1
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Azzaz F, Yahi N, Chahinian H, Fantini J. The Epigenetic Dimension of Protein Structure Is an Intrinsic Weakness of the AlphaFold Program. Biomolecules 2022; 12:biom12101527. [PMID: 36291736 PMCID: PMC9599222 DOI: 10.3390/biom12101527] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/12/2022] [Accepted: 10/16/2022] [Indexed: 12/02/2022] Open
Abstract
One of the most important lessons we have learned from sequencing the human genome is that not all proteins have a 3D structure. In fact, a large part of the human proteome is made up of intrinsically disordered proteins (IDPs) which can adopt multiple structures, and therefore, multiple functions, depending on the ligands with which they interact. Under these conditions, one can wonder about the value of algorithms developed for predicting the structure of proteins, in particular AlphaFold, an AI which claims to have solved the problem of protein structure. In a recent study, we highlighted a particular weakness of AlphaFold for membrane proteins. Based on this observation, we have proposed a paradigm, referred to as “Epigenetic Dimension of Protein Structure” (EDPS), which takes into account all environmental parameters that control the structure of a protein beyond the amino acid sequence (hence “epigenetic”). In this new study, we compare the reliability of the AlphaFold and Robetta algorithms’ predictions for a new set of membrane proteins involved in human pathologies. We found that Robetta was generally more accurate than AlphaFold for ascribing a membrane-compatible topology. Raft lipids (e.g., gangliosides), which control the structural dynamics of membrane protein structure through chaperone effects, were identified as major actors of the EDPS paradigm. We conclude that the epigenetic dimension of a protein structure is an intrinsic weakness of AI-based protein structure prediction, especially AlphaFold, which warrants further development.
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2
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Nakatani Y, Ye Z, Ishizue Y, Higashi T, Imai T, Fujii I, Michigami M. “Human and Mouse Cross-Reactive” Albumin-Binding Helix–Loop–Helix Peptide Tag for Prolonged Bioactivity of Therapeutic Proteins. Mol Pharm 2022; 19:2279-2286. [PMID: 35635006 PMCID: PMC9257745 DOI: 10.1021/acs.molpharmaceut.2c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The effectiveness
of protein and peptide pharmaceuticals depends
essentially on their intrinsic pharmacokinetics. Small-sized pharmaceuticals
in particular often suffer from short serum half-lives due to rapid
renal clearance. To improve the pharmacokinetics by association with
serum albumin (SA) in vivo, we generated an SA-binding
tag of a helix–loop–helix (HLH) peptide to be linked
with protein pharmaceuticals. For use in future preclinical studies,
screening of yeast-displayed HLH peptide libraries against human SA
(HSA) and mouse SA (MSA) was alternately repeated to give the SA-binding
peptide AY-VE, which exhibited cross-binding activities to HSA and
MSA with KD of 65 and 20 nM, respectively.
As a proof of concept, we site-specifically conjugated peptide AY-VE
with insulin to examine its bioactivity in vivo.
In mouse bioassay monitoring the blood glucose level, the AY-VE conjugate
was found to have a prolonged hypoglycemic effect for 12 h. The HLH
peptide tag is a general platform for extending the bioactivity of
therapeutic peptides or proteins.
