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Guo Z, Kundu S. Recent research progress in glycosylphosphatidylinositol-anchored protein biosynthesis, chemical/chemoenzymatic synthesis, and interaction with the cