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Caoduro C, Hervouet E, Girard-Thernier C, Gharbi T, Boulahdour H, Delage-Mourroux R, Pudlo M. Carbon nanotubes as gene carriers: Focus on internalization pathways related to functionalization and properties. Acta Biomater 2017; 49:36-44. [PMID: 27826000 DOI: 10.1016/j.actbio.2016.11.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/15/2016] [Accepted: 11/03/2016] [Indexed: 12/25/2022]
Abstract
Carbon nanotubes represent promising transporters for delivery of DNA and other biomolecules into living cells. Various methods of CNTs surface functionalization have been developed. These are essential to improve CNTs dispersibility and permit their interactions with biological structures that broaden their use in advanced biomedical applications. The present review discusses the different single walled carbon nanotubes and multiwalled carbon nanotubes functionalization methods, leading to the formation of optimized and functionalized-CNT complexes with DNA. F-CNTs are recognized as efficient and promising gene carriers. Emphasis is then placed on the processes used by f-CNTs/DNA complexes to cross cell membranes. Energy independent pathways and uptake mechanisms dependent on energy, such as endocytosis or phagocytosis, are reported by many studies, and if these mechanisms seem contradictory at first sight, a detailed review of the literature illustrates that they are rather complementary. Preferential use of one or the other depends on the DNA and CNTs chemical nature and physical parameters, experimental procedures and cell types. STATEMENT OF SIGNIFICANCE Efficient non-viral gene delivery is desirable, yet challenging. CNTs appear as a promising solution to penetrate into cells and successfully deliver DNA. Moreover, the field of use of CNTs as gene carrier is large and is currently growing. This critical review summarizes the development and evaluation of CNTs as intracellular gene delivery system and provides an overview of functionalized CNTs/DNA cellular uptake mechanisms, depending on several parameters of CNTs/DNA complexes.
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Affiliation(s)
- Cécile Caoduro
- Nanomedicine, Imagery and Therapeutics Laboratory, EA4662, Université de Bourgogne Franche Comté, F-25000 Besançon, France
| | - Eric Hervouet
- Laboratoire de Biochimie, EA3922, Expression Génique et Pathologies du Système Nerveux Central, SFRIBCT FED 4234, Université de Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Corine Girard-Thernier
- Fonctions et Dysfonctions Epithéliales, EA4267, Université de Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Tijani Gharbi
- Nanomedicine, Imagery and Therapeutics Laboratory, EA4662, Université de Bourgogne Franche Comté, F-25000 Besançon, France
| | - Hatem Boulahdour
- Nanomedicine, Imagery and Therapeutics Laboratory, EA4662, Université de Bourgogne Franche Comté, F-25000 Besançon, France
| | - Régis Delage-Mourroux
- Laboratoire de Biochimie, EA3922, Expression Génique et Pathologies du Système Nerveux Central, SFRIBCT FED 4234, Université de Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Marc Pudlo
- Fonctions et Dysfonctions Epithéliales, EA4267, Université de Bourgogne Franche-Comté, F-25000 Besançon, France.
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Baoum AA, Middaugh CR, Berkland C. DNA complexed with TAT peptide and condensed using calcium possesses unique structural features compared to PEI polyplexes. Int J Pharm 2014; 465:11-7. [DOI: 10.1016/j.ijpharm.2014.01.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 12/17/2013] [Accepted: 01/29/2014] [Indexed: 11/29/2022]
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Prudovsky I, Kumar TKS, Sterling S, Neivandt D. Protein-phospholipid interactions in nonclassical protein secretion: problem and methods of study. Int J Mol Sci 2013; 14:3734-72. [PMID: 23396106 PMCID: PMC3588068 DOI: 10.3390/ijms14023734] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 12/30/2022] Open
Abstract
Extracellular proteins devoid of signal peptides use nonclassical secretion mechanisms for their export. These mechanisms are independent of the endoplasmic reticulum and Golgi. Some nonclassically released proteins, particularly fibroblast growth factors (FGF) 1 and 2, are exported as a result of their direct translocation through the cell membrane. This process requires specific interactions of released proteins with membrane phospholipids. In this review written by a cell biologist, a structural biologist and two membrane engineers, we discuss the following subjects: (i) Phenomenon of nonclassical protein release and its biological significance; (ii) Composition of the FGF1 multiprotein release complex (MRC); (iii) The relationship between FGF1 export and acidic phospholipid externalization; (iv) Interactions of FGF1 MRC components with acidic phospholipids; (v) Methods to study the transmembrane translocation of proteins; (vi) Membrane models to study nonclassical protein release.
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Affiliation(s)
- Igor Prudovsky
- Maine Medical Center Research Institute, 81 Research Drive, Scarborough, ME 04074, USA
| | | | - Sarah Sterling
- Department of Chemical and Biological Engineering, University of Maine, Orono, ME 04469, USA; E-Mails: (S.S.); (D.N.)
| | - David Neivandt
- Department of Chemical and Biological Engineering, University of Maine, Orono, ME 04469, USA; E-Mails: (S.S.); (D.N.)
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Biophilic carbon nanotubes. Colloids Surf B Biointerfaces 2013; 105:310-8. [PMID: 23384693 DOI: 10.1016/j.colsurfb.2012.12.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 11/29/2012] [Accepted: 12/29/2012] [Indexed: 11/21/2022]
Abstract
Carbon nanotubes (CNTs) have been proposed and are actively being explored as innovative multipurpose carriers for biomolecules and diagnostic applications. Their versatile physico-chemical features enable them as a carrier of several pharmaceutically relevant entities and allow them for rational design of novel nanoscale candidates for drug development. Functionalized carbon nanotubes (f-CNT) are emerging as a new family of nanovectors for the delivery of different types of therapeutic molecules. The application of CNTs in the field of carrier-mediated delivery has become possible after the recent discovery of their capacity to penetrate into the cells. CNT can be loaded with active molecules by forming stable covalent bonds or supramolecular assemblies based on noncovalent interactions. Once the cargos are carried into various cells, tissues and organs they are able to express their biological function. In this review, we will describe the potential of f-CNT as a vehicle to deliver different types of therapeutic agents into the biological species.
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Jo J, Song H, Park SG, Lee S, Ko J, Park J, Jeong J, Cheon Y, Lee DR. Regulation of Differentiation Potential of Human Mesenchymal Stem Cells by Intracytoplasmic Delivery of Coactivator‐Associated Arginine Methyltransferase 1 Protein Using Cell‐Penetrating Peptide. Stem Cells 2012; 30:1703-1713. [DOI: 10.1002/stem.1146] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- Junghyun Jo
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
| | - Haengseok Song
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
| | - Sang Gyu Park
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
| | - Soo‐Hong Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
| | - Jung‐Jae Ko
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
| | - Jong‐Hyuk Park
- Division of Development and Physiology, School of Biological Sciences and Chemistry, Institute for Basic Sciences, College of Natural Science, Sungshin Women's University, Seoul, Korea
| | - Jaemin Jeong
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Science, Seoul, Korea
| | - Yong‐Pil Cheon
- Division of Development and Physiology, School of Biological Sciences and Chemistry, Institute for Basic Sciences, College of Natural Science, Sungshin Women's University, Seoul, Korea
| | - Dong Ryul Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
- CHA Stem Cell Institute, CHA University, Seoul, Korea
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Ménard-Moyon C, Venturelli E, Fabbro C, Samorì C, Da Ros T, Kostarelos K, Prato M, Bianco A. The alluring potential of functionalized carbon nanotubes in drug discovery. Expert Opin Drug Discov 2010; 5:691-707. [DOI: 10.1517/17460441.2010.490552] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Yeh HY, Yates MV, Chen W, Mulchandani A. Real-time molecular methods to detect infectious viruses. Semin Cell Dev Biol 2009; 20:49-54. [PMID: 19429491 DOI: 10.1016/j.semcdb.2009.01.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 01/23/2009] [Indexed: 01/18/2023]
Abstract
Waterborne transmitted viruses pose a public health threat due to their stability in aquatic environment and the easy transmission with high morbidity rates at low infectious doses. Two major challenge of virus analysis include a lack of adequate information in infectivity and the inability to cultivate certain epidemiologically important viruses in vitro. The use of fluorescent probes in conjunction with fluorescence microscopy allows us to reveal dynamic interactions of the viruses with different cellular structures in living cells that are impossible to detect by immunological or PCR-based experiments. Real-time viral detection in vivo provides sufficient information regarding multiple steps in infection process at molecular level, which will be valuable for the prevention and control of viral infection.
