1
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Kim NH, Shim G, Park GH, Yu YG. A nondestructive membrane engineering method using an amphiphilic polymer. Protein Sci 2024; 33:e5143. [PMID: 39150080 PMCID: PMC11328118 DOI: 10.1002/pro.5143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/09/2024] [Accepted: 07/28/2024] [Indexed: 08/17/2024]
Abstract
The cellular signaling process or ion transport is mediated by membrane proteins (MPs) located on the cell surface, and functional studies of MPs have mainly been conducted using cells endogenously or transiently expressing target proteins. Reconstitution of purified MPs in the surface of live cells would have advantages of short manipulation time and ability to target cells in which gene transfection is difficult. However, direct reconstitution of MPs in live cells has not been established. The traditional detergent-mediated reconstitution method of MPs into a lipid bilayer cannot be applied to live cells because this disrupts and reforms the lipid bilayer structure, which is detrimental to cell viability. In this study, we demonstrated that GPCRs (prostaglandin E2 receptor 4 [EP4] and glucagon-like peptide-1 receptor [GLP1R]) or serotonin receptor 3A (5HT3A), a ligand-gated ion channel, stabilized with amphiphilic poly-γ-glutamate (APG), can be reconstituted into mammalian cell plasma membranes without affecting cell viability. Furthermore, 5HT3A reconstituted in mammalian cells showed ligand-dependent Ca2+ ion transport activity. APG-mediated reconstitution of GPCR in synthetic liposomes showed that electrostatic interaction between APG and membrane surface charge contributed to the reconstitution process. This APG-mediated membrane engineering method could be applied to the functional modification of cell membranes with MPs in live cells.
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Affiliation(s)
- Nam Hyuk Kim
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
| | - Goeun Shim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ga Hyeon Park
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Yeon Gyu Yu
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
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2
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Tsumagari K, Isobe Y, Imami K, Arita M. Exploring protein lipidation by mass spectrometry-based proteomics. J Biochem 2024; 175:225-233. [PMID: 38102731 PMCID: PMC10908362 DOI: 10.1093/jb/mvad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Protein lipidation is a common co- or post-translational modification that plays a crucial role in regulating the localization, interaction and function of cellular proteins. Dysregulation of lipid modifications can lead to various diseases, including cancer, neurodegenerative diseases and infectious diseases. Therefore, the identification of proteins undergoing lipidation and their lipidation sites should provide insights into many aspects of lipid biology, as well as providing potential targets for therapeutic strategies. Bottom-up proteomics using liquid chromatography/tandem mass spectrometry is a powerful technique for the global analysis of protein lipidation. Here, we review proteomic methods for profiling protein lipidation, focusing on the two major approaches: the use of chemical probes, such as lipid alkyne probes, and the use of enrichment techniques for endogenous lipid-modified peptides. The challenges facing these methods and the prospects for developing them further to achieve a comprehensive analysis of lipid modifications are discussed.
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Affiliation(s)
- Kazuya Tsumagari
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yosuke Isobe
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Koshi Imami
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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3
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Wang Y, Zhang J, Li K, Xia S, Gou S. Multitargeting HDAC Inhibitors Containing a RAS/RAF Protein Interfering Unit. J Med Chem 2024; 67:2066-2082. [PMID: 38261411 DOI: 10.1021/acs.jmedchem.3c01941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
In this work, a series of multitargeting histone deacetylase (HDAC) inhibitors capable of regulating the signal transduction between RAS protein and downstream effectors were obtained by introducing a zinc-ion-binding group into the framework of rigosertib via different linkers. Among them, two representative compounds, XSJ-7 and XSJ-10, not only showed stronger antiproliferative activity against many types of cancer cells including solid tumor cells but also presented more potent inhibition on different subtypes of HDAC than suberoylanilide hydroxamic acid (SAHA). Significantly, XSJ-10 presented moderate pharmacokinetic behaviors and showed stronger antitumor activity than oxaliplatin, SAHA, and rigosertib in the HT-29 xenograft mouse models without significant systemic toxicity. Research on the anticancer mechanism of XSJ-10 revealed that it can effectively induce the apoptosis of cancer cells and suppress the tumor by strongly inhibiting the RAS-RAF-MEK-ERK signaling pathway and the acetylation level of HDAC3.
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Affiliation(s)
- Yuanjiang Wang
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, PR China
| | - Jianluo Zhang
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Kun Li
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Shengjin Xia
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Shaohua Gou
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, PR China
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4
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Stillger L, Viau L, Kamm L, Holtmann D, Müller D. Optimization of antimicrobial peptides for the application against biocorrosive bacteria. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12562-9. [PMID: 37154907 DOI: 10.1007/s00253-023-12562-9] [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: 01/12/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/10/2023]
Abstract
Microbiologically influenced corrosion is a common problem in the industrial field due to the deterioration of metals in the presence of various microorganisms, in particular sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB). A common method to reduce microbiologically influenced corrosion is the application of biocides. The limited number of suitable biocides and the resulting development of resistance, high dosage, and high application rate hinder an effective application. An environmentally friendly alternative could be the application of antimicrobial peptides (AMP), which have already been established in the field of medical devices for a while. Here, the successful treatment of different AMPs against 3 SRB and 1 SOB was demonstrated. The peptide L5K5W was favored due to its broad activity, high stability, and simple structure resulting in low synthesis costs. An alanine scan showed that substitution of leucine with tryptophan increased the activity of this peptide twofold compared to the original peptide against D. vulgaris, the main representative of SRB. Additional optimization of this modified peptide through changes in amino acid composition and lipidations significantly increased the effectiveness, finally resulting in a minimum inhibitory concentration (MIC) of 15.63 μg/mL against Desulfovibrio vulgaris. Even against the marine SRB Desulfovibrio indonesiensis with a required salt concentration of min. 2%, an activity of the peptides can be observed (MIC: 31.25 μg/mL). The peptides also remained stable and active for 7 days in the supernatant of the bacterial culture. KEY POINTS: • Antimicrobial peptides provide an alternative to combat biocorrosive bacteria. • Optimization of the peptide sequence leads to a significant increase in activity. • The investigated peptides exhibit high stability, both in the medium and in the bacterial supernatant.
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Affiliation(s)
- L Stillger
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany
| | - L Viau
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany
| | - L Kamm
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany
| | - D Holtmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany
| | - D Müller
- Institute of Pharmaceutical Technology and Biopharmacy, Philipps-University Marburg, Biegenstraße 10, 35307, Marburg, Germany.
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5
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Jamaluddin A, Chuang CL, Williams ET, Siow A, Yang SH, Harris PWR, Petersen JSSM, Bower RL, Chand S, Brimble MA, Walker CS, Hay DL, Loomes KM. Lipidated Calcitonin Gene-Related Peptide (CGRP) Peptide Antagonists Retain CGRP Receptor Activity and Attenuate CGRP Action In Vivo. Front Pharmacol 2022; 13:832589. [PMID: 35341216 PMCID: PMC8942775 DOI: 10.3389/fphar.2022.832589] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Signaling through calcitonin gene-related peptide (CGRP) receptors is associated with pain, migraine, and energy expenditure. Small molecule and monoclonal antibody CGRP receptor antagonists that block endogenous CGRP action are in clinical use as anti-migraine therapies. By comparison, the potential utility of peptide antagonists has received less attention due to suboptimal pharmacokinetic properties. Lipidation is an established strategy to increase peptide half-life in vivo. This study aimed to explore the feasibility of developing lipidated CGRP peptide antagonists that retain receptor antagonist activity in vitro and attenuate endogenous CGRP action in vivo. CGRP peptide analogues based on the archetypal CGRP receptor antagonist, CGRP8-37, were palmitoylated at the N-terminus, position 24, and near the C-terminus at position 35. The antagonist activities of the lipidated peptide analogues were tested in vitro using transfected Cos-7 cells expressing either the human or mouse CGRP receptor, amylin subtype 1 (AMY1) receptor, adrenomedullin (AM) receptors, or calcitonin receptor. Antagonist activities were also evaluated in SK-N-MC cells that endogenously express the human CGRP receptor. Lipidated peptides were then tested for their ability to antagonize endogenous CGRP action in vivo using a capsaicin-induced dermal vasodilation (CIDV) model in C57/BL6J mice. All lipidated peptides except for the C-terminally modified analogue retained potent antagonist activity compared to CGRP8-37 towards the CGRP receptor. The lipidated peptides also retained, and sometimes gained, antagonist activities at AMY1, AM1 and AM2 receptors. Several lipidated peptides produced robust inhibition of CIDV in mice. This study demonstrates that selected lipidated peptide antagonists based on αCGRP8-37 retain potent antagonist activity at the CGRP receptor and are capable of inhibition of endogenous CGRP action in vivo. These findings suggest that lipidation can be applied to peptide antagonists, such as αCGRP8-37 and are a potential strategy for antagonizing CGRP action.
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Affiliation(s)
- Aqfan Jamaluddin
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Chia-Lin Chuang
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Elyse T Williams
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Andrew Siow
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Sung Hyun Yang
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Paul W R Harris
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | - Rebekah L Bower
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Shanan Chand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | - Debbie L Hay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Pharmacology and Toxicology, University of Otago, Dunedin, New Zealand
| | - Kerry M Loomes
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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6
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Protein Lipidation Types: Current Strategies for Enrichment and Characterization. Int J Mol Sci 2022; 23:ijms23042365. [PMID: 35216483 PMCID: PMC8880637 DOI: 10.3390/ijms23042365] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
Post-translational modifications regulate diverse activities of a colossal number of proteins. For example, various types of lipids can be covalently linked to proteins enzymatically or non-enzymatically. Protein lipidation is perhaps not as extensively studied as protein phosphorylation, ubiquitination, or glycosylation although it is no less significant than these modifications. Evidence suggests that proteins can be attached by at least seven types of lipids, including fatty acids, lipoic acids, isoprenoids, sterols, phospholipids, glycosylphosphatidylinositol anchors, and lipid-derived electrophiles. In this review, we summarize types of protein lipidation and methods used for their detection, with an emphasis on the conjugation of proteins with polyunsaturated fatty acids (PUFAs). We discuss possible reasons for the scarcity of reports on PUFA-modified proteins, limitations in current methodology, and potential approaches in detecting PUFA modifications.
