitously expressed integral membrane protein that regulates intracellular pH in mammals by extruding an intracellular H(+) in exchange for one extracellular Na(+). We characterized structural and functional aspects of the critical transmembrane (TM) segment XI (residues 449-470) by using cysteine scanning mutagenesis and high resolution NMR. Each residue of TM XI was mutated to cysteine in the background of the cysteine-less protein and the sensitivity to water-soluble sulfhydryl reactive compounds MTSET ((2-(trimethylammonium) ethyl)methanethiosulfonate) and MTSES ((2-sulfonatoethyl) methanethiosulfonate) was determined for those residues with at least moderate activity remaining. Of the residues tested, only proteins with mutations L457C, I461C, and L465C were inhibited by MTSET. The activity of the L465C mutant was almost completely eliminated, whereas that of the L457C and I461C mutants was partially affected. The structure of a peptide representing TM XI (residues Lys(447)-Lys(472)) was determined using high resolution NMR spectroscopy in dodecylphosphocholine micelles. The structure consisted of helical regions between Asp(447)-Tyr(454) and Phe(460)-Lys(471) at the N and C termini of the peptide, respectively, connected by a region with poorly defined, irregular structure consisting of residues Gly(455)-Gly(459). TM XI of NHE1 had a structural similarity to TM XI of the Escherichia coli Na(+)/H(+) exchanger NhaA. The results suggest that TM XI is a discontinuous helix, with residue Leu(465) contributing to the pore.
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Affiliation(s)
- Brian L Lee
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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40
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Toschi F, Lugli F, Biscarini F, Zerbetto F. Effects of Electric Field Stress on a β-Amyloid Peptide. J Phys Chem B 2008; 113:369-76. [DOI: 10.1021/jp807896g] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesca Toschi
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy, and ISMN CNR, V. Gobetti, Bologna, Italy
| | - Francesca Lugli
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy, and ISMN CNR, V. Gobetti, Bologna, Italy
| | - Fabio Biscarini
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy, and ISMN CNR, V. Gobetti, Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy, and ISMN CNR, V. Gobetti, Bologna, Italy
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41
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Secondary structure transitions and aggregation induced in dynorphin neuropeptides by the detergent sodium dodecyl sulfate. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2580-7. [DOI: 10.1016/j.bbamem.2008.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 07/16/2008] [Accepted: 07/16/2008] [Indexed: 11/22/2022]
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42
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Zerbe O, Neumoin A, Mares J, Walser R, Walser R, Zou C. Recognition of Neurohormones of the NPY Family by Their Receptors. J Recept Signal Transduct Res 2008; 26:487-504. [PMID: 17118795 DOI: 10.1080/10799890600928194] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this review a structural approach developed to answer the question whether hormones from the neuropeptide Y (NPY) family are recognized directly from solution or from the membrane-bound state is described. The chosen strategy is built onto a comparison of a set of peptides with well-known pharmacology and investigates whether similarities of structures of pharmacologically related peptides are higher in solution or in the membrane-bound state. Moreover, we have established the membrane-association mode of these peptides and contributed to our understanding of the structural features of these hormones both when placed in bulk solution and when bound to membranes. As a result we propose a receptor recognition pathway that includes initial association with the membrane and requires the peptides to come off the membrane to diffuse into the binding pocket of the receptor. This review also presents methodology recently developed by us to simulate the structural transition the peptides undergo when diffusing from bulk solution onto the membrane.
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Affiliation(s)
- Oliver Zerbe
- Institute of Organic Chemistry, University of Zurich, Zurich, Switzerland.