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Affiliation(s)
- Hsiao-Yun Yeh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, United States
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Posnett DN, Engelhorn ME, Lin Y, Merghoub T, Duan F, Wolchok JD, Houghton AN. Development of effective vaccines for old mice in a tumor model. Vaccine 2008; 27:1093-100. [PMID: 19103244 DOI: 10.1016/j.vaccine.2008.11.112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 11/21/2008] [Accepted: 11/26/2008] [Indexed: 10/21/2022]
Abstract
Vaccines are often inefficient in old people and old mice. Few studies have focused on testing vaccines in old populations. Here we used DNA tumor antigen vaccines against melanoma and showed that old mice were not protected. Vaccines incorporating fusions of the tumor antigen with microbial adjuvant proteins OmpA (E. Coli) or Vp22 (Herpes simplex virus-1) dramatically improved protection of old mice. The mechanisms by which these adjuvant proteins act are distinct. TLR2 was not required for either OmpA or Vp22. Antigen processing and presentation were not boosted by these fusion constructs. However, fusion constructs with Vp22 gave a strong CD4 response to B16 melanoma and the OmpA response is MHC-II dependent. Both adjuvant fusion constructs stimulated CD4 and CD8 responses otherwise diminished in old mice.
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Affiliation(s)
- David N Posnett
- Dep. of Medicine, Weill Medical College of Cornell University, New York, NY 10021, United States.
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Yu BZ, Yang JS, Li WX. In vitro capability of multi-walled carbon nanotubes modified with gonadotrophin releasing hormone on killing cancer cells. CARBON 2007. [DOI: 10.1016/j.carbon.2007.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Chakraborty T, Kumar SU, Mohan BK, Sarma GD, Kiran MU, Jagadeesh B. Synthesis and conformational studies of 3,4-di-O-acylated furanoid sugar amino acid-containing analogs of the receptor binding inhibitor of vasoactive intestinal peptide. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.07.158] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Rajalingam D, Graziani I, Prudovsky I, Yu C, Kumar TKS. Relevance of partially structured states in the non-classical secretion of acidic fibroblast growth factor. Biochemistry 2007; 46:9225-38. [PMID: 17636870 PMCID: PMC3656169 DOI: 10.1021/bi7002586] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acidic fibroblast growth factor (aFGF) is a signal peptide-less protein that is secreted into the extracellular compartment as part of a multiprotein release complex, consisting of aFGF, S100A13 (a calcium binding protein), and a 40 kDa (p40) form of synaptotagmin (Syt1), a protein that participates in the docking of a variety of secretory vesicles. p40 Syt1, and specifically its C2A domain, is believed to play a major role in the non-classical secretion of the aFGF release complex mediated by the interaction of aFGF and p40 Syt1with the phospholipids of the cell membrane inner leaflet. In the present study, we investigate the structural characteristics of aFGF and the C2A domain of p40 Syt1 under acidic conditions, using a variety of biophysical techniques including multidimensional NMR spectroscopy. Urea-induced equilibrium unfolding (at pH 3.4) of both aFGF and the C2A domain are non-cooperative and proceed with the accumulation of stable intermediate states. 1-Anilino-8-napthalene sulfonate (ANS) binding and size-exclusion chromatography results suggest that both aFGF and the C2A domain exist as partially structured states under acidic conditions (pH 3.4). Limited trypsin digestion analysis and 1H-15N chemical shift perturbation data reveal that the flexibility of certain portions of the protein backbone is increased in the partially structured state(s) of aFGF. The residues that are perturbed in the partially structured state(s) in aFGF are mostly located at the N- and C-terminal ends of the protein. In marked contrast, most of the interactions stabilizing the native secondary structure are preserved in the partially structured state of the C2A domain. Isothermal titration calorimetry data indicate that the binding affinity between aFGF and the C2A domain is significantly enhanced at pH 3.4. In addition, both aFGF and the C2A domain exhibit much higher lipid binding affinity in their partially structured states. The translocation of the multiprotein FGF release complex across the membrane appears to be facilitated by the formation of partially structured states of aFGF and the C2A domain of p40 Syt1.