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Affiliation(s)
- Yuto Nakatani
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Zhengmao Ye
- Interprotein Corporation, 3-10-2 Toyosaki, Kita-ku, Osaka 531-0072, Japan
| | - Yuki Ishizue
- Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-Honmachi, Kumamoto 862-0973, Japan
| | - Taishi Higashi
- Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-Honmachi, Kumamoto 862-0973, Japan
| | - Teruko Imai
- Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-Honmachi, Kumamoto 862-0973, Japan
- Daiichi University of Pharmacy, 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Masataka Michigami
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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3
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Mihara K, Nakajima N, Fujii I, Fujiwara D. Generation of inhibitory peptides for
IKKε
from a kinase‐focused phage library of helix‐loop‐helix peptides. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kousuke Mihara
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Natsumi Nakajima
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
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4
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Fujiwara D, Mihara K, Takayama R, Nakamura Y, Ueda M, Tsumuraya T, Fujii I. Chemical Modification of Phage-Displayed Helix-Loop-Helix Peptides to Construct Kinase-Focused Libraries. Chembiochem 2021; 22:3406-3409. [PMID: 34605137 PMCID: PMC9297947 DOI: 10.1002/cbic.202100450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/01/2021] [Indexed: 11/11/2022]
Abstract
Conformationally constrained peptides hold promise as molecular tools in chemical biology and as a new modality in drug discovery. The construction and screening of a target‐focused library could be a promising approach for the generation of de novo ligands or inhibitors against target proteins. Here, we have prepared a protein kinase‐focused library by chemically modifying helix‐loop‐helix (HLH) peptides displayed on phage and subsequently tethered to adenosine. The library was screened against aurora kinase A (AurA). The selected HLH peptide Bip‐3 retained the α‐helical structure and bound to AurA with a KD value of 13.7 μM. Bip‐3 and the adenosine‐tethered peptide Bip‐3‐Adc provided IC50 values of 103 μM and 7.7 μM, respectively, suggesting that Bip‐3‐Adc bivalently inhibited AurA. In addition, the selectivity of Bip‐3‐Adc to several protein kinases was tested, and was highest against AurA. These results demonstrate that chemical modification can enable the construction of a kinase‐focused library of phage‐displayed HLH peptides.
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Affiliation(s)
- Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Kousuke Mihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ryo Takayama
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Yusuke Nakamura
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Mitsuhiro Ueda
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Takeshi Tsumuraya
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
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5
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Matsuura K, Hisamoto K, Tanaka T, Sakamoto R, Okazaki M, Inaba H. Turn-On Fluorescent Probe Based on a Dansyl Triarginine Peptide for Ganglioside Imaging. ACS ORGANIC & INORGANIC AU 2021; 1:60-67. [PMID: 36855753 PMCID: PMC9954261 DOI: 10.1021/acsorginorgau.1c00013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gangliosides play pivotal biological roles in the animal cell membranes, and it is vital to develop fluorescent probes for imaging them. To date, various artificial receptors for ganglioside imaging have been developed; however, turn-on fluorescence imaging for gangliosides with high contrast has not been achieved. We developed a simple fluorescent probe on the basis of a dansyl triarginine peptide for turn-on ganglioside imaging on the liposome membrane. The probe bound to monosialyl gangliosides and other anionic lipids with association constants was 105 M-1, which enhanced from 6-fold to 7-fold the fluorescence intensity. Upon binding to monosialyl ganglioside-containing giant liposomes, the turn-on probe selectively enhanced the fluorescence intensity compared with the other anionic lipids. This simple peptide probe for turn-on fluorescence imaging of gangliosides would provide a novel molecular tool for chemical biology.
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Affiliation(s)
- Kazunori Matsuura
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan,Centre
for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan,E-mail:
| | - Koichi Hisamoto
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Tomoya Tanaka
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Ryota Sakamoto
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Mizuki Okazaki
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Hiroshi Inaba
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan,Centre
for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
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6
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Ramanayake Mudiyanselage TM, Michigami M, Ye Z, Uyeda A, Inoue N, Sugiura K, Fujii I, Fujiwara D. An Immune-Stimulatory Helix-Loop-Helix Peptide: Selective Inhibition of CTLA-4-B7 Interaction. ACS Chem Biol 2020; 15:360-368. [PMID: 31841301 DOI: 10.1021/acschembio.9b00743] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular-targeting peptides and mini-proteins are promising alternatives to antibodies in a wide range of applications in bioscience and medicine. We have developed a helix-loop-helix (HLH) peptide as an alternative to antibodies to inhibit specific protein interactions. Cytotoxic T lymphocyte antigen-4 (CTLA-4) downregulates immune responses of cytotoxic T-cells by interaction with B7-1, a co-stimulatory molecule expressed on antigen presenting cells (APCs). To induce immune stimulatory activity, we used directed evolution methods to generate a HLH peptide that binds to CTLA-4, inhibiting the CTLA-4-B7-1 interaction and inducing immune stimulatory activity. Yeast-displayed libraries of HLH peptides were constructed and screened against CTLA-4 and identified the binding peptide Y-2, which exhibits a moderate affinity. The affinity of Y-2 was improved by in vitro affinity maturation to afford a stronger binder, ERY2-4. Peptide ERY2-4 specifically bound to CTLA-4 with a KD of 196.8 ± 2.3 nM, comparable to the affinity of the CTLA-4-B7-1 interaction. Furthermore, ERY2-4 inhibited the CTLA-4-B7-1 interaction with an IC50 of 1.1 ± 0.03 μM and blocked the interaction between CTLA-4 and dendritic cells (DCs) presenting B7 on their surface. Importantly, ERY2-4 showed no cross-reactivity against CD28, suggesting it does not suppress T-cell activation. Finally, in a mixed lymphocyte reaction assay with DCs and T cells, ERY2-4 enhanced an allogeneic lymphocyte response. Since CTLA-4 is a critical immune checkpoint for restricting the cancer immune response, this inhibitory HLH peptide represents a new class of drug candidates for immunotherapy.
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Affiliation(s)
- Tharanga M.R. Ramanayake Mudiyanselage
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-oraikita, Izumisano, Osaka 598-8531, Japan
| | - Masataka Michigami
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Zhengmao Ye
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Atsuko Uyeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norimitsu Inoue
- Department of Tumor Immunology, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka-shi, Osaka 541-8567, Japan
| | - Kikuya Sugiura
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-oraikita, Izumisano, Osaka 598-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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7
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Wang W, Suga T, Hagimori M, Kuroda N, Fuchigami Y, Kawakami S. Investigation of Intracellular Delivery of NuBCP-9 by Conjugation with Oligoarginines Peptides in MDA-MB-231 Cells. Biol Pharm Bull 2018; 41:1448-1455. [PMID: 30175779 DOI: 10.1248/bpb.b18-00335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Oligoarginines (Rn) are becoming promising tools for the intracellular delivery of biologically active molecules. NuBCP-9, a peptide that induces apoptosis in B-cell lymphoma 2 (Bcl-2)-expressing cancer cells, has been reported to promote the uptake and non-specific cytotoxicity of R8, also called octaarginine. However, it is unknown whether a similar synergistic effect can be seen with other Rn. In this study, we conjugated NuBCP-9 with various Rn (n=8, 10, 12, 14) to investigate and compare their cellular uptake characteristics. In addition, their non-specific cytotoxicity and apoptosis-inducing abilities were evaluated. We found that NuBCP-9 conjugated with Rn enhanced cellular uptake mainly through clathrin-mediated endocytosis and macropinocytosis, and that the uptake pathways were not different from those used by unconjugated Rn. However, the cytotoxicity study showed that NuBCP-9-R12 and NuBCP-9-R14 conjugates enhanced non-specific cytotoxicity. We found that NuBCP-9-R10 conjugate had the highest uptake efficiency and induced correspondingly high levels of apoptosis, while resulting in a tolerable degree of non-specific toxicity.
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Affiliation(s)
- Wei Wang
- Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, Nagasaki University.,Department of Analytical Chemistry for Pharmaceutics, Graduate School of Biomedical Sciences, Nagasaki University
| | - Tadaharu Suga
- Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, Nagasaki University.,Department of Analytical Chemistry for Pharmaceutics, Graduate School of Biomedical Sciences, Nagasaki University
| | - Masayori Hagimori
- Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, Nagasaki University
| | - Naotaka Kuroda
- Department of Analytical Chemistry for Pharmaceutics, Graduate School of Biomedical Sciences, Nagasaki University
| | - Yuki Fuchigami
- Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, Nagasaki University
| | - Shigeru Kawakami
- Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, Nagasaki University
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8
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Nishihara T, Kitada H, Fujiwara D, Fujii I. Macrocyclization and labeling of helix-loop-helix peptide with intramolecular bis-thioether linkage. Biopolymers 2017; 106:415-21. [PMID: 26917088 DOI: 10.1002/bip.22826] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/27/2016] [Accepted: 02/13/2016] [Indexed: 11/07/2022]
Abstract
Conformationally constrained peptides have been developed as an inhibitor for protein-protein interactions (PPIs), and we have de novo designed cyclized helix-loop-helix (cHLH) peptide with a disulfide bond consisting of 40 amino acids to generate molecular-targeting peptides. However, synthesis of long peptides has sometimes resulted in low yield according to the respective amino acid sequences. Here we developed a method for efficient synthesis and labeling for cHLH peptides. First, we synthesized two peptide fragments and connected them by the copper-mediated alkyne and azide cycloaddition (CuAAC) reaction. Cyclization was performed by bis-thioether linkage using 1,3-dibromomethyl-5-propargyloxybenzene, and subsequently, the cHLH peptide was labeled with an azide-labeled probe. Finally, we designed and synthesized a peptide inhibitor for the p53-HDM2 interaction using a structure-guided design and successfully labeled it with a fluorescent probe or a functional peptide, respectively, by click chemistry. This macrocyclization and labeling method for cHLH peptide would facilitate the discovery of de novo bioactive ligands and therapeutic leads. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 415-421, 2016.
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Affiliation(s)
- Toshio Nishihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Hidekazu Kitada
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
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9
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Matsubara T, Otani R, Yamashita M, Maeno H, Nodono H, Sato T. Selective Intracellular Delivery of Ganglioside GM3-Binding Peptide through Caveolae/Raft-Mediated Endocytosis. Biomacromolecules 2017; 18:355-362. [DOI: 10.1021/acs.biomac.6b01262] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Teruhiko Matsubara
- Department of Biosciences
and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Ryohei Otani
- Department of Biosciences
and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Miki Yamashita
- Department of Biosciences
and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Haruka Maeno
- Department of Biosciences
and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Hanae Nodono
- Department of Biosciences
and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Toshinori Sato
- Department of Biosciences
and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
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10
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Fujiwara D, Kitada H, Oguri M, Nishihara T, Michigami M, Shiraishi K, Yuba E, Nakase I, Im H, Cho S, Joung JY, Kodama S, Kono K, Ham S, Fujii I. A Cyclized Helix-Loop-Helix Peptide as a Molecular Scaffold for the Design of Inhibitors of Intracellular Protein-Protein Interactions by Epitope and Arginine Grafting. Angew Chem Int Ed Engl 2016; 55:10612-5. [DOI: 10.1002/anie.201603230] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 06/07/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Daisuke Fujiwara
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Hidekazu Kitada
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Masahiro Oguri
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Toshio Nishihara
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Masataka Michigami
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Kazunori Shiraishi
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Eiji Yuba
- Department of Applied Chemistry; Graduate School of Engineering; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Ikuhiko Nakase
- N2RC; Osaka Prefecture University; 1-2, Gakuen-cho, Naka-ku Osaka 599-8570 Japan
| | - Haeri Im
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Sunhee Cho
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Jong Young Joung
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Seiji Kodama
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Kenji Kono
- Department of Applied Chemistry; Graduate School of Engineering; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Sihyun Ham
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Ikuo Fujii
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
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11
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Fujiwara D, Kitada H, Oguri M, Nishihara T, Michigami M, Shiraishi K, Yuba E, Nakase I, Im H, Cho S, Joung JY, Kodama S, Kono K, Ham S, Fujii I. A Cyclized Helix-Loop-Helix Peptide as a Molecular Scaffold for the Design of Inhibitors of Intracellular Protein-Protein Interactions by Epitope and Arginine Grafting. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Daisuke Fujiwara
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Hidekazu Kitada
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Masahiro Oguri
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Toshio Nishihara
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Masataka Michigami
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Kazunori Shiraishi
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Eiji Yuba
- Department of Applied Chemistry; Graduate School of Engineering; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Ikuhiko Nakase
- N2RC; Osaka Prefecture University; 1-2, Gakuen-cho, Naka-ku Osaka 599-8570 Japan
| | - Haeri Im
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Sunhee Cho
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Jong Young Joung
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Seiji Kodama
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Kenji Kono
- Department of Applied Chemistry; Graduate School of Engineering; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Sihyun Ham
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Ikuo Fujii
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
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12