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7
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Smith BJ, Carregari VC. Post-Translational Modifications During Brain Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:29-38. [DOI: 10.1007/978-3-031-05460-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Barz S, Kriegenburg F, Sánchez-Martín P, Kraft C. Small but mighty: Atg8s and Rabs in membrane dynamics during autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119064. [PMID: 34048862 PMCID: PMC8261831 DOI: 10.1016/j.bbamcr.2021.119064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/04/2021] [Accepted: 05/21/2021] [Indexed: 11/17/2022]
Abstract
Autophagy is a degradative pathway during which autophagosomes are formed that enwrap cytosolic material destined for turnover within the lytic compartment. Autophagosome biogenesis requires controlled lipid and membrane rearrangements to allow the formation of an autophagosomal seed and its subsequent elongation into a fully closed and fusion-competent double membrane vesicle. Different membrane remodeling events are required, which are orchestrated by the distinct autophagy machinery. An important player among these autophagy proteins is the small lipid-modifier Atg8. Atg8 proteins facilitate various aspects of autophagosome formation and serve as a binding platform for autophagy factors. Also Rab GTPases have been implicated in autophagosome biogenesis. As Atg8 proteins interact with several Rab GTPase regulators, they provide a possible link between autophagy progression and Rab GTPase activity. Here, we review central aspects in membrane dynamics during autophagosome biogenesis with a focus on Atg8 proteins and selected Rab GTPases.
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Affiliation(s)
- Saskia Barz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Franziska Kriegenburg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Pablo Sánchez-Martín
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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9
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Yang J, Hirata T, Liu YS, Guo XY, Gao XD, Kinoshita T, Fujita M. Human SND2 mediates ER targeting of GPI-anchored proteins with low hydrophobic GPI attachment signals. FEBS Lett 2021; 595:1542-1558. [PMID: 33838053 DOI: 10.1002/1873-3468.14083] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 11/08/2022]
Abstract
Over 100 glycosylphosphatidylinositol-anchored proteins (GPI-APs) are encoded in the mammalian genome. It is not well understood how these proteins are targeted and translocated to the endoplasmic reticulum (ER). Here, we reveal that many GPI-APs, such as CD59, CD55, and CD109, utilize human SND2 (hSND2)-dependent ER targeting machinery. We also found that signal recognition particle receptors seem to cooperate with hSND2 to target GPI-APs to the ER. Both the N-terminal signal sequence and C-terminal GPI attachment signal of GPI-APs contribute to ER targeting via the hSND2-dependent pathway. Particularly, the hydrophobicity of the C-terminal GPI attachment signal acts as the determinant of hSND2 dependency. Our results explain the route and mechanism of the ER targeting of GPI-APs in mammalian cells.
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Affiliation(s)
- Jing Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Tetsuya Hirata
- Institute for Glyco-core Research (iGCORE), Gifu University, Japan.,Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Japan
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xin-Yu Guo
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan.,WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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10
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de Jong F, Munnik T. Attracted to membranes: lipid-binding domains in plants. PLANT PHYSIOLOGY 2021; 185:707-723. [PMID: 33793907 PMCID: PMC8133573 DOI: 10.1093/plphys/kiaa100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/11/2020] [Indexed: 05/18/2023]
Abstract
Membranes are essential for cells and organelles to function. As membranes are impermeable to most polar and charged molecules, they provide electrochemical energy to transport molecules across and create compartmentalized microenvironments for specific enzymatic and cellular processes. Membranes are also responsible for guided transport of cargoes between organelles and during endo- and exocytosis. In addition, membranes play key roles in cell signaling by hosting receptors and signal transducers and as substrates and products of lipid second messengers. Anionic lipids and their specific interaction with target proteins play an essential role in these processes, which are facilitated by specific lipid-binding domains. Protein crystallography, lipid-binding studies, subcellular localization analyses, and computer modeling have greatly advanced our knowledge over the years of how these domains achieve precision binding and what their function is in signaling and membrane trafficking, as well as in plant development and stress acclimation.
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Affiliation(s)
- Femke de Jong
- Cluster Green Life Sciences, Section Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Teun Munnik
- Cluster Green Life Sciences, Section Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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11
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Gouguet P, Gronnier J, Legrand A, Perraki A, Jolivet MD, Deroubaix AF, German-Retana S, Boudsocq M, Habenstein B, Mongrand S, Germain V. Connecting the dots: from nanodomains to physiological functions of REMORINs. PLANT PHYSIOLOGY 2021; 185:632-649. [PMID: 33793872 PMCID: PMC8133660 DOI: 10.1093/plphys/kiaa063] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/31/2020] [Indexed: 05/11/2023]
Abstract
REMORINs (REMs) are a plant-specific protein family, proposed regulators of membrane-associated molecular assemblies and well-established markers of plasma membrane nanodomains. REMs play a diverse set of functions in plant interactions with pathogens and symbionts, responses to abiotic stresses, hormone signaling and cell-to-cell communication. In this review, we highlight the established and more putative roles of REMs throughout the literature. We discuss the physiological functions of REMs, the mechanisms underlying their nanodomain-organization and their putative role as regulators of nanodomain-associated molecular assemblies. Furthermore, we discuss how REM phosphorylation may regulate their functional versatility. Overall, through data-mining and comparative analysis of the literature, we suggest how to further study the molecular mechanisms underpinning the functions of REMs.