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Affiliation(s)
| | - Irene Graziani
- Department of Chemistry and Biochemistry, Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine 04074
| | - Igor Prudovsky
- Department of Chemistry and Biochemistry, Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine 04074
| | - Chin Yu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
- Department of Chemistry, National Tsing Hua University, Hsinchu 30043, Taiwan
- To whom correspondence should be addressed. Phone: 479-575-5646. Fax: 479-575-4049. (T.K.S.K.). Phone: 886-35-711082. Fax: 886-35-721524. cyu@ mx.nthu.edu.tw (C.Y.)
| | - Thallapuranam Krishnaswamy S. Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
- To whom correspondence should be addressed. Phone: 479-575-5646. Fax: 479-575-4049. (T.K.S.K.). Phone: 886-35-711082. Fax: 886-35-721524. cyu@ mx.nthu.edu.tw (C.Y.)
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Bayele HK, Ramaswamy C, Wilderspin AF, Srai KS, Toth I, Florence AT. Protein transduction by lipidic peptide dendrimers. J Pharm Sci 2006; 95:1227-37. [PMID: 16639724 DOI: 10.1002/jps.20606] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We investigated the potential of a new family of lipidic peptide dendrimers in protein transduction into cultured cells. Dendrimer-protein interaction was determined by gel retardation assays using purified recombinant protein. To assess intracellular protein delivery, two marker proteins were used: recombinant firefly luciferase and a Cy3-labeled monoclonal antibody to the c-myc proto-oncogene. Protein delivery was determined by luciferase assays and fluorescence microscopy, respectively. While there was minimal delivery of luciferase or antibody in the absence of the dendrimers, the latter increased protein delivery substantially. Luciferase delivery was concentration and cell type-dependent; the efficiency of delivery also varied with the number of terminal amino groups on the dendrimers. In previous reports, we showed that these dendrimers could be used for gene and drug delivery; the data we report herein suggest that they may also be capable of intracellular protein delivery. This finding has important implications for the use of these dendrimers in protein therapeutics and vaccinology.
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Affiliation(s)
- Henry K Bayele
- Department of Biochemistry and Molecular Biology, University College London, London NW3 2PF, United Kingdom.
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Bullok KE, Gammon ST, Violini S, Prantner AM, Villalobos VM, Sharma V, Piwnica-Worms D. Permeation Peptide Conjugates for In Vivo Molecular Imaging Applications. Mol Imaging 2006. [DOI: 10.2310/7290.2006.00001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Zaro JL, Shen WC. Evidence that membrane transduction of oligoarginine does not require vesicle formation. Exp Cell Res 2005; 307:164-73. [PMID: 15922736 DOI: 10.1016/j.yexcr.2005.02.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Revised: 02/17/2005] [Accepted: 02/21/2005] [Indexed: 01/04/2023]
Abstract
The involvement of vesicular formation processes in the membrane transduction and nuclear transport of oligoarginine is currently a subject of controversy. In this report, a novel quantitative method which allows for the selective measurement of membrane transduction excluding concurrent endocytosis was used to determine the effects of temperature, endosomal acidification, endosomolysis, and several known inhibitors of endocytic pathways on the internalization of oligoarginine. The results show that, unlike endocytosis, transduction of oligoarginine was not affected by incubation at 16 degrees C as compared to the 37 degrees C control, and was only partially inhibited at 4 degrees C incubation. Additionally, membrane transduction was not inhibited to the same extent as endocytosis following treatment with ammonium chloride, hypertonic medium, amiloride, or filipin. The endosomolytic activity of oligoarginine was investigated by examining the leakage of FITC-dextran into the cytosolic compartment, which was not higher in the presence of oligoarginine. Furthermore, ammonium chloride showed no effect on the nuclear transport of oligoarginine. The data presented in this report indicate that membrane transduction is likely to occur at the plasma membrane without the formation of membrane vesicles, and the nuclear localization involves membrane transduction, rather than endocytosis of oligoarginine.
