1
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Li Y, Gao Q, Ruan Z. Effects of side-chain lengths on the structure and properties of anhydrides modified starch micelles: Experimental and DPD simulation studies. Carbohydr Polym 2024; 343:122451. [PMID: 39174130 DOI: 10.1016/j.carbpol.2024.122451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/04/2024] [Accepted: 06/28/2024] [Indexed: 08/24/2024]
Abstract
Anhydride-modified starch micelles have great potential in the delivery of hydrophobic guest molecules. This study aimed to experimentally explore the effects of side-chain lengths on the structure and properties of anhydride-modified starch micelles, and to visualize the self-assembly and loading process of these micelles through Dissipative particle dynamics (DPD) simulations. Starch micelles could only form when the carbon chain length exceeded four. The highly hydrophobic C18 starch micelle exhibited the minimum particle size (65 nm) and maximum loading capability (59.10 μg/mg). For each addition carbon atom in the anhydride side chains, the critical micelle concentration (CMC) of starch micelles decreased average of 1.79 %. Thermodynamic results showed that the micellization was an entropy-dominated driven process, and longer carbon chains enhanced the stability of starch micelles. DPD results showed that the starch chains formed the small clusters then spherical aggregates and finally core-shell structure spherical micelle. Curcumin was loaded into micelles by adjoint aggregation-micellization-adsorption mechanism. Overall, this study provides microscopic insight into the micellization and drug-loading mechanisms for anhydrides modified starch micelles.
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Affiliation(s)
- Yang Li
- Carbohydrate Laboratory, School of Food Science and Engineering, South China University of Technology, 381 Wushan Rd., Tianhe District, Guangzhou 510640, PR China
| | - Qunyu Gao
- Carbohydrate Laboratory, School of Food Science and Engineering, South China University of Technology, 381 Wushan Rd., Tianhe District, Guangzhou 510640, PR China; Collaborative Innovation Center of Functional Food by Green Manufacturing, Xuchang, Henan Province 461000, PR China.
| | - Zheng Ruan
- Carbohydrate Laboratory, School of Food Science and Engineering, South China University of Technology, 381 Wushan Rd., Tianhe District, Guangzhou 510640, PR China
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2
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Li F, Harvey RD, Modicano P, Hamdi F, Kyrilis F, Müller S, Gruhle K, Kastritis P, Drescher S, Dailey LA. Investigating bolalipids as solubilizing agents for poorly soluble drugs: Effects of alkyl chain length on solubilization and cytotoxicity. Colloids Surf B Biointerfaces 2022; 212:112369. [PMID: 35123195 DOI: 10.1016/j.colsurfb.2022.112369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/17/2022] [Accepted: 01/23/2022] [Indexed: 01/31/2023]
Abstract
Synthetic single-chain bolalipids with symmetrical headgroups have shown potential in various pharmaceutical applications, such as the stabilization of liposome bilayers. Despite their amphiphilic character, synthetic bolalipids have not yet been investigated for their suitability as solubilizing agents for poorly soluble drug compounds. In this study, three synthetic single-chain bolalipids with increasing alkyl chain lengths (C22, C24 and C26) were investigated. All three bolalipids were able to achieve an increased solubility of the model drug, mefenamic acid, by approximately 180% in a pH 7.4 buffer compared to only a 102-105% increase achieved by sodium dodecyl sulfate (SDS) or the non-ionic surfactant pegylated hydroxystearate (PEG-HS). Subsequently, interfacial activity of bolalipids and their ability to destabilize liposomal bilayers were investigated. The C22 bolalipid exhibited a consistently lower interfacial activity, which was consistent with its significantly lower cytotoxicity in the macrophage-like cell line, J774. A1, compared to C24 and C26 counterparts. The mean IC50 values of the bolalipids tested (0.035-0.093 mM) were approximately 4-100-fold lower than that of SDS (0.401 mM) or PEG-HS (0.922 mM), with the mechanism of toxicity linked to increased cell membrane permeability, as is expected for surfactants. In summary, evidence from this study shows that decreasing the length of the bolalipid alkyl linker from C26 to C22 resulted in a significantly decreased cytotoxicity with no loss in drug solubilization efficiency.
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Affiliation(s)
- Feng Li
- Department of Pharmaceutical Sciences, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - Richard D Harvey
- Department of Pharmaceutical Sciences, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - Paola Modicano
- Institute of Pharmacy, Department of Pharmaceutical Technology and Biopharmaceutics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Farzad Hamdi
- Biozentrum, MLU Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany; Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Fotios Kyrilis
- Biozentrum, MLU Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany; Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Sindy Müller
- Institute of Pharmacy, Department of Pharmaceutical Chemistry, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Kai Gruhle
- Institute of Pharmacy, Department of Pharmaceutical Chemistry, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Panagiotis Kastritis
- Biozentrum, MLU Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany; Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Simon Drescher
- Phospholipid Research Center, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Lea Ann Dailey
- Department of Pharmaceutical Sciences, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria.
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3
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Zhang X, Kindt JT. Free energy of micellization of dodecyl phosphocholine (DPC) from molecular simulation: Hybrid PEACH-BAR method. J Comput Chem 2021; 42:2221-2232. [PMID: 34561897 DOI: 10.1002/jcc.26751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/08/2021] [Accepted: 09/05/2021] [Indexed: 11/06/2022]
Abstract
A new method to extract the free energy of aggregation versus aggregate size from molecular simulation data is proposed and applied to a united atom model of the zwitterionic surfactant dodecyl phosphocholine in water. This system's slow dissociation rate and low critical micelle concentration (CMC of approximately 1-2 mM) make extraction of cluster free energies directly from simulation results using the "partition-enabled analysis of cluster histogram" (PEACH) method impractical. The new approach applies PEACH to a model with weakened attractions between aggregants, which allows sampling of a continuous range of cluster sizes, then recovers the free energy of aggregation under the original fully-attractive force field using the BAR free energy difference method. PEACH-BAR results are compared with free energy differences calculated via umbrella sampling, and are used to make predictions of CMC, average cluster size, and SAXS scattering profiles that are in fair agreement with experiment.
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Affiliation(s)
- Xiaokun Zhang
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| | - James T Kindt
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
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4
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Nonin-Lecomte S, Fermon L, Felden B, Pinel-Marie ML. Bacterial Type I Toxins: Folding and Membrane Interactions. Toxins (Basel) 2021; 13:toxins13070490. [PMID: 34357962 PMCID: PMC8309996 DOI: 10.3390/toxins13070490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
Bacterial type I toxin-antitoxin systems are two-component genetic modules that encode a stable toxic protein whose ectopic overexpression can lead to growth arrest or cell death, and an unstable RNA antitoxin that inhibits toxin translation during growth. These systems are widely spread among bacterial species. Type I antitoxins are cis- or trans-encoded antisense small RNAs that interact with toxin-encoding mRNAs by pairing, thereby inhibiting toxin mRNA translation and/or inducing its degradation. Under environmental stress conditions, the up-regulation of the toxin and/or the antitoxin degradation by specific RNases promote toxin translation. Most type I toxins are small hydrophobic peptides with a predicted α-helical transmembrane domain that induces membrane depolarization and/or permeabilization followed by a decrease of intracellular ATP, leading to plasmid maintenance, growth adaptation to environmental stresses, or persister cell formation. In this review, we describe the current state of the art on the folding and the membrane interactions of these membrane-associated type I toxins from either Gram-negative or Gram-positive bacteria and establish a chronology of their toxic effects on the bacterial cell. This review also includes novel structural results obtained by NMR concerning the sprG1-encoded membrane peptides that belong to the sprG1/SprF1 type I TA system expressed in Staphylococcus aureus and discusses the putative membrane interactions allowing the lysis of competing bacteria and host cells.
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Affiliation(s)
| | - Laurence Fermon
- BRM (Bacterial Regulatory RNAs and Medicine), Inserm, UMR_S 1230, Université de Rennes 1, 35000 Rennes, France; (L.F.); (B.F.)
| | - Brice Felden
- BRM (Bacterial Regulatory RNAs and Medicine), Inserm, UMR_S 1230, Université de Rennes 1, 35000 Rennes, France; (L.F.); (B.F.)
| | - Marie-Laure Pinel-Marie
- BRM (Bacterial Regulatory RNAs and Medicine), Inserm, UMR_S 1230, Université de Rennes 1, 35000 Rennes, France; (L.F.); (B.F.)
- Correspondence:
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5
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Harris JJ, Pantelopulos GA, Straub JE. Finite-Size Effects and Optimal System Sizes in Simulations of Surfactant Micelle Self-Assembly. J Phys Chem B 2021; 125:5068-5077. [PMID: 33961427 DOI: 10.1021/acs.jpcb.1c01186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The spontaneous formation of micelles in aqueous solutions is governed by the amphipathic nature of surfactants and is practically interesting due to the regular use of micelles as membrane mimics, for the characterization of protein structure, and for drug design and delivery. We performed a systematic characterization of the finite-size effect observed in single-component dodecylphosphocholine (DPC) micelles with the coarse-grained MARTINI model. Of multiple coarse-grained solvent models investigated using large system sizes, the nonpolarizable solvent model was found to most accurately reproduce SANS spectra of 100 mM DPC in aqueous solution. We systematically investigated the finite-size effect at constant 100 mM concentration in 23 systems of sizes 40-150 DPC, confirming the finite-size effect to manifest as an oscillation in the mean micelle aggregation number about the thermodynamic aggregation number as the system size increases. The oscillations in aggregation number mostly diminish once the system supports the formation of three micelles. Similar oscillations were observed in the estimated critical micelle concentration with a mean value of 1.10 mM, which is in agreement with experiment to 0.1 mM. The accuracy of using a multiscale simulation approach to avoid finite-size effects in the micelle size distribution and SANS spectra using MARTINI and CHARMM36 was explored using multiple long time scale 500 DPC coarse-grained simulations, which were back-mapped to CHARMM36 all-atom systems. It was found that the MARTINI model generally occupies more volume than the all-atom model, leading to the formation of micelles that are of a reasonable radius of gyration but are smaller in aggregation number. The systematic characterization of the finite-size effect and exploration of multiscale modeling presented in this work provide guidance for the accurate modeling of micelles in simulations.
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Affiliation(s)
- Jonathan J Harris
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - George A Pantelopulos
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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6
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de Souza RM, Ratochinski RH, Karttunen M, Dias LG. Self-Assembly of Phosphocholine Derivatives Using the ELBA Coarse-Grained Model: Micelles, Bicelles, and Reverse Micelles. J Chem Inf Model 2020; 60:522-536. [PMID: 31714768 DOI: 10.1021/acs.jcim.9b00790] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The ELBA coarse-grained force field was originally developed for lipids, and its water model is described as a single-site Lennard-Jones particle with electrostatics modeled by an embedded point-dipole, while other molecules in this force field have a three (or four)-to-one mapping scheme. Here, ELBA was applied to investigate the self-assembly processes of dodecyl-phosphocholine (DPC) micelle, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dihexaoyl-sn-glycero-3-phosphocholine (DPPC/DHPC) bicelles, and DPPC/cyclohexane/water reverse micelles through coarse-grained molecular dynamics (MD) simulations. New parameters were obtained using a simplex algorithm-based calibration procedure to determine the Lennard-Jones parameters for cyclohexane, dodecane, and cyclohexane-dodecane cross-interactions. Density, self-diffusion coefficient, surface tension, and mixture excess volume were found to be in fair agreement with experimental data. These new parameters were used in the simulations, and the obtained structures were analyzed for shape, size, volume, and surface area. Except for the shape of DPC micelles, all other properties match well with available experimental data and all-atom simulations. Remarkably, in agreement with experiments the rodlike shape of the DPPC reverse micelle is well described by ELBA, while all-atom data in the literature predicts a disclike shape. To further check the consistency of the force field in reproducing the correct shapes of reverse micelles, additional simulations were performed doubling the system size. Two distinct reverse micelles were obtained both presenting the rodlike shape and correct aggregation number.