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Affiliation(s)
- Paul Gouguet
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
- ZMBP, Universität Tübingen, Auf der Morgenstelle 32 72076 Tübingen, Germany
| | - Julien Gronnier
- Department of Plant and Microbial Biology University of Zürich, Zollikerstrasse, Zürich, Switzerland
| | - Anthony Legrand
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université de Bordeaux, Institut Polytechnique de Bordeaux, A11, Geoffroy Saint-Hilaire, Pessac, France
| | - Artemis Perraki
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, UK
- Present address: Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas, Heraklion, Crete, Greece
| | - Marie-Dominique Jolivet
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
| | - Anne-Flore Deroubaix
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
| | - Sylvie German-Retana
- Equipe de Virologie, Institut Scientifique de Recherche Agronomique and Université de Bordeaux, BP81, 33883 Villenave d’Ornon, France
| | - Marie Boudsocq
- Université Paris-Saclay, CNRS, INRAE, Université d’Evry, Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, Orsay, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université de Bordeaux, Institut Polytechnique de Bordeaux, A11, Geoffroy Saint-Hilaire, Pessac, France
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
- Author for communication: (S.M.)
| | - Véronique Germain
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
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12
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Monje-Galvan V, Voth GA. Binding mechanism of the matrix domain of HIV-1 gag on lipid membranes. eLife 2020; 9:58621. [PMID: 32808928 PMCID: PMC7476761 DOI: 10.7554/elife.58621] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/14/2020] [Indexed: 01/10/2023] Open
Abstract
Specific protein-lipid interactions are critical for viral assembly. We present a molecular dynamics simulation study on the binding mechanism of the membrane targeting domain of HIV-1 Gag protein. The matrix (MA) domain drives Gag onto the plasma membrane through electrostatic interactions at its highly-basic-region (HBR), located near the myristoylated (Myr) N-terminus of the protein. Our study suggests Myr insertion is involved in the sorting of membrane lipids around the protein-binding site to prepare it for viral assembly. Our realistic membrane models confirm interactions with PIP2 and PS lipids are highly favored around the HBR and are strong enough to keep the protein bound even without Myr insertion. We characterized Myr insertion events from microsecond trajectories and examined the membrane response upon initial membrane targeting by MA. Insertion events only occur with one of the membrane models, showing a combination of surface charge and internal membrane structure modulate this process.
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Affiliation(s)
- Viviana Monje-Galvan
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, United States
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13
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Bitencourt-Ferreira G, de Azevedo WF. Molecular Dynamics Simulations with NAMD2. Methods Mol Biol 2020; 2053:109-124. [PMID: 31452102 DOI: 10.1007/978-1-4939-9752-7_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
X-ray diffraction crystallography is the primary technique to determine the three-dimensional structures of biomolecules. Although a robust method, X-ray crystallography is not able to access the dynamical behavior of macromolecules. To do so, we have to carry out molecular dynamics simulations taking as an initial system the three-dimensional structure obtained from experimental techniques or generated using homology modeling. In this chapter, we describe in detail a tutorial to carry out molecular dynamics simulations using the program NAMD2. We chose as a molecular system to simulate the structure of human cyclin-dependent kinase 2.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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14
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Ning W, Jiang P, Guo Y, Wang C, Tan X, Zhang W, Peng D, Xue Y. GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins. Brief Bioinform 2020; 22:1836-1847. [PMID: 32248222 DOI: 10.1093/bib/bbaa038] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
As an important reversible lipid modification, S-palmitoylation mainly occurs at specific cysteine residues in proteins, participates in regulating various biological processes and is associated with human diseases. Besides experimental assays, computational prediction of S-palmitoylation sites can efficiently generate helpful candidates for further experimental consideration. Here, we reviewed the current progress in the development of S-palmitoylation site predictors, as well as training data sets, informative features and algorithms used in these tools. Then, we compiled a benchmark data set containing 3098 known S-palmitoylation sites identified from small- or large-scale experiments, and developed a new method named data quality discrimination (DQD) to distinguish data quality weights (DQWs) between the two types of the sites. Besides DQD and our previous methods, we encoded sequence similarity values into images, constructed a deep learning framework of convolutional neural networks (CNNs) and developed a novel algorithm of graphic presentation system (GPS) 6.0. We further integrated nine additional types of sequence-based and structural features, implemented parallel CNNs (pCNNs) and designed a new predictor called GPS-Palm. Compared with other existing tools, GPS-Palm showed a >31.3% improvement of the area under the curve (AUC) value (0.855 versus 0.651) for general prediction of S-palmitoylation sites. We also produced two species-specific predictors, with corresponding AUC values of 0.900 and 0.897 for predicting human- and mouse-specific sites, respectively. GPS-Palm is free for academic research at http://gpspalm.biocuckoo.cn/.