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Affiliation(s)
- Jennica L Zaro
- University of Southern California, School of Pharmacy, Department of Pharmaceutical Sciences, 1985 Zonal Avenue, PSC 404B, Los Angeles, CA 90033-1039, USA
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Abstract
Reversible lipid attachment was investigated as a means to deliver small peptides into cells. Two labile straight chain alkyl motifs were developed: a cysteine dodecane disulfide (Cdd) building block and a tyrosine- or serine-myristate ester. Both moieties are cleaved on cell internalization and are compatible with Fmoc solid phase peptide synthesis. A series of fluorophore-labeled peptides that varied in lipophilic content, net charge, and charge distribution were synthesized. The peptides were screened for cellular uptake efficiency as monitored by fluorescence microscopy. Effective peptide transport is based on a distributed net positive charge introduced as lysine residues at the C and/or N terminus of the peptide and the presence of a hydrophobic domain exhibiting an estimated log P4.0. The incorporation of labile lipid motifs into peptides enhances lipophilic character of the peptides and contributes to cellular uptake with minimal alteration to the native sequence.
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Affiliation(s)
- Christina N Carrigan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Loiarro M, Sette C, Gallo G, Ciacci A, Fantò N, Mastroianni D, Carminati P, Ruggiero V. Peptide-mediated Interference of TIR Domain Dimerization in MyD88 Inhibits Interleukin-1-dependent Activation of NF-κB. J Biol Chem 2005; 280:15809-14. [PMID: 15755740 DOI: 10.1074/jbc.c400613200] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myeloid differentiation factor 88 (MyD88) plays a crucial role in the signaling pathways triggered by interleukin (IL)-1 and Toll-like receptors in several steps of innate host defense. A crucial event in this signaling pathway is represented by dimerization of MyD88, which allows the recruitment of downstream kinases like IRAK-1 and IRAK-4. Herein, we have investigated the function of the Toll/IL-1 receptor (TIR) domain in MyD88 homodimerization in cell-free and in vitro experimental settings by using epta-peptides that mimic the BB-loop region of the conserved TIR domain of different proteins. By using a pull-down assay with purified glutathione S-transferase-MyD88 TIR or co-immunoprecipitation experiments, we found that epta-peptides derived from the TIR domain of MyD88 and IL-18R are the most effective in inhibiting homodimerization with either the isolated TIR or full-length MyD88. Moreover, we demonstrated that a cell permeable analog of MyD88 epta-peptide inhibits homodimerization of MyD88 TIR domains in an in vitro cell system and significantly reduces IL-1 signaling, as assayed by activation of the downstream transcription factor NF-kappaB. Our results indicate that the BB-loop in TIR domain of MyD88 is a good target for specific inhibition of MyD88-mediated signaling in vivo.