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Affiliation(s)
- R M de Souza
- Department of Chemistry , The University of Western Ontario , London , Ontario , Canada N6A 3K7.,Departamento de Química, FFCLRP , Universidade de São Paulo , Avenida Bandeirantes 3900 , 14040-901 Ribeirão Preto , SP , Brazil.,The Center for Advanced Materials and Biomaterials Research , The University of Western Ontario , London , Ontario , Canada N6K 3K7
| | - R H Ratochinski
- Departamento de Química, FFCLRP , Universidade de São Paulo , Avenida Bandeirantes 3900 , 14040-901 Ribeirão Preto , SP , Brazil
| | - Mikko Karttunen
- Department of Chemistry , The University of Western Ontario , London , Ontario , Canada N6A 3K7.,The Center for Advanced Materials and Biomaterials Research , The University of Western Ontario , London , Ontario , Canada N6K 3K7.,Department of Applied Mathematics , The University of Western Ontario , London , Ontario , Canada N6A 5B7
| | - L G Dias
- Departamento de Química, FFCLRP , Universidade de São Paulo , Avenida Bandeirantes 3900 , 14040-901 Ribeirão Preto , SP , Brazil
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7
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Sofroniou C, Chazapi I, Leontidis E. Binding of lanthanide salts to zwitterionic phospholipid micelles. J Colloid Interface Sci 2019; 557:568-579. [PMID: 31550649 DOI: 10.1016/j.jcis.2019.09.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/01/2019] [Accepted: 09/15/2019] [Indexed: 10/26/2022]
Abstract
As the use of lanthanide salts in biophysical systems increases and the separation of lanthanides from nuclear and other wastes with extraction processes has become an important technological challenge, a deeper understanding of the behavior of lanthanides at lipid interfaces is urgently needed. In this work the interaction of lanthanide salts with zwitterionic phospholipids is probed using aqueous micelles of the surfactant dodecyl phosphocholine (DPC), which are useful membrane-mimetic model systems, widely used for the solubilization of membrane proteins in aqueous solutions. Because more than one species exists in lanthanide salt solutions, even at the pH value of 4 used in this experiment, the major goal of this investigation is to examine which species are actually binding to the micelles. Using static and time-dependent europium fluorescence, strong indications are obtained that both the Eu3+ cation and its 1:1 chloride, nitrate, or sulfate complexes bind to the micelles, whereas the europium species do not appear to interact strongly with DPC molecules below the cmc. From isothermal titration calorimetry (ITC) measurements it is found that the lanthanide interaction with DPC micelles increases to the right of the lanthanide series and is - surprisingly - endothermic, underlying the important role of hydration effects in the interaction. The anion of the lanthanide salt strongly influences the thermodynamics: perchlorate and sulfate salts give extraordinary results, switching the interaction to exothermic. A multi-level phenomenological electrostatic model of the europium fluorescence lifetimes strongly suggests that in the case of nitrate salts both Ln3+ and LnNO32+ ions bind to the micelles. Overall a detailed molecular picture of the complexity of lanthanide-lipid interactions at interfaces is emerging from these experiments and the associated modelling effort.
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Affiliation(s)
- Constantina Sofroniou
- Department of Chemistry, University of Cyprus, PO Box 20537, Nicosia 1678, Cyprus; Department of Chemistry, University of Florence, Via della Lastruccia, 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Ioanna Chazapi
- Department of Chemistry, University of Cyprus, PO Box 20537, Nicosia 1678, Cyprus
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8
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Peptide Assembly on the Membrane Determines the HIV-1 Inhibitory Activity of Dual-Targeting Fusion Inhibitor Peptides. Sci Rep 2019; 9:3257. [PMID: 30824796 PMCID: PMC6397244 DOI: 10.1038/s41598-019-40125-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/08/2019] [Indexed: 12/31/2022] Open
Abstract
Novel strategies in the design of HIV-1 fusion/entry inhibitors are based on the construction of dual-targeting fusion proteins and peptides with synergistic antiviral effects. In this work we describe the design of dual-targeting peptides composed of peptide domains of E2 and E1 envelope proteins from Human Pegivirus with the aim of targeting both the loop region and the fusion peptide domains of HIV-1 gp41. In a previous work, we described the inhibitory role of a highly conserved fragment of the E1 protein (domain 139–156) which interacts with the HIV-1 fusion peptide at the membrane level. Here, two different dual-targeting peptides, where this E1 peptide is located on the N- or the C-terminus respectively, have been chemically synthesized and their antiviral activities have been evaluated with HIV pseudotyped viruses from different clades. The study of the functional behaviour of peptides in a membranous environment attending to the peptide recognition of the target sites on gp41, the peptide conformation as well as the peptide affinity to the membrane, demonstrate that antiviral activity of the dual-targeting peptides is directly related to the peptide affinity and its subsequent assembly into the model membrane. The overall results point out to the necessity that fusion inhibitor peptides that specifically interfere with the N-terminal region of gp41 are embedded within the membrane in order to properly interact with their viral target.
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9
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Fiore M. The synthesis of mono-alkyl phosphates and their derivatives: an overview of their nature, preparation and use, including synthesis under plausible prebiotic conditions. Org Biomol Chem 2018; 16:3068-3086. [DOI: 10.1039/c8ob00469b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nucleic acids, phospholipids and other organic phosphates play central roles in biological pathways.
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Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires
- Université de Lyon
- F-69622 Villeurbanne Cedex
- France
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10
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Yang G, Yu K, Kubicek J, Labahn J. Expression, purification, and preliminary characterization of human presenilin-2. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Yang G, Yu K, Kaitatzi CS, Singh A, Labahn J. Influence of solubilization and AD-mutations on stability and structure of human presenilins. Sci Rep 2017; 7:17970. [PMID: 29269939 PMCID: PMC5740079 DOI: 10.1038/s41598-017-18313-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
Presenilin (PS1 or PS2) functions as the catalytic subunit of γ-secretase, which produces the toxic amyloid beta peptides in Alzheimer’s disease (AD). The dependence of folding and structural stability of PSs on the lipophilic environment and mutation were investigated by far UV CD spectroscopy. The secondary structure content and stability of PS2 depended on the lipophilic environment. PS2 undergoes a temperature-dependent structural transition from α-helical to β-structure at 331 K. The restructured protein formed structures which tested positive in spectroscopic amyloid fibrils assays. The AD mutant PS1L266F, PS1L424V and PS1ΔE9 displayed reduced stability which supports a proposed ‘loss of function’ mechanism of AD based on protein instability. The exon 9 coded sequence in the inhibitory loop of the zymogen was found to be required for the modulation of the thermal stability of PS1 by the lipophilic environment.
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Affiliation(s)
- Ge Yang
- Centre for Structural Systems Biology (CSSB), CSSB-FZJ, Notkestr. 85, 22607, Hamburg, Germany.,Institute of Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425, Jülich, Germany
| | - Kun Yu
- Centre for Structural Systems Biology (CSSB), CSSB-FZJ, Notkestr. 85, 22607, Hamburg, Germany.,Institute of Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425, Jülich, Germany
| | - Christina-Symina Kaitatzi
- Centre for Structural Systems Biology (CSSB), CSSB-FZJ, Notkestr. 85, 22607, Hamburg, Germany.,Physics Department, University of Patras, University Campus, 26504, Rio Achaia, Greece
| | - Abhilasha Singh
- Centre for Structural Systems Biology (CSSB), CSSB-FZJ, Notkestr. 85, 22607, Hamburg, Germany.,Institute of Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425, Jülich, Germany
| | - Jörg Labahn
- Centre for Structural Systems Biology (CSSB), CSSB-FZJ, Notkestr. 85, 22607, Hamburg, Germany. .,Institute of Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425, Jülich, Germany. .,Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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12
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Faramarzi S, Bonnett B, Scaggs CA, Hoffmaster A, Grodi D, Harvey E, Mertz B. Molecular Dynamics Simulations as a Tool for Accurate Determination of Surfactant Micelle Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:9934-9943. [PMID: 28836794 DOI: 10.1021/acs.langmuir.7b02666] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular dynamics (MD) simulations were used to characterize the equilibrium size, shape, hydration, and self-assembly of dodecylphosphocholine (DPC) and dodecyl-β-D-maltoside (DDM) micelles. We show that DPC molecules self-assemble to form micelles with sizes within the range reported in the experimental literature. The equilibrium shape of DPC and DDM micelles as well as associated micellar radii are in agreement with small-angle X-ray scattering (SAXS) experiments and theoretical packing parameters. In addition, we show that hydration of the micelle interior is limited; however, flexibility of the acyl chains leads to dynamic encounters with the solvated outer shell of the micelle, providing an explanation for long-standing differences in models of micelle hydration. Altogether, our results provide fundamental understanding of physical characteristics of micelles that can be utilized to study other types of detergents and proteomicelle complexes.
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Affiliation(s)
- Sadegh Faramarzi
- C. Eugene Bennett Department of Chemistry, West Virginia University , 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Brittany Bonnett
- Biology, Chemistry, and Geoscience Department, Fairmont State University , 1201 Locust Avenue, Fairmont, West Virginia 26554, United States
| | - Carl A Scaggs
- Biology, Chemistry, and Geoscience Department, Fairmont State University , 1201 Locust Avenue, Fairmont, West Virginia 26554, United States
| | - Ashley Hoffmaster
- Biology, Chemistry, and Geoscience Department, Fairmont State University , 1201 Locust Avenue, Fairmont, West Virginia 26554, United States
| | - Danielle Grodi
- Biology, Chemistry, and Geoscience Department, Fairmont State University , 1201 Locust Avenue, Fairmont, West Virginia 26554, United States
| | - Erica Harvey
- Biology, Chemistry, and Geoscience Department, Fairmont State University , 1201 Locust Avenue, Fairmont, West Virginia 26554, United States
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University , 217 Clark Hall, Morgantown, West Virginia 26506, United States
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13
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Kordts M, Kerth A, Drescher S, Ott M, Blume A. The cmc-value of a bolalipid with two phosphocholine headgroups and a C 24 alkyl chain: Unusual binding properties of fluorescence probes to bolalipid aggregates. J Colloid Interface Sci 2017; 501:294-303. [PMID: 28460222 DOI: 10.1016/j.jcis.2017.04.077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 10/19/2022]
Abstract
Bolalipids with a long alkyl chain and two phosphocholine polar groups self-assemble in water into two different types of aggregate structures, namely helical nanofibers at low temperature and two types of micellar aggregates at higher temperature. We tried to determine the critical aggregation concentration (cac) or critical micellar concentration (cmc) of the bolalipid tetracosane-1,24-bis(phosphocholine) (PC-C24-PC) by using different fluorescent probes. The use of pyrene or pyrene derivatives as fluorophores failed, whereas the probes 1,8-ANS and particularly bis-ANS gave consistent results. The structure of the bolalipid aggregates obviously hinders partitioning or binding of pyrene derivatives into the micellar interior, whereas 1,8-ANS and bis-ANS can bind to the surface of the aggregate structures. The observed large increase in fluorescence intensity of bis-ANS indicates that binding to the hydrophobic surface of the aggregates leads to a reduction of the dye mobility. However, binding of bis-ANS is relatively weak, so that the determination of a cac/cmc-value is difficult. Simulations of the intensity curves for PC-C24-PC lead to estimates of the cac/cmc-value of 0.3-1.0×10-6M, depending on the structure of the aggregates. Single molecule fluorescence correlation spectroscopy was used to determine the mobility of bis-ANS as a function of concentration of PC-C24-PC. The dye diffusion time and the molecular brightness are lower at low bolalipid concentration, when only free dye is present, and increase at higher concentration when bis-ANS is bound to the aggregates. The experimental cac/cmc-values are higher than those estimated, using an incremental method for the change in Gibbs free energy for micellization with n-alkyl-phosphocholines with only one polar group as a comparison. Apparently, for PC-C24-PC in micellar or fibrous aggregates, more CH2 groups are exposed to water than in a conventional micelle of an n-alkyl-phosphocholine.
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Affiliation(s)
- Martin Kordts
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Andreas Kerth
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Simon Drescher
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Maria Ott
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle (Saale), Germany
| | - Alfred Blume
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany.
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14
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Pérez Y, Gómara MJ, Yuste E, Gómez-Gutierrez P, Pérez JJ, Haro I. Structural Study of a New HIV-1 Entry Inhibitor and Interaction with the HIV-1 Fusion Peptide in Dodecylphosphocholine Micelles. Chemistry 2017; 23:11703-11713. [DOI: 10.1002/chem.201702531] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Yolanda Pérez
- Nuclear Magnetic Resonance Facility; IQAC-CSIC; Jordi Girona, 18-26 08034 Barcelona Spain
| | - Maria José Gómara
- Unit of Synthesis and Biomedical Applications of Peptides; IQAC-CSIC; Jordi Girona, 18-26 08034 Barcelona Spain
| | - Eloísa Yuste
- Department of Chemical Engineering (ETSEIB); Universitat Politecnica de Catalunya; 08034 Barcelona Spain
- Present address: AIDS Immunopathology Unit; Centro Nacional Microbiología; Instituto de Salud Carlos III; 28029 Madrid Spain
| | | | | | - Isabel Haro
- Unit of Synthesis and Biomedical Applications of Peptides; IQAC-CSIC; Jordi Girona, 18-26 08034 Barcelona Spain
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15
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Lebecque S, Crowet J, Nasir M, Deleu M, Lins L. Molecular dynamics study of micelles properties according to their size. J Mol Graph Model 2017; 72:6-15. [DOI: 10.1016/j.jmgm.2016.12.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 11/26/2022]
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16
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Wimmer R, Uggerhøj LE. Determination of Structure and Micellar Interactions of Small Antimicrobial Peptides by Solution-State NMR. Methods Mol Biol 2017; 1548:73-88. [PMID: 28013498 DOI: 10.1007/978-1-4939-6737-7_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
NMR spectroscopy is a well-established technique to determine the structure of peptides and small proteins in solution, also when bound to detergent micelles or phospholipid bicelles. The structure of the peptide alone is, however, not conveying the full picture, if the peptide is bound to a micelle, since it does not tell anything about the orientation of the peptide in the micelle. This article describes how to obtain that information together with information on peptide structure.
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Affiliation(s)
- Reinhard Wimmer
- Department of Chemistry and Bioscience, University of Aalborg, Frederik Bajers vej 7H, 9220, Aalborg, Denmark.
| | - Lars Erik Uggerhøj
- Department of Chemistry and Bioscience, University of Aalborg, Frederik Bajers vej 7H, 9220, Aalborg, Denmark
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17
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Gabel F. Applications of SANS to Study Membrane Protein Systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:201-214. [DOI: 10.1007/978-981-10-6038-0_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Ryan TM, Griffin MDW, McGillivray DJ, Knott RB, Wood K, Masters CL, Kirby N, Curtain CC. Apolipoprotein C-II Adopts Distinct Structures in Complex with Micellar and Submicellar Forms of the Amyloid-Inhibiting Lipid-Mimetic Dodecylphosphocholine. Biophys J 2016; 110:85-94. [PMID: 26745412 PMCID: PMC4805880 DOI: 10.1016/j.bpj.2015.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/03/2015] [Accepted: 11/09/2015] [Indexed: 01/21/2023] Open
Abstract
The formation of amyloid deposits is a common feature of a broad range of diseases, including atherosclerosis, Alzheimer's disease, and Parkinson's disease. The basis and role of amyloid deposition in the pathogenesis of these diseases is still being defined, however an interesting feature of amyloidogenic proteins is that the majority of the pathologically associated proteins are involved in lipid homeostasis, be it in lipid transport, incorporation into membranes, or the regulation of lipid pathways. Thus, amyloid-forming proteins commonly bind lipids, and lipids are generally involved in the proper folding of these proteins. However, understanding of the basis for these lipid-related aspects of amyloidogenesis is lacking. Thus, we have used the apolipoprotein C-II amyloid model system in conjunction with x-ray and neutron scattering analyses to address this problem. Apolipoprotein C-II is a well-studied model system of systemic amyloid fibril formation, with a clear and well-defined pathway for fibril formation, where the effects of lipid interaction are characterized, particularly for the lipid mimetic dodecylphosphocholine. We show that the micellar state of an inhibitory lipid can have a very significant effect on protein conformation, with micelles stabilizing a particular α-helical structure, whereas submicellar lipids stabilize a very different dimeric, α-helical structure. These results indicate that lipids may have an important role in the development and progression of amyloid-related diseases.
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Affiliation(s)
- Timothy M Ryan
- Australian Synchrotron, Clayton, Victoria, Australia; The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia; The MacDiarmid Institute of Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Duncan J McGillivray
- School of Chemical Science, The University of Auckland, Auckland, New Zealand; The MacDiarmid Institute of Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - Robert B Knott
- Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | - Colin L Masters
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Nigel Kirby
- Australian Synchrotron, Clayton, Victoria, Australia
| | - Cyril C Curtain
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
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19
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Pambou E, Crewe J, Yaseen M, Padia FN, Rogers S, Wang D, Xu H, Lu JR. Structural Features of Micelles of Zwitterionic Dodecyl-phosphocholine (C₁₂PC) Surfactants Studied by Small-Angle Neutron Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9781-9789. [PMID: 26301341 DOI: 10.1021/acs.langmuir.5b02077] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Small-angle neutron scattering (SANS) was used to investigate the size and shape of zwitterionic dodecyl phosphocholine (C12PC) micelles formed at various concentrations above its critical micelle concentration (CMC = 0.91 mM). The predominant spherical shape of micelles is revealed by SANS while the average micellar size was found to be broadly consistent with the hydrodynamic diameters determined by dynamic light scattering (DLS). Cryogenic tunneling electron microscopy (cryo-TEM) shows a uniform distribution of structures, proposing micelle monodispersity ( Supporting Information ). H/D substitution was utilized to selectively label the chain, head, or entire surfactant so that structural distributions within the micellar assembly could be investigated using fully protonated, head-deuterated, and tail-deuterated PC surfactants in D2O and fully deuterated surfactants in H2O. Using the analysis software we have developed, the four C12PC contrasts at a given concentration were simultaneously analyzed using various core-shell models consisting of a hydrophobic core and a shell representing hydrated polar headgroups. Results show that at 10 mM, C12PC micelles can be well represented by a spherical core-shell model with a core radius and shell thicknesses of 16.9 ± 0.5 and 10.2 ± 2.0 Å (total radius 27.1 ± 2.0 Å), respectively, with a surfactant aggregation number of 57 ± 5. As the concentration was increased, the SANS data revealed an increase in core-shell mixing, characterized by the emergence of an intermediate mixing region at the spherical core-shell interface. C12PC micelles at 100 mM were found to have a core radius and shell thicknesses of 19.6 ± 0.5 and 7.8 ± 2.0 Å, with an intermediate mixing region of 3.0 ± 0.5 Å. Further reduction in the shell thickness with concentration was also observed, coupled with an increased mixing of the core and shell regions and a reduction in miceller hydration, suggesting that concentration has a significant influence on surfactant packing and aggregation within micelles.
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Affiliation(s)
- Elias Pambou
- Biological Physics Group, School of Physics and Astronomy, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - John Crewe
- Biological Physics Group, School of Physics and Astronomy, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Mohammed Yaseen
- Biological Physics Group, School of Physics and Astronomy, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Faheem N Padia
- Biological Physics Group, School of Physics and Astronomy, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sarah Rogers
- STFC ISIS Facility, Rutherford Appleton Laboratory , Didcot OX11 0QX, United Kingdom
| | - Dong Wang
- Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266555, China
| | - Hai Xu
- Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266555, China
| | - Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
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20
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Boeszoermenyi A, Nagy HM, Arthanari H, Pillip CJ, Lindermuth H, Luna RE, Wagner G, Zechner R, Zangger K, Oberer M. Structure of a CGI-58 motif provides the molecular basis of lipid droplet anchoring. J Biol Chem 2015; 290:26361-72. [PMID: 26350461 PMCID: PMC4646293 DOI: 10.1074/jbc.m115.682203] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 11/29/2022] Open
Abstract
Triacylglycerols (TGs) stored in lipid droplets (LDs) are hydrolyzed in a highly regulated metabolic process called lipolysis to free fatty acids that serve as energy substrates for β-oxidation, precursors for membrane lipids and signaling molecules. Comparative gene identification-58 (CGI-58) stimulates the enzymatic activity of adipose triglyceride lipase (ATGL), which catalyzes the hydrolysis of TGs to diacylglycerols and free fatty acids. In adipose tissue, protein-protein interactions between CGI-58 and the LD coating protein perilipin 1 restrain the ability of CGI-58 to activate ATGL under basal conditions. Phosphorylation of perilipin 1 disrupts these interactions and mobilizes CGI-58 for the activation of ATGL. We have previously demonstrated that the removal of a peptide at the N terminus (residues 10–31) of CGI-58 abrogates CGI-58 localization to LDs and CGI-58-mediated activation of ATGL. Here, we show that this tryptophan-rich N-terminal peptide serves as an independent LD anchor, with its three tryptophans serving as focal points of the left (harboring Trp21 and Trp25) and right (harboring Trp29) anchor arms. The solution state NMR structure of a peptide comprising the LD anchor bound to dodecylphosphocholine micelles as LD mimic reveals that the left arm forms a concise hydrophobic core comprising tryptophans Trp21 and Trp25 and two adjacent leucines. Trp29 serves as the core of a functionally independent anchor arm. Consequently, simultaneous tryptophan alanine permutations in both arms abolish localization and activity of CGI-58 as opposed to tryptophan substitutions that occur in only one arm.
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Affiliation(s)
- Andras Boeszoermenyi
- From the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria, the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Harald Manuel Nagy
- From the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Haribabu Arthanari
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | | | - Hanna Lindermuth
- From the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria, the Institute of Biophysics, Medical University of Graz, 8010 Graz, Austria
| | - Rafael Eulogio Luna
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Gerhard Wagner
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Rudolf Zechner
- From the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Klaus Zangger
- the Institute of Chemistry, University of Graz, 8010 Graz, Austria, and
| | - Monika Oberer
- From the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria,
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21
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Glanzer S, Pulido SA, Tutz S, Wagner GE, Kriechbaum M, Gubensäk N, Trifunovic J, Dorn M, Fabian WMF, Novak P, Reidl J, Zangger K. Structural and functional implications of the interaction between macrolide antibiotics and bile acids. Chemistry 2015; 21:4350-8. [PMID: 25655041 PMCID: PMC4471570 DOI: 10.1002/chem.201406413] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 01/13/2023]
Abstract
Macrolide antibiotics, such as azithromycin and erythromycin, are in widespread use for the treatment of bacterial infections. Macrolides are taken up and excreted mainly by bile. Additionally, they have been implicated in biliary system diseases and to modify the excretion of other drugs through bile. Despite mounting evidence for the interplay between macrolide antibiotics and bile acids, the molecular details of this interaction remain unknown. Herein, we show by NMR measurements that macrolides directly bind to bile acid micelles. The topology of this interaction has been determined by solvent paramagnetic relaxation enhancements (solvent PREs). The macrolides were found to be bound close to the surface of the micelle. Increasing hydrophobicity of both the macrolide and the bile acid strengthen this interaction. Both bile acid and macrolide molecules show similar solvent PREs across their whole structures, indicating that there are no preferred orientations of them in the bile micelle aggregates. The binding to bile aggregates does not impede macrolide antibiotics from targeting bacteria. In fact, the toxicity of azithromycin towards enterotoxic E. coli (ETEC) is even slightly increased in the presence of bile, as was shown by effective concentration (EC50 ) values.
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Affiliation(s)
| | | | - Sarah Tutz
- Institute of Molecular BiosciencesUniversity of Graz (Austria)
| | | | | | | | - Jovana Trifunovic
- Dept. of Pharmacology, Medical FacultyUniversity of Novi Sad (Serbia)
| | - Markus Dorn
- Institute of NavigationGraz University of Technology (Austria)
| | | | - Predrag Novak
- Department of Chemistry, Faculty of Natural ScienceUniversity of Zagreb (Croatia)
| | - Joachim Reidl
- Institute of Molecular BiosciencesUniversity of Graz (Austria)
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22
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Uggerhøj LE, Poulsen TJ, Munk JK, Fredborg M, Sondergaard TE, Frimodt-Moller N, Hansen PR, Wimmer R. Rational Design of Alpha-Helical Antimicrobial Peptides: Do's and Don'ts. Chembiochem 2014; 16:242-53. [DOI: 10.1002/cbic.201402581] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 11/06/2022]
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23
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Yamaguchi Y, Tokunaga N, Inouye M, Phadtare S. Characterization of LdrA (long direct repeat A) protein of Escherichia coli. J Mol Microbiol Biotechnol 2014; 24:91-7. [PMID: 24513967 DOI: 10.1159/000357949] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Reminiscent of apoptotic genes in higher systems, almost all bacteria contain 'suicide' genes, which encode toxins. Toxins inhibit cell growth and may cause cell death. These are coexpressed with their cognate antitoxins from a toxin-antitoxin (TA) operon in normally growing cells. The cellular targets of toxins are diverse. The study of the TA system is important as in addition to their involvement in the normal bacterial physiology, TA systems may also play a role in bacterial pathogenicity. The long direct repeat (Ldr) family of proteins belongs to one such TA system. Here we report characterization of LdrA, the prototypical protein of the Ldr family, and show that it is highly toxic for cell growth. The data suggests that LdrA may exert toxicity by inhibiting ATP synthesis, possibly due to its localization in the cell membrane. This inhibition of energy production leads to the inhibition of biosynthetic reactions in the cell such as DNA replication, transcription and translation, and eventually cell growth.
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Affiliation(s)
- Yoshihiro Yamaguchi
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, N.J., USA
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24
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Wang Y, Tjandra N. Structural insights of tBid, the caspase-8-activated Bid, and its BH3 domain. J Biol Chem 2013; 288:35840-51. [PMID: 24158446 DOI: 10.1074/jbc.m113.503680] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Bcl-2 family proteins regulate mitochondria-mediated apoptosis through intricate molecular mechanisms. One of the pro-apoptotic proteins, tBid, can induce apoptosis by promoting Bax activation, Bax homo-oligomerization, and mitochondrial outer membrane permeabilization. Association of tBid on the mitochondrial outer membrane is key to its biological function. Therefore knowing the conformation of tBid on the membrane will be the first step toward understanding its crucial role in triggering apoptosis. Here, we present NMR characterization of the structure and dynamics of human tBid in 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-RAC-(1-glycerol)] micelles. Our data showed that tBid is monomeric with six well defined α-helices in the micelles. Compared with the full-length Bid structure, a longer flexible loop between tBid helix α4 and α5 was observed. Helices in tBid do not pack into a compact-fold but form an extended structure with a C-shape configuration in the micelles. All six tBid helices were shown to interact with LPPG micelles, with helix α6 and α7 being more embedded. Of note, the BH3-containing helix α3, which was previously believed to be exposed above the membrane surface, is also membrane associated, suggesting an "on the membrane" binding mode for tBid interaction with Bax. Our data provided structural details on the membrane-associated state of tBid and the functional implications of its membrane-associated BH3 domain.