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Affiliation(s)
- Wanshan Ning
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Peiran Jiang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Yaping Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Xiaodan Tan
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Weizhi Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Di Peng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
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15
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Giannini E, González LJ, Vila AJ. A simple protocol to characterize bacterial cell-envelope lipoproteins in a native-like environment. Protein Sci 2019; 28:2004-2010. [PMID: 31518027 DOI: 10.1002/pro.3728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 01/04/2023]
Abstract
Physiological conditions in living cells are strictly regulated to allow, optimize, and coordinate biological processes. The bacterial cell envelope is the compartment where the communication with the external environment takes place. This involves membrane proteins, key players in many biological processes that ensure bacterial survival. The biochemical characterization of membrane proteins, either integral, lipidated or peripheral is challenging due to their mixed protein-lipid nature, making it difficult to purify and obtain considerable amounts of samples. In contrast to integral membrane proteins, lipidated proteins are usually purified as truncated soluble versions, neglecting the impact of the membrane environment. Here we report a simple and robust protocol to characterize bacterial lipidated proteins in spheroplasts from Escherichia coli using a β-lactamase as a model. The Metallo-β-lactamase NDM-1 is an enzyme anchored to the inner leaflet of the outer membrane of Gram-negative bacteria. Kinetic parameters and stability of the lipidated NDM-1 and the soluble unbound version (NDM-1 C26A) were measured in spheroplasts and periplasm, respectively. These studies revealed that membrane anchoring increases the KM of the enzyme, consequently decreasing the catalytic efficiency, while not affecting its kinetic stability. This approach can be used to characterize lipidated proteins avoiding the purification step while mimicking its native environment. This approach also helps in filling the gap between in vitro and in vivo studies.
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Affiliation(s)
- Estefanía Giannini
- Laboratorio de Metaloproteínas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
| | - Lisandro J González
- Laboratorio de Metaloproteínas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Alejandro J Vila
- Laboratorio de Metaloproteínas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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16
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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17
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Domains of the TF protein important in regulating its own palmitoylation. Virology 2019; 531:31-39. [PMID: 30852269 DOI: 10.1016/j.virol.2019.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 11/23/2022]
Abstract
Sindbis virus particles contain the viral proteins capsid, E1 and E2, and low levels of a small membrane protein called TF. TF is produced during a (-1) programmed ribosomal frameshifting event during the translation of the structural polyprotein. TF from Sindbis virus-infected cells is present in two palmitoylated states, basal and maximal; unpalmitoylated TF is not detectable. Mutagenesis studies demonstrated that without palmitoylation, TF is not incorporated into released virions, suggesting palmitoylation of TF is a regulated step in virus assembly. In this work, we identified Domains within the TF protein that regulate its palmitoylation state. Mutations and insertions in Domain III, a region proposed to be in the cytoplasmic loop of TF, increase levels of unpalmitoylated TF found during an infection but still unpalmitoylated TF was not incorporated into virions. Mutations in Domain IV, the TF unique region, are likely to impact the balance between basal and maximal palmitoylation.
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18
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Mamode Cassim A, Gouguet P, Gronnier J, Laurent N, Germain V, Grison M, Boutté Y, Gerbeau-Pissot P, Simon-Plas F, Mongrand S. Plant lipids: Key players of plasma membrane organization and function. Prog Lipid Res 2018; 73:1-27. [PMID: 30465788 DOI: 10.1016/j.plipres.2018.11.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 12/29/2022]
Abstract
The plasma membrane (PM) is the biological membrane that separates the interior of all cells from the outside. The PM is constituted of a huge diversity of proteins and lipids. In this review, we will update the diversity of molecular species of lipids found in plant PM. We will further discuss how lipids govern global properties of the plant PM, explaining that plant lipids are unevenly distributed and are able to organize PM in domains. From that observation, it emerges a complex picture showing a spatial and multiscale segregation of PM components. Finally, we will discuss how lipids are key players in the function of PM in plants, with a particular focus on plant-microbe interaction, transport and hormone signaling, abiotic stress responses, plasmodesmata function. The last chapter is dedicated to the methods that the plant membrane biology community needs to develop to get a comprehensive understanding of membrane organization in plants.
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Affiliation(s)
- Adiilah Mamode Cassim
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Paul Gouguet
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Julien Gronnier
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Nelson Laurent
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRS, Dijon, France
| | - Véronique Germain
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Magali Grison
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Yohann Boutté
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Patricia Gerbeau-Pissot
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRS, Dijon, France
| | - Françoise Simon-Plas
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRS, Dijon, France.
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France.