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43
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Wahlström A, Hugonin L, Perálvarez-Marín A, Jarvet J, Gräslund A. Secondary structure conversions of Alzheimer's Abeta(1-40) peptide induced by membrane-mimicking detergents. FEBS J 2008; 275:5117-28. [PMID: 18786140 DOI: 10.1111/j.1742-4658.2008.06643.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The amyloid beta peptide (Abeta) with 39-42 residues is the major component of amyloid plaques found in brains of Alzheimer's disease patients, and soluble oligomeric peptide aggregates mediate toxic effects on neurons. The Abeta aggregation involves a conformational change of the peptide structure to beta-sheet. In the present study, we report on the effect of detergents on the structure transitions of Abeta, to mimic the effects that biomembranes may have. In vitro, monomeric Abeta(1-40) in a dilute aqueous solution is weakly structured. By gradually adding small amounts of sodium dodecyl sulfate (SDS) or lithium dodecyl sulfate to a dilute aqueous solution, Abeta(1-40) is converted to beta-sheet, as observed by CD at 3 degrees C and 20 degrees C. The transition is mainly a two-state process, as revealed by approximately isodichroic points in the titrations. Abeta(1-40) loses almost all NMR signals at dodecyl sulfate concentrations giving rise to the optimal beta-sheet content (approximate detergent/peptide ratio = 20). Under these conditions, thioflavin T fluorescence measurements indicate a maximum of aggregated amyloid-like structures. The loss of NMR signals suggests that these are also involved in intermediate chemical exchange. Transverse relaxation optimized spectroscopy NMR spectra indicate that the C-terminal residues are more dynamic than the others. By further addition of SDS or lithium dodecyl sulfate reaching concentrations close to the critical micellar concentration, CD, NMR and FTIR spectra show that the peptide rearranges to form a micelle-bound structure with alpha-helical segments, similar to the secondary structures formed when a high concentration of detergent is added directly to the peptide solution.
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Affiliation(s)
- Anna Wahlström
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
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44
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Brunsveld L, Waldmann H, Huster D. Membrane binding of lipidated Ras peptides and proteins--the structural point of view. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:273-88. [PMID: 18771652 DOI: 10.1016/j.bbamem.2008.08.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 08/01/2008] [Accepted: 08/06/2008] [Indexed: 10/21/2022]
Abstract
Biological membranes are interesting interfaces, at which important biological processes occur. In addition to integral membrane proteins, a number of proteins bind to the membrane surface and associate with it. Posttranslational lipid modification is one important mechanism, by which soluble molecules develop a propensity towards the membrane and reversibly bind to it. Membrane binding by insertion of hydrophobic lipid moieties is relevant for up to 10% of all cellular proteins. A particular interesting lipid-modified protein is the small GTPase Ras, which plays a key role in cellular signal transduction. Until recently, the structural basis for membrane binding of Ras was not well-defined. However, with the advent of new synthesis techniques and the advancement of several biophysical methods, a number of structural and dynamical features about membrane binding of Ras proteins have been revealed. This review will summarize the chemical biology of Ras and discuss in more detail the biophysical and structural features of the membrane bound C-terminus of the protein.
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Affiliation(s)
- Luc Brunsveld
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
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45
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Reddy T, Ding J, Li X, Sykes BD, Rainey JK, Fliegel L. Structural and functional characterization of transmembrane segment IX of the NHE1 isoform of the Na+/H+ exchanger. J Biol Chem 2008; 283:22018-30. [PMID: 18508767 DOI: 10.1074/jbc.m803447200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na(+)/H(+) exchanger isoform 1 (NHE1) is an integral membrane protein that regulates intracellular pH by removing one intracellular H(+) in exchange for one extracellular Na(+). It has a large N-terminal membrane domain of 12 transmembrane segments and an intracellular C-terminal regulatory domain. We characterized the cysteine accessibility of amino acids of the putative transmembrane segment IX (residues 339-363). Each residue was mutated to cysteine in a functional cysteineless NHE1 protein. Of 25 amino acids mutated, 5 were inactive or nearly so after mutation to cysteine. Several of these showed aberrant targeting to the plasma membrane and reduced expression of the intact protein, whereas others were expressed and targeted correctly but had defective NHE1 function. Of the active mutants, Glu(346) and Ser(351) were inhibited >70% by positively charged [2-(trimethylammonium)-ethyl]methanethiosulfonate but not by anionic [2-sulfonatoethyl]methanethiosulfonate, suggesting that they are pore lining and make up part of the cation conduction pathway. Both mutants also had decreased affinity for Na(+) and decreased activation by intracellular protons. The structure of a peptide representing amino acids 338-365 was determined by using high resolution NMR in dodecylphosphocholine micelles. The structure contained two helical regions (amino acids Met(340)-Ser(344) and Ile(353)-Ser(359)) kinked with a large bend angle around a pivot point at amino acid Ser(351). The results suggest that transmembrane IX is critical with pore-lining residues and a kink at the functionally important residue Ser(351).