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Kirkeby S. Binding of fluorescently labeled cholera toxin subunit B to glycolipids in the human submandibular gland and inhibition of binding by periodate oxidation and by galactose. Biotech Histochem 2015; 91:1-8. [DOI: 10.3109/10520295.2015.1065000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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13
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Deciphering the glycolipid code of Alzheimer's and Parkinson's amyloid proteins allowed the creation of a universal ganglioside-binding peptide. PLoS One 2014; 9:e104751. [PMID: 25140899 PMCID: PMC4139322 DOI: 10.1371/journal.pone.0104751] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
A broad range of microbial and amyloid proteins interact with cell surface glycolipids which behave as infectivity and/or toxicity cofactors in human pathologies. Here we have deciphered the biochemical code that determines the glycolipid-binding specificity of two major amyloid proteins, Alzheimer's β-amyloid peptide (Aβ) and Parkinson's disease associated protein α-synuclein. We showed that both proteins interact with selected glycolipids through a common loop-shaped motif exhibiting little sequence homology. This 12-residue domain corresponded to fragments 34-45 of α-synuclein and 5-16 of Aβ. By modulating the amino acid sequence of α-synuclein at only two positions in which we introduced a pair of histidine residues found in Aβ, we created a chimeric α-synuclein/Aβ peptide with extended ganglioside-binding properties. This chimeric peptide retained the property of α-synuclein to recognize GM3, and acquired the capacity to recognize GM1 (an Aβ-inherited characteristic). Free histidine (but not tryptophan or asparagine) and Zn2+ (but not Na+) prevented this interaction, confirming the key role of His-13 and His-14 in ganglioside binding. Molecular dynamics studies suggested that the chimeric peptide recognized cholesterol-constrained conformers of GM1, including typical chalice-shaped dimers, that are representative of the condensed cholesterol-ganglioside complexes found in lipid raft domains of the plasma membrane of neural cells. Correspondingly, the peptide had a particular affinity for raft-like membranes containing both GM1 and cholesterol. The chimeric peptide also interacted with several other gangliosides, including major brain gangliosides (GM4, GD1a, GD1b, and GT1b) but not with neutral glycolipids such as GlcCer, LacCer or asialo-GM1. It could inhibit the binding of Aβ1-42 onto neural SH-SY5Y cells and did not induce toxicity in these cells. In conclusion, deciphering the glycolipid code of amyloid proteins allowed us to create a universal ganglioside-binding peptide of only 12-residues with potential therapeutic applications in infectious and neurodegenerative diseases that involve cell surface gangliosides as receptors.
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14
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Affiliation(s)
- Daisuke Fujiwara
- Department of Biological Science, Graduate School of ScienceOsaka Prefecture University Osaka Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of ScienceOsaka Prefecture University Osaka Japan
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15
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Kuzmanov U, Kosanam H, Diamandis EP. The sweet and sour of serological glycoprotein tumor biomarker quantification. BMC Med 2013; 11:31. [PMID: 23390961 PMCID: PMC3751898 DOI: 10.1186/1741-7015-11-31] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 02/07/2013] [Indexed: 12/25/2022] Open
Abstract
Aberrant and dysregulated protein glycosylation is a well-established event in the process of oncogenesis and cancer progression. Years of study on the glycobiology of cancer have been focused on the development of clinically viable diagnostic applications of this knowledge. However, for a number of reasons, there has been only sparse and varied success. The causes of this range from technical to biological issues that arise when studying protein glycosylation and attempting to apply it to practical applications. This review focuses on the pitfalls, advances, and future directions to be taken in the development of clinically applicable quantitative assays using glycan moieties from serum-based proteins as analytes. Topics covered include the development and progress of applications of lectins, mass spectrometry, and other technologies towards this purpose. Slowly but surely, novel applications of established and development of new technologies will eventually provide us with the tools to reach the ultimate goal of quantification of the full scope of heterogeneity associated with the glycosylation of biomarker candidate glycoproteins in a clinically applicable fashion.