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19
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Gronnier J, Gerbeau-Pissot P, Germain V, Mongrand S, Simon-Plas F. Divide and Rule: Plant Plasma Membrane Organization. TRENDS IN PLANT SCIENCE 2018; 23:899-917. [PMID: 30174194 DOI: 10.1016/j.tplants.2018.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 05/24/2023]
Abstract
Since the publication of the fluid mosaic as a relevant model for biological membranes, accumulating evidence has revealed the outstanding complexity of the composition and organization of the plant plasma membrane (PM). Powerful new methodologies have uncovered the remarkable multiscale and multicomponent heterogeneity of PM subcompartmentalization, and this is emerging as a general trait with different features and properties. It is now evident that the dynamics of such a complex organization are intrinsically related to signaling pathways that regulate key physiological processes. Listing and linking recent progress in precisely qualifying these heterogeneities will help to draw an integrated picture of the plant PM. Understanding the key principles governing such a complex dynamic organization will contribute to deciphering the crucial role of the PM in cell physiology.
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Affiliation(s)
- Julien Gronnier
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche (UMR) 5200, Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux, Bordeaux, France; Present address: Laboratory of Cyril Zipfel, Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Patricia Gerbeau-Pissot
- Agroécologie, Institut National Supérieur des Sciences Agronomiques, de l'Alimentation, et de l'Environnement (AgroSup) Dijon, CNRS, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, Dijon, France
| | - Véronique Germain
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche (UMR) 5200, Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux, Bordeaux, France
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche (UMR) 5200, Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux, Bordeaux, France; These authors contributed equally to this work
| | - Françoise Simon-Plas
- Agroécologie, Institut National Supérieur des Sciences Agronomiques, de l'Alimentation, et de l'Environnement (AgroSup) Dijon, CNRS, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, Dijon, France; These authors contributed equally to this work.
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20
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Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors. Proc Natl Acad Sci U S A 2018; 115:E8172-E8180. [PMID: 30104359 DOI: 10.1073/pnas.1807981115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite not spanning phospholipid bilayers, monotopic integral proteins (MIPs) play critical roles in organizing biochemical reactions on membrane surfaces. Defining the structural basis by which these proteins are anchored to membranes has been hampered by the paucity of unambiguously identified MIPs and a lack of computational tools that accurately distinguish monolayer-integrating motifs from bilayer-spanning transmembrane domains (TMDs). We used quantitative proteomics and statistical modeling to identify 87 high-confidence candidate MIPs in lipid droplets, including 21 proteins with predicted TMDs that cannot be accommodated in these monolayer-enveloped organelles. Systematic cysteine-scanning mutagenesis showed the predicted TMD of one candidate MIP, DHRS3, to be a partially buried amphipathic α-helix in both lipid droplet monolayers and the cytoplasmic leaflet of endoplasmic reticulum membrane bilayers. Coarse-grained molecular dynamics simulations support these observations, suggesting that this helix is most stable at the solvent-membrane interface. The simulations also predicted similar interfacial amphipathic helices when applied to seven additional MIPs from our dataset. Our findings suggest that interfacial helices may be a common motif by which MIPs are integrated into membranes, and provide high-throughput methods to identify and study MIPs.
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21
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Ozdemir ES, Jang H, Gursoy A, Keskin O, Nussinov R. Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ. J Phys Chem B 2018; 122:7503-7513. [PMID: 29961325 PMCID: PMC8087113 DOI: 10.1021/acs.jpcb.8b04347] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Proper localization of Ras proteins at the plasma membrane (PM) is crucial for their functions. To get to the PM, KRas4B and some other Ras family proteins bind to the PDEδ shuttling protein through their farnesylated hypervariable regions (HVRs). The docking of their farnesyl (and to a lesser extent geranylgeranyl) in the hydrophobic pocket of PDEδ's stabilizes the interaction. At the PM, guanosine 5'-triphosphate (GTP)-bound Arf-like protein 2 (Arl2) assists in the release of Ras from the PDEδ. However, exactly how is still unclear. Using all-atom molecular dynamics simulations, we unraveled the detailed mechanism of Arl2-mediated release of KRas4B, the most abundant oncogenic Ras isoform, from PDEδ. We simulated ternary Arl2-PDEδ-KRas4B HVR complexes and observed that Arl2 binding weakens the PDEδ-farnesylated HVR interaction. Our detailed analysis showed that allosteric changes (involving β6 of PDEδ and additional PDEδ residues) compress the hydrophobic PDEδ pocket and push the HVR out. Mutating PDEδ residues that mediate allosteric changes in PDEδ terminates the release process. Mutant Ras proteins are enriched in human cancers, with currently no drugs in the clinics. This mechanistic account may inspire efforts to develop drugs suppressing oncogenic KRas4B release.
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Affiliation(s)
- E. Sila Ozdemir
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
- Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
- Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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22
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Socas LBP, Ambroggio EE. Myristoylation and Oligonucleotide Interaction Modulate Peptide and Protein Surface Properties: The Case of the HIV-1 Matrix Domain. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6051-6062. [PMID: 29727193 DOI: 10.1021/acs.langmuir.8b01005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Myristoylated proteins typically develop a tight association with membranes. One example is the matrix domain (MA) of the HIV-1 Gag protein. In addition, MA is able to bind the Sel25 RNA sequence, a ligand that can act as a competitor for the interaction with the membrane. These properties make HIV-1 MA an attractive molecule to understand how protein and peptide surface properties can be controlled by myristoylation and oligonucleotide interaction. In this line, we analyzed the stability, thermodynamics, and the topography of Langmuir monolayers composed of the myristoylated or unmyristoylated versions of MA in the presence or the absence of a single-strand DNA (ssDNASel25) analogue of the Sel25 RNA sequence. With a similar approach, we compared the MA surface properties with those obtained from monolayers of myristoylated and unmyristoylated MA-derived peptides (first 21 residues of the MA sequence). Our results show that the protein or peptide films are destabilized by the presence of ssDNASel25, inducing solubilization of the monolayer components into the bulk phase. In addition, the oligonucleotide affects the protein-protein or peptide-peptide lateral interactions, provoking interfacial topography changes of the monolayers, visualized by Brewster angle microscopy. Furthermore, we also show how the myristoyl group has major effects on the lateral stability and the elasticity of the monolayers. Altogether, here we propose a general model considering the effect of myristoylation and the interaction with oligonucleotides on the interfacial properties of MA and derived peptides. In this model, we introduce a new role of the core region of MA (sequence of MA after the 21st residue) that confers higher lateral interfacial stability to the protein.
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Affiliation(s)
- Luis B P Socas
- Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas , Universidad Nacional de Córdoba , Haya de la Torre y Medina Allende s/n , Córdoba X5000HUA , Argentina
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC) , Haya de la Torre y Medina Allende s/n , Córdoba X5000HUA , Argentina
| | - Ernesto E Ambroggio
- Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas , Universidad Nacional de Córdoba , Haya de la Torre y Medina Allende s/n , Córdoba X5000HUA , Argentina
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC) , Haya de la Torre y Medina Allende s/n , Córdoba X5000HUA , Argentina
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23
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Zou Y, Pan R, Ruan Q, Wan Z, Guo J, Yang X. Interaction of Soybean 7S Globulin Peptide with Cell Membrane Model via Isothermal Titration Calorimetry, Quartz Crystal Microbalance with Dissipation, and Langmuir Monolayer Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:4913-4922. [PMID: 29634259 DOI: 10.1021/acs.jafc.8b00414] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To understand the underlying molecular mechanism of the cholesterol-lowering effect of soybean 7S globulins, the interactions of their pepsin-released peptides (7S-peptides) with cell membrane models consisting of dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and cholesterol (CHOL) were systematically studied. The results showed that 7S-peptides were bound to DPPC/DOPC/CHOL liposomes mainly through van der Waals forces and hydrogen bonds, and the presence of higher CHOL concentrations enhanced the binding affinity (e.g., DPPC/DOPC/CHOL = 1:1:0, binding ratio = 0.114; DPPC/DOPC/CHOL = 1:1:1, binding ratio = 2.02). Compression isotherms indicated that the incorporation of 7S-peptides increased the DPPC/DOPC/CHOL monolayer fluidity and the lipid raft size. The presence of CHOL accelerated the 7S-peptide accumulation on lipid rafts, which could serve as platforms for peptides to develop into β-sheet rich structures. These results allow us to hypothesize that 7S-peptides may indirectly influence membrane protein functions via altering the membrane organization in the enterocytes.
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Affiliation(s)
- Yuan Zou
- Food Protein Research and Development Center, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , P. R China
| | - Runting Pan
- Food Protein Research and Development Center, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , P. R China
| | - Qijun Ruan
- Food Protein Research and Development Center, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , P. R China
| | - Zhili Wan
- Food Protein Research and Development Center, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , P. R China
| | - Jian Guo
- Food Protein Research and Development Center, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , P. R China
| | - Xiaoquan Yang
- Food Protein Research and Development Center, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , P. R China
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Hadpech S, Jinathep W, Saoin S, Thongkum W, Chupradit K, Yasamut U, Moonmuang S, Tayapiwatana C. Impairment of a membrane-targeting protein translated from a downstream gene of a "self-cleaving" T2A peptide conjunction. Protein Expr Purif 2018; 150:17-25. [PMID: 29733907 DOI: 10.1016/j.pep.2018.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 04/26/2018] [Accepted: 05/03/2018] [Indexed: 12/20/2022]
Abstract
The requirement for reliable bicistronic or multicistronic vectors in gene delivery systems is at the forefront of bio/biomedical technology. A method that provides an efficient co-expression of multiple heterologous proteins would be valuable for many applications, especially in medical science for treating various types of disease. In this study, we designed and constructed a bicistronic expression vector using a self-cleaving 2A peptide derived from a virus of the insect Thosea asigna (T2A). This exhibited the most efficient cleavage of the 2A sequence. Two versions of the T2A-based vector were constructed by switching the DNA sequences encoding the proteins of interest, the N-myristoylated protein and the nuclear-homing protein, upstream and downstream of the 2A linker, respectively. Our results showed that similar levels of mRNA expression were found and 100% of cleavage efficiency of T2A was observed. Nevertheless, we also reported the cleared evidence that the N-myristoylated protein cannot be placed downstream of the 2A sequence. Since the protein product fails to translocate to the plasma membrane due to altered myristoylation process, the gene position of the T2A-based vector is meaningful for the subcellular localization of the N-myristoylated protein. Therefore, the observation was marked as a precaution for using the 2A peptide. To adopt the 2A peptide technology for generating the bicistronic or multicistronic expression, the vector design should be carefully considered for the transgene position, signal sequences, and post-translational modifications of each individual protein.