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Affiliation(s)
- Tyler Reddy
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
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46
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Carotenuto A, Malfi S, Saviello MR, Campiglia P, Gomez-Monterrey I, Mangoni ML, Gaddi LMH, Novellino E, Grieco P. A different molecular mechanism underlying antimicrobial and hemolytic actions of temporins A and L. J Med Chem 2008; 51:2354-62. [PMID: 18370376 DOI: 10.1021/jm701604t] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, the naturally occurring antimicrobial peptides temporin A (TA) and L (TL) are studied by spectroscopic (CD and NMR) techniques and molecular dynamics simulation. We analyzed the interactions of TA and TL with sodium dodecyl sulfate (SDS) and dodecylphosphocholine (DPC) micelles, which mimic bacterial and mammalian membranes, respectively. In SDS, the peptides prefer a location at the micelle-water interface; in DPC, they prefer a location perpendicular to the micelle surface, with the N-terminus imbedded in the hydrophobic core. TL shows higher propensity, with respect to TA, in forming alpha-helical structures in both membrane mimetic systems and the highest propensity to penetrate the micelles. Hence, we have proposed a different molecular mechanism underlying the antimicrobial and hemolytic activities of the two peptides. We also designed new analogues of TA and TL and found interesting differences in their efficacy against microbial species and human erythrocytes.
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Affiliation(s)
- Alfonso Carotenuto
- Department of Pharmaceutical and Toxicological Chemistry, University of Naples "Federico II", I-80131 Naples, Italy
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47
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Gangabadage CS, Najda A, Bogdan D, Wijmenga SS, Tessari M. Dependence of the size of a protein-SDS complex on detergent and Na+ concentrations. J Phys Chem B 2008; 112:4242-5. [PMID: 18348561 DOI: 10.1021/jp710045e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sodium dodecyl sulfate (SDS) micelles provide ideal mimetic media for high-resolution NMR studies of membrane proteins and proteins or peptides interacting with micellar aggregates. (15)N NMR relaxation of the backbone amides of a protein-SDS complex has been measured under different experimental conditions. The rotational diffusion time of this complex has been found highly sensitive to detergent and NaCl concentrations. A comparison with calculated rotational diffusion times of protein-free SDS micelles under the same conditions suggests that the size of both aggregates must follow a similar functional dependence on detergent/NaCl concentration.
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Affiliation(s)
- Chinthaka Sanath Gangabadage
- Department of Chemistry, University of Ruhuna, Matara, Sri Lanka, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5a Pawińskiego, 02-106 Warsaw, Poland
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48
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Jarvet J, Danielsson J, Damberg P, Oleszczuk M, Gräslund A. Positioning of the Alzheimer Abeta(1-40) peptide in SDS micelles using NMR and paramagnetic probes. JOURNAL OF BIOMOLECULAR NMR 2007; 39:63-72. [PMID: 17657567 DOI: 10.1007/s10858-007-9176-4] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2007] [Revised: 06/18/2007] [Accepted: 06/19/2007] [Indexed: 05/16/2023]
Abstract
NMR spectroscopy combined with paramagnetic relaxation agents was used to study the positioning of the 40-residue Alzheimer Amyloid beta-peptide Abeta(1-40) in SDS micelles. 5-Doxyl stearic acid incorporated into the micelle or Mn(2+) ions in the aqueous solvent were used to determine the position of the peptide relative to the micelle geometry. In SDS solvent, the two alpha-helices induced in Abeta(1-40), comprising residues 15-24, and 29-35, respectively, are surrounded by flexible unstructured regions. NMR signals from these unstructured regions are strongly attenuated in the presence of Mn(2+) showing that these regions are positioned mostly outside the micelle. The central helix (residues 15-24) is significantly affected by 5-doxyl stearic acid however somewhat less for residues 16, 20, 22 and 23. This alpha-helix therefore resides in the SDS headgroup region with the face with residues 16, 20, 22 and 23 directed away from the hydrophobic interior of the micelle. The C-terminal helix is protected both from 5-doxyl stearic acid and Mn(2+), and should be buried in the hydrophobic interior of the micelle. The SDS micelles were characterized by diffusion and (15)N-relaxation measurements. Comparison of experimentally determined translational diffusion coefficients for SDS and Abeta(1-40) show that the size of SDS micelle is not significantly changed by interaction with Abeta(1-40).