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Affiliation(s)
- Yu Wang
- From the Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
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25
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Solution NMR studies on the orientation of membrane-bound peptides and proteins by paramagnetic probes. Molecules 2013; 18:7407-35. [PMID: 23799448 PMCID: PMC6269851 DOI: 10.3390/molecules18077407] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/13/2013] [Accepted: 06/20/2013] [Indexed: 12/24/2022] Open
Abstract
Many peptides and proteins are attached to or immersed in a biological membrane. In order to understand their function not only the structure but also their topology in the membrane is important. Solution NMR spectroscopy is one of the most often used approaches to determine the orientation and localization of membrane-bound peptides and proteins. Here we give an application-oriented overview on the use of paramagnetic probes for the investigation of membrane-bound peptides and proteins. The examples discussed range from the large pool of antimicrobial peptides, bacterial toxins, cell penetrating peptides to domains of larger proteins or the calcium regulating protein phospholamban. Topological information is obtained in all these examples by the use of either attached or freely mobile paramagnetic tags. For some examples information obtained from the paramagnetic probes was included in the structure determination.
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26
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Alvares RD, Tulumello DV, Macdonald PM, Deber CM, Prosser RS. Effects of a polar amino acid substitution on helix formation and aggregate size along the detergent-induced peptide folding pathway. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:373-81. [DOI: 10.1016/j.bbamem.2012.09.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 09/06/2012] [Accepted: 09/24/2012] [Indexed: 12/15/2022]
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27
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Abel S, Dupradeau FY, Marchi M. Molecular Dynamics Simulations of a Characteristic DPC Micelle in Water. J Chem Theory Comput 2012; 8:4610-23. [DOI: 10.1021/ct3003207] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Stéphane Abel
- Commissariat à l’Energie Atomique et aux Energies Alternatives, DSV/iBiTEC-S/SB2SM/LBMS, Saclay, France, CNRS UMR 8221, Saclay,
France
| | - François-Yves Dupradeau
- Laboratoire des glucides, UFR de Pharmacie & CNRS FRE 3517, Université de Picardie-Jules Verne, Amiens, France
| | - Massimo Marchi
- Commissariat à l’Energie Atomique et aux Energies Alternatives, DSV/iBiTEC-S/SB2SM/LBMS, Saclay, France, CNRS UMR 8221, Saclay,
France
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28
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Kosol S, Schrank E, Krajačić MB, Wagner GE, Meyer NH, Göbl C, Rechberger GN, Zangger K, Novak P. Probing the Interactions of Macrolide Antibiotics with Membrane-Mimetics by NMR Spectroscopy. J Med Chem 2012; 55:5632-6. [DOI: 10.1021/jm300647f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Simone Kosol
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | - Evelyne Schrank
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | | | - Gabriel E. Wagner
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | - N. Helge Meyer
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | - Christoph Göbl
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | - Gerald N. Rechberger
- Institute of Molecular Biosciences,
University of Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - Klaus Zangger
- Institute
of Chemistry/Organic
and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28,
A-8010 Graz, Austria
| | - Predrag Novak
- Department of Chemistry, Faculty
of Natural Science, University of Zagreb, Laboratory for Analytical
Chemistry, Horvatovac 102a, HR-10000 Zagreb, Croatia
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29
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Hohlweg W, Kosol S, Zangger K. Determining the orientation and localization of membrane-bound peptides. Curr Protein Pept Sci 2012; 13:267-79. [PMID: 22044140 PMCID: PMC3394173 DOI: 10.2174/138920312800785049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 10/01/2011] [Accepted: 10/10/2011] [Indexed: 01/06/2023]
Abstract
Many naturally occurring bioactive peptides bind to biological membranes. Studying and elucidating the mode of interaction is often an essential step to understand their molecular and biological functions. To obtain the complete orientation and immersion depth of such compounds in the membrane or a membrane-mimetic system, a number of methods are available, which are separated in this review into four main classes: solution NMR, solid-state NMR, EPR and other methods. Solution NMR methods include the Nuclear Overhauser Effect (NOE) between peptide and membrane signals, residual dipolar couplings and the use of paramagnetic probes, either within the membrane-mimetic or in the solvent. The vast array of solid state NMR methods to study membrane-bound peptide orientation and localization includes the anisotropic chemical shift, PISA wheels, dipolar waves, the GALA, MAOS and REDOR methods and again the use of paramagnetic additives on relaxation rates. Paramagnetic additives, with their effect on spectral linewidths, have also been used in EPR spectroscopy. Additionally, the orientation of a peptide within a membrane can be obtained by the anisotropic hyperfine tensor of a rigidly attached nitroxide label. Besides these magnetic resonance techniques a series of other methods to probe the orientation of peptides in membranes has been developed, consisting of fluorescence-, infrared- and oriented circular dichroism spectroscopy, colorimetry, interface-sensitive X-ray and neutron scattering and Quartz crystal microbalance.
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Affiliation(s)
| | | | - Klaus Zangger
- Institute of Chemistry / Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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30
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Sauvé S, Buijs D, Gingras G, Aubin Y. Interactions between the conserved hydrophobic region of the prion protein and dodecylphosphocholine micelles. J Biol Chem 2011; 287:1915-22. [PMID: 22128151 DOI: 10.1074/jbc.m111.279364] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The three-dimensional structure of PrP110-136, a peptide encompassing the conserved hydrophobic region of the human prion protein, has been determined at high resolution in dodecylphosphocholine micelles by NMR. The results support the conclusion that the (Ctm)PrP, a transmembrane form of the prion protein, adopts a different conformation than the reported structures of the normal prion protein determined in solution. Paramagnetic relaxation enhancement studies with gadolinium-diethylenetriaminepentaacetic acid indicated that the conserved hydrophobic region peptide is not inserted symmetrically in the micelle, thus suggesting the presence of a guanidium-phosphate ion pair involving the side chain of the terminal arginine and the detergent headgroup. Titration of dodecylphosphocholine into a solution of PrP110-136 revealed the presence of a surface-bound species. In addition, paramagnetic probes located the surface-bound peptide somewhere below the micelle-water interface when using the inserted helix as a positional reference. This localization of the unknown population would allow a similar ion pair interaction.
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Affiliation(s)
- Simon Sauvé
- Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
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31
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Willerich I, Schindler T, Gröhn F. Effect of Polyelectrolyte Architecture and Size on Macroion–Dye Assemblies. J Phys Chem B 2011; 115:9710-9. [DOI: 10.1021/jp204368t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Immanuel Willerich
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander University Erlangen-Nürnberg, Egerlandstrasse 3, 91058 Erlangen, Germany
| | - Torben Schindler
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander University Erlangen-Nürnberg, Egerlandstrasse 3, 91058 Erlangen, Germany
| | - Franziska Gröhn
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander University Erlangen-Nürnberg, Egerlandstrasse 3, 91058 Erlangen, Germany
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Myllykoski M, Baumgärtel P, Kursula P. Conformations of peptides derived from myelin-specific proteins in membrane-mimetic conditions probed by synchrotron radiation CD spectroscopy. Amino Acids 2011; 42:1467-74. [PMID: 21505824 DOI: 10.1007/s00726-011-0911-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 04/02/2011] [Indexed: 12/22/2022]
Abstract
Myelin is a tightly packed membrane multilayer in the nervous system, which harbours a specific set of quantitatively major proteins. All these proteins interact with the lipid bilayer, being either peripheral or integral membrane proteins. In this study, we examined the conformational properties of peptides from the myelin proteins P0, CNPase, MOBP, P2 and MOG, using trifluoroethanol and micelles of different detergents as membrane-like mimics. The peptides showed significant differences in their folding under the employed conditions, as evidenced by synchrotron radiation circular dichroism spectroscopy. Our experiments provide new structural information on the interactions between myelin proteins and membranes, using a simplified model system of synthetic peptides and micelles.
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Sarker M, Rose J, McDonald M, Morrow MR, Booth V. Modifications to surfactant protein B structure and lipid interactions under respiratory distress conditions: consequences of tryptophan oxidation. Biochemistry 2010; 50:25-36. [PMID: 21128671 DOI: 10.1021/bi101426s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
These studies detail the altered structure-function relationships caused by oxidation of surfactant protein B (SP-B), a mode of damage thought to be important in acute respiratory distress syndrome (ARDS), a common and frequently fatal condition. An 18-residue fragment comprising the N-terminal helix of SP-B was investigated in oxidized and unmodified forms by solution and solid-state nuclear magnetic resonance (NMR), circular dichroism (CD), and molecular dynamics (MD) simulation. Taken together, the results indicate that tryptophan oxidation causes substantial disruptions in helical structure and lipid interactions. The structural modifications induced by tryptophan oxidation were severe, with a reduction in helical extent from approximately three helical turns to, at most, one turn, and were observed in a variety of solvent environments, including sodium dodecyl sulfate (SDS) micelles, dodecyl phosphocholine (DPC) micelles, and a 40% hexafluoro-2-propanol (HFIP) aqueous solution. The unmodified peptide takes on an orientation within lipid bilayers that is tilted approximately 30° away from an in-plane position. Tryptophan oxidation causes significant modifications to the peptide-lipid interactions, and the peptide likely shifts to a more in-plane orientation within the lipids. Interestingly, the character of the disruptions to peptide-lipid interactions caused by tryptophan oxidation was highly dependent on the charge of the lipid headgroup.
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Affiliation(s)
- Muzaddid Sarker
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL, Canada
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Göbl C, Kosol S, Stockner T, Rückert HM, Zangger K. Solution structure and membrane binding of the toxin fst of the par addiction module. Biochemistry 2010; 49:6567-75. [PMID: 20677831 PMCID: PMC2914490 DOI: 10.1021/bi1005128] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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The par toxin−antitoxin system is required for the stable inheritance of the plasmid pAD1 in its native host Enterococcus faecalis. It codes for the toxin Fst and a small antisense RNA which inhibits translation of toxin mRNA, and it is the only known antisense regulated toxin−antitoxin system in Gram-positive bacteria. This study presents the structure of the par toxin Fst, the first atomic resolution structure of a component of an antisense regulated toxin−antitoxin system. The mode of membrane binding was determined by relaxation enhancements in a paramagnetic environment and molecular dynamics simulation. Fst forms a membrane-binding α-helix in the N-terminal part and contains an intrinsically disordered region near the C-terminus. It binds in a transmembrane orientation with the C-terminus likely pointing toward the cytosol. Membrane-bound, α-helical peptides are frequently found in higher organisms as components of the innate immune system. Despite similarities to these antimicrobial peptides, Fst shows neither hemolytic nor antimicrobial activity when applied externally to a series of bacteria, fungal cells, and erythrocytes. Moreover, its charge distribution, orientation in the membrane, and structure distinguish it from antimicrobial peptides.
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Affiliation(s)
- Christoph Göbl
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Großauer J, Kosol S, Schrank E, Zangger K. The peptide hormone ghrelin binds to membrane-mimetics via its octanoyl chain and an adjacent phenylalanine. Bioorg Med Chem 2010; 18:5483-8. [PMID: 20621491 PMCID: PMC3038380 DOI: 10.1016/j.bmc.2010.06.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 06/15/2010] [Accepted: 06/16/2010] [Indexed: 02/01/2023]
Abstract
The peptide hormone ghrelin, which is the natural ligand of the membrane-bound growth hormone secretagogue receptor (GHS-R), regulates overall body and cell growth, energy homeostasis, carbohydrate, protein and lipid metabolism and water electrolyte balance. It contains an O-acyl linked octanoyl group on Ser3 and is the only peptide known to contain such a modification. Using solution state NMR spectroscopy and ultrafiltration we found that human ghrelin binds to membrane-mimetic environments via its octanoyl group as well as the aromatic moiety of Phe4. Relaxation enhancements in a paramagnetic environment reveal that both the octanoyl group on Ser3 and the aromatic group on Phe4 are inserted deep into the hydrophobic core of phosphocholine assemblies while the remaining peptide is freely mobile in solution. In contrast, no binding was observed for des-octanoyl ghrelin. Thus, the octanoyl chain, together with the Phe4 aromatic group of ghrelin, functions as a membrane anchor. Our results are in parallel with the previous finding that a bulky hydrophobic group on Ser3 and Phe4 of ghrelin are necessary for its function and thus indicate that membrane-binding is essential for ghrelin function.
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Affiliation(s)
| | | | | | - Klaus Zangger
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria
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Kosol S, Zangger K. Dynamics and orientation of a cationic antimicrobial peptide in two membrane-mimetic systems. J Struct Biol 2010; 170:172-9. [PMID: 20045466 PMCID: PMC7128155 DOI: 10.1016/j.jsb.2009.12.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 12/21/2009] [Accepted: 12/28/2009] [Indexed: 01/23/2023]
Abstract
In order to investigate the functional and structural properties of cationic α-helical peptides in two different membranes, we studied the 20-residue peptide maximin H6 in two membrane-mimetic systems by NMR spectroscopy using partially 15N-labeled peptide and paramagnetic relaxation enhancements. Maximin H6, which is found in skin secretions of frogs of the Bombinae family, attacks gram-negative bacteria and acts haemolytically. While the peptide spontaneously folds into similar structures in both neutral dodecylphosphocholine (DPC) and negatively charged sodium dodecyl sulphate (SDS) micelles, its structure is more flexible in SDS as shown by 15N relaxation measurements. In addition, it is bound closer to the surface of the micelle and rotated by ∼70° around its helix axis in the negatively charged membrane surrogate compared to the structure in DPC. This might form the basis for peptide–peptide interactions through a GxxxG motif, which could finally lead to membrane disruption and, thus, preferential attack of negatively charged microbial cell walls.
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Affiliation(s)
- Simone Kosol
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria.
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