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Affiliation(s)
- Maria Loiarro
- Department of Public Health and Cell Biology, University of Rome "Tor Vergata," 00173 Rome, Italy
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Gromiha MM, Suwa M. Structural analysis of residues involving cation-π interactions in different folding types of membrane proteins. Int J Biol Macromol 2005; 35:55-62. [PMID: 15769516 DOI: 10.1016/j.ijbiomac.2004.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Revised: 12/01/2004] [Accepted: 12/02/2004] [Indexed: 11/30/2022]
Abstract
Cation-pi interactions play an important role to the stability of protein structures. In our earlier work, we have analyzed the influence and energetic contribution of cation-pi interactions in three-dimensional structures of membrane proteins. In this work, we investigate the characteristic features of residues that are involved in cation-pi interactions. We have computed several parameters, such as surrounding hydrophobicity, number of long-range contacts, conservation score and normalized B-factor for all these residues and identified their location, whether in the membrane or at surface. We found that the cation-pi interactions are mainly formed by long-range interactions. The cationic residues involved in cation-pi interactions have higher surrounding hydrophobicity than their average values in the whole dataset and an opposite trend is observed for aromatic residues. In transmembrane helical proteins, except Phe, all other residues that are responsible for cation-pi interactions are highly conserved with other related protein sequences whereas in transmembrane strand proteins, an appreciable conservation is observed only for Arg. The analysis on the flexibility of residues reveals that the cation-pi interaction forming residues are more stable than other residues. The results obtained in the present study would be helpful to understand the role of cation-pi interactions in the structure and folding of membrane proteins.
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Affiliation(s)
- M Michael Gromiha
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Aomi Frontier Building 17F, 2-43 Aomi, Koto-ku, Tokyo 135-0064, Japan.
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Roth CM, Sundaram S. Engineering synthetic vectors for improved DNA delivery: insights from intracellular pathways. Annu Rev Biomed Eng 2004; 6:397-426. [PMID: 15255775 DOI: 10.1146/annurev.bioeng.6.040803.140203] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Significant progress has been made in the area of nonviral gene delivery to date. Yet, synthetic vectors remain less efficient by orders of magnitude than their viral counterparts. Research continues toward unraveling and overcoming various barriers to the efficient delivery of DNA, whether in plasmid form encoding a gene or as an oligonucleotide for the selective inhibition of target gene expression. Novel components for overcoming these hurdles are continually being incorporated into the design of synthetic vectors, leading to increasingly more virus-like particles. Despite these advances, general principles defining the design of synthetic vectors are yet to be developed fully. A more quantitative analysis of the cellular uptake and intracellular processing of these vectors is required for the rational manipulation of vector design. Mathematical frameworks with a more conceptual basis will help obtain an integrated perspective on these complex systems. In this review, we critically examine the progress made toward the improved design of synthetic vectors by the strategic exploitation of intracellular mechanisms and explore newer possibilities to overcome obstacles in the practical realization of this field.
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Affiliation(s)
- Charles M Roth
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, USA.
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Chakraborty T, Krishna Mohan B, Uday Kumar S, Prabhakar A, Jagadeesh B. Synthesis of 3,4-di- O -acylated glucose-derived furanoid sugar amino acids (Gaa): conformational analysis of a Leu-enkephalin analog containing di- O -myristoylated Gaa. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.05.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
The behavior of the proteome reflects spatial and temporal organization both within and without cells. We propose that various macromolecular entities possessing polyanionic character such as proteoglycans, lipid bilayer surfaces, microtubules, microfilaments, and polynucleotides may provide a functional network that mediates a variety of cellular phenomena. The interaction of proteins with this array of polyanions is characterized by a lower degree of specificity than seen with most commonly recognized macromolecular interactions. In this commentary, potential roles for this polyanion network in diverse functions such as protein/protein interactions, protein folding and stabilization, macromolecular transport, and various disease processes are all considered, as well as the use of polyanions as therapeutic agents. The role of small polyanions in the regulation of protein/polyanion interactions is also postulated. We provide preliminary experimental analysis of the extent to which proteins interact with polyanions inside cells using a combination of two-dimensional chromatographic and electrophoretic methods and antibody arrays. We conclude that many hundreds to thousands of such interactions are present in cells and argue that future understanding of the proteome will require that the "polyanion world" be taken into account.
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Affiliation(s)
- LaToya S Jones
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047-3729, USA
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