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Affiliation(s)
- Uros Kuzmanov
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, 6th floor, 60 Murray Street, Box 32, Toronto, ON M5T 3L9, Canada
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16
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Arnaud J, Audfray A, Imberty A. Binding sugars: from natural lectins to synthetic receptors and engineered neolectins. Chem Soc Rev 2013; 42:4798-813. [PMID: 23353569 DOI: 10.1039/c2cs35435g] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The large diversity and complexity of glycan structures together with their crucial role in many biological or pathological processes require the development of new high-throughput techniques for analyses. Lectins are classically used for characterising, imaging or targeting glycoconjugates and, when printed on microarrays, they are very useful tools for profiling glycomes. Development of recombinant lectins gives access to reliable and reproducible material, while engineering of new binding sites on existing scaffolds allows tuning of specificity. From the accumulated knowledge on protein-carbohydrate interactions, it is now possible to use nucleotide and peptide (bio)synthesis for producing new carbohydrate-binding molecules. Such a biomimetic approach can also be addressed by boron chemistry and supra-molecular chemistry for the design of fully artificial glycosensors.
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Affiliation(s)
- Julie Arnaud
- Centre de Recherche sur les Macromolécules Végétales (CERMAV-CNRS), affiliated to Grenoble-Université and ICMG, Grenoble, France
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17
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Carbohydrate recognition by pentadecapeptide ligands for a series of sialylated oligosaccharides. Bioorg Med Chem 2012; 20:6452-8. [DOI: 10.1016/j.bmc.2012.08.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 08/18/2012] [Accepted: 08/21/2012] [Indexed: 11/18/2022]
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18
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Takayama K, Hirose H, Tanaka G, Pujals S, Katayama S, Nakase I, Futaki S. Effect of the Attachment of a Penetration Accelerating Sequence and the Influence of Hydrophobicity on Octaarginine-Mediated Intracellular Delivery. Mol Pharm 2012; 9:1222-30. [DOI: 10.1021/mp200518n] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Kentaro Takayama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hisaaki Hirose
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Gen Tanaka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Sílvia Pujals
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Sayaka Katayama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Ikuhiko Nakase
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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19
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Sawada T, Ishiguro K, Takahashi T, Mihara H. A novel β-loop scaffold of phage-displayed peptides for highly specific affinities. MOLECULAR BIOSYSTEMS 2011; 7:2558-62. [PMID: 21655618 DOI: 10.1039/c1mb05085k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Loop peptides stabilized by two β-strands were used as a scaffold for a phage displayed peptide library. Affinity-based screening for insulin provided peptides, which showed affinity constants of 10(5) M(-1) order for insulin over 100 times greater than their affinity for the structurally similar insulin-like growth factor 1. The results suggested that the scaffold offers a powerful tool for generating and screening peptides as ligands for drugs and biologics.
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Affiliation(s)
- Toshiki Sawada
- Department of Bioengineering, Tokyo Institute of Technology, 4259-B40 Nagatsuta-cho, Midori-ku, Yokohama, Japan
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20
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Cunningham S, Gerlach JQ, Kane M, Joshi L. Glyco-biosensors: recent advances and applications for the detection of free and bound carbohydrates. Analyst 2010; 135:2471-80. [PMID: 20714521 DOI: 10.1039/c0an00276c] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The field of biosensor development now encompasses several areas specifically geared toward the rapid and sensitive detection, identification, and quantification of target analytes. In contrast to the more mature research and development of nucleic acid and protein biosensors, the development of 'glyco-biosensors' for detecting carbohydrates and conjugates of carbohydrates (glycoconjugates) is at a relatively nascent stage. The application of glyco-biosensors aims to open novel analytical and diagnostic avenues, encompassing industrial bioprocesses, biomedical and clinical applications. This area of research has been greatly aided by advancement brought by interdisciplinary mergers of engineering, biology, chemistry and physical sciences and enabling the miniaturization of detection platforms. In this review, we briefly introduce the need for glyco-biosensors, discuss current analytical technologies, and examine advances in glyco-biosensor approaches aimed at the detection and/or quantification of glycoconjugates or carbohydrates derived from glycoconjugates since 2005.