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Affiliation(s)
- Jüri Jarvet
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Stockholm 106 91, Sweden.
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De Pinto V, Tomasello F, Messina A, Guarino F, Benz R, La Mendola D, Magrì A, Milardi D, Pappalardo G. Determination of the conformation of the human VDAC1 N-terminal peptide, a protein moiety essential for the functional properties of the pore. Chembiochem 2007; 8:744-56. [PMID: 17387661 DOI: 10.1002/cbic.200700009] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mitochondrial porin or VDAC (voltage-dependent anion-selective channel) is the most abundant protein in the mitochondrial outer membrane. The structure of VDAC has been predicted to be a transmembrane beta-barrel with an alpha-helix at the N terminus. It is a matter of debate as to whether this putative alpha-helix plays a structural role as a component of the pore walls or a function in the pore activity. We have synthesised the human VDAC1 (HVDAC1) N-terminal peptide Ac-AVPPTYADLGKSARDVFTK-NH2 (Prn2-20) and determined its structure by CD and NMR spectroscopy. CD studies show that the Prn2-20 peptide exists in aqueous solvent as an unstructured peptide with no stable secondary structure. In membrane-mimetic SDS micelles or water/trifluoroethanol, however, it assumes an amphipathic alpha-helix conformation between Tyr5 and Val16, as deduced from NMR. No ordered structure was observed in dodecyl beta-maltoside. Differential scanning calorimetric measurements were carried out in order to examine the membrane affinity of the peptide. Upon interaction with the negatively charged 1,2 dipalmitoyl-sn-glycero-3-phosphoserine membrane, Prn2-20 exhibited distinctive behaviour, suggesting that electrostatics play an important role. Interaction between the peptide and artificial bilayers indicates that the peptide lies on the membrane surface. Recombinant HVDAC1 deletion mutants, devoid of seven or 19 N-terminal amino acids, were used for transfection of eukaryotic cells. Over-expression of HVDAC1 increases the number of Cos cells with depolarised mitochondria, and this effect is progressively reduced in cells transfected with HVDAC1 lacking those seven or 19 amino acids. The mitochondrial targeting of the deletion mutants is unaffected. The overall picture emerging from our experiments is that the VDAC N-terminal peptide plays a role in the proper function of this protein during apoptotic events.
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Affiliation(s)
- Vito De Pinto
- Department of Chemical Sciences, Laboratory of Molecular Biology, University of Catania, Viale A. Doria, 6, 95125 Catania, Italy.
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Da Costa G, Mouret L, Chevance S, Le Rumeur E, Bondon A. NMR of molecules interacting with lipids in small unilamellar vesicles. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:933-42. [PMID: 17565495 DOI: 10.1007/s00249-007-0186-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Revised: 05/03/2007] [Accepted: 05/07/2007] [Indexed: 11/24/2022]
Abstract
Detailed characterization of protein, peptide or drug interactions with natural membrane is still a challenge. This review focuses on the use of nuclear magnetic resonance (NMR) for the analysis of interaction of molecules with small unilamellar vesicles (SUV). These phospholipid vesicles are often used as model membranes for fluorescence or circular dichroism experiments. The various NMR approaches for studying molecule-lipid association are reviewed. After a brief survey of the SUV characterization, the use of heteronuclear NMR (phosphorous, carbon, fluorine) is described. Applications of proton NMR through transferred nuclear Overhauser effect to perform structural determination of peptide are presented. Special care is finally given to the influence of the kinetic of the interactions for the proton NMR of bound molecules in SUV, which can constitute a good model for the study of dynamical processes at the membrane surface.
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Affiliation(s)
- Grégory Da Costa
- RMN-Interactions Lipides Protéines, UMR CNRS 6026, IFR 140, PRISM, Université de Rennes 1, 35043, Rennes Cedex, France
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