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Affiliation(s)
- Sudarat Hadpech
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wannarat Jinathep
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Somphot Saoin
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Weeraya Thongkum
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Koollawat Chupradit
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Umpa Yasamut
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sutpirat Moonmuang
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand.
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25
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Yakubu RR, Weiss LM, Silmon de Monerri NC. Post-translational modifications as key regulators of apicomplexan biology: insights from proteome-wide studies. Mol Microbiol 2017; 107:1-23. [PMID: 29052917 DOI: 10.1111/mmi.13867] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 12/12/2022]
Abstract
Parasites of the Apicomplexa phylum, such as Plasmodium spp. and Toxoplasma gondii, undergo complex life cycles involving multiple stages with distinct biology and morphologies. Post-translational modifications (PTMs), such as phosphorylation, acetylation and glycosylation, regulate numerous cellular processes, playing a role in every aspect of cell biology. PTMs can occur on proteins at any time in their lifespan and through alterations of target protein activity, localization, protein-protein interactions, among other functions, dramatically increase proteome diversity and complexity. In addition, PTMs can be induced or removed on changes in cellular environment and state. Thus, PTMs are likely to be key regulators of developmental transitions, biology and pathogenesis of apicomplexan parasites. In this review we examine the roles of PTMs in both parasite-specific and conserved eukaryotic processes, and the potential crosstalk between PTMs, that together regulate the intricate lives of these protozoa.
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Affiliation(s)
- Rama R Yakubu
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10128, USA.,Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10128, USA
| | - Louis M Weiss
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10128, USA.,Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10128, USA
| | - Natalie C Silmon de Monerri
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10128, USA.,Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10128, USA
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26
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N-terminal S-acylation facilitates tonoplast targeting of the calcium sensor CBL6. FEBS Lett 2017; 591:3745-3756. [DOI: 10.1002/1873-3468.12880] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 09/22/2017] [Accepted: 09/22/2017] [Indexed: 12/21/2022]
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27
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Muallem S, Chung WY, Jha A, Ahuja M. Lipids at membrane contact sites: cell signaling and ion transport. EMBO Rep 2017; 18:1893-1904. [PMID: 29030479 DOI: 10.15252/embr.201744331] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/10/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022] Open
Abstract
Communication between organelles is essential to coordinate cellular functions and the cell's response to physiological and pathological stimuli. Organellar communication occurs at membrane contact sites (MCSs), where the endoplasmic reticulum (ER) membrane is tethered to cellular organelle membranes by specific tether proteins and where lipid transfer proteins and cell signaling proteins are located. MCSs have many cellular functions and are the sites of lipid and ion transfer between organelles and generation of second messengers. This review discusses several aspects of MCSs in the context of lipid transfer, formation of lipid domains, generation of Ca2+ and cAMP second messengers, and regulation of ion transporters by lipids.
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Affiliation(s)
- Shmuel Muallem
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Woo Young Chung
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Archana Jha
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Malini Ahuja
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
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28
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Muratcioglu S, Jang H, Gursoy A, Keskin O, Nussinov R. PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization. J Phys Chem B 2017; 121:5917-5927. [PMID: 28540724 PMCID: PMC7891760 DOI: 10.1021/acs.jpcb.7b03035] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
To signal, Ras isoforms must be enriched at the plasma membrane (PM). It was suggested that phosphodiesterase-δ (PDEδ) can bind and shuttle some farnesylated Ras isoforms to the PM, but not all. Among these, interest focused on K-Ras4B, the most abundant oncogenic Ras isoform. To study PDEδ/Ras interactions, we modeled and simulated the PDEδ/K-Ras4B complex. We obtained structures, which were similar to two subsequently determined crystal structures. We next modeled and simulated complexes of PDEδ with the farnesylated hypervariable regions of K-Ras4A and N-Ras. Earlier data suggested that PDEδ extracts K-Ras4B and N-Ras from the PM, but surprisingly not K-Ras4A. Earlier analysis of the crystal structures advanced that the presence of large/charged residues adjacent to the farnesylated site precludes the PDEδ interaction. Here, we show that PDEδ can bind to farnesylated K-Ras4A and N-Ras like K-Ras4B, albeit not as strongly. This weaker binding, coupled with the stronger anchoring of K-Ras4A in the membrane (but not of electrostatically neutral N-Ras), can explain the observation why PDEδ is unable to effectively extract K-Ras4A. We thus propose that farnesylated Ras isoforms can bind PDEδ to fulfill the required PM enrichment, and argue that the different environments, PM versus solution, can resolve apparently puzzling Ras observations. These are novel insights that would not be expected based on the crystal structures alone, which provide an elegant rationale for previously puzzling observations of the differential effects of PDEδ on farnesylated Ras family proteins.
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Affiliation(s)
- Serena Muratcioglu
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick and Basic Science Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702, United States
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick and Basic Science Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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