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Affiliation(s)
- Stephen Cunningham
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland, Galway
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21
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Rich RL, Myszka DG. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J Mol Recognit 2010; 23:1-64. [PMID: 20017116 DOI: 10.1002/jmr.1004] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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22
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Fujiwara D, Ye Z, Gouda M, Yokota K, Tsumuraya T, Fujii I. Selection of inhibitory peptides for Aurora-A kinase from a phage-displayed library of helix–loop–helix peptides. Bioorg Med Chem Lett 2010; 20:1776-8. [DOI: 10.1016/j.bmcl.2010.01.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Revised: 12/29/2009] [Accepted: 01/05/2010] [Indexed: 11/16/2022]
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23
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Ueno K, Tamura Y, Chibana H. Target validation and ligand development for a pathogenic fungal profilin, using a knock-down strain of pathogenic yeast Candida glabrata and structure-based ligand design. Yeast 2010; 27:369-78. [DOI: 10.1002/yea.1759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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24
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van Ameijde J, Poot AJ, van Wandelen LTM, Wammes AEM, Ruijtenbeek R, Rijkers DTS, Liskamp RMJ. Preparation of novel alkylated arginine derivatives suitable for click-cycloaddition chemistry and their incorporation into pseudosubstrate- and bisubstrate-based kinase inhibitors. Org Biomol Chem 2010; 8:1629-39. [PMID: 20237675 DOI: 10.1039/b922928k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient strategies for the introduction of arginine residues featuring acetylene or azide moieties in their side chains are described. The substituents are introduced in a way that maintains the basicity of the guanidine moiety. The methodology can be used e.g. for non-invasive labeling of arginine-containing peptides. Its applicability is demonstrated by the introduction of 'click' handles into a Protein Kinase C (PKC) pseudosubstrate peptide, and the subsequent preparation and evaluation of a novel bisubstrate-based inhibitor based on such a peptide.
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Affiliation(s)
- Jeroen van Ameijde
- Medicinal Chemistry and Chemical Biology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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25
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Fantini J, Barrantes FJ. Sphingolipid/cholesterol regulation of neurotransmitter receptor conformation and function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2345-61. [PMID: 19733149 DOI: 10.1016/j.bbamem.2009.08.016] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Revised: 07/17/2009] [Accepted: 08/28/2009] [Indexed: 10/20/2022]
Abstract
Like all other monomeric or multimeric transmembrane proteins, receptors for neurotransmitters are surrounded by a shell of lipids which form an interfacial boundary between the protein and the bulk membrane. Among these lipids, cholesterol and sphingolipids have attracted much attention because of their well-known propensity to segregate into ordered platform domains commonly referred to as lipid rafts. In this review we present a critical analysis of the molecular mechanisms involved in the interaction of cholesterol/sphingolipids with neurotransmitter receptors, in particular acetylcholine and serotonin receptors, chosen as representative members of ligand-gated ion channels and G protein-coupled receptors. Cholesterol and sphingolipids interact with these receptors through typical binding sites located in both the transmembrane helices and the extracellular loops. By altering the conformation of the receptors ("chaperone-like" effect), these lipids can regulate neurotransmitter binding, signal transducing functions, and, in the case of multimeric receptors, subunit assembly and subsequent receptor trafficking to the cell surface. Several sphingolipids (especially gangliosides) also exhibit low/moderate affinity for neurotransmitters. We suggest that such lipids could facilitate (i) the attachment of neurotransmitters to the post-synaptic membrane and in some cases (ii) their subsequent delivery to specific protein receptors. Overall, various experimental approaches provide converging evidence that the biological functions of neurotransmitters and their receptors are highly dependent upon sphingolipids and cholesterol, which are active partners of synaptic transmission. Several decades of research have been necessary to untangle the skein of a complex network of molecular interactions between neurotransmitters, their receptors, cholesterol and sphingolipids. This sophisticated crosstalk between all four distinctive partners may allow a fine biochemical tuning of synaptic transmission.
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Affiliation(s)
- Jacques Fantini
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M), University of Aix-Marseille 2 and Aix-Marseille 3, CNRS UMR 6231, INRA USC 2027, Faculté des Sciences de St. Jérôme, Laboratoire des Interactions Moléculaires et Systèmes Membranaires, Marseille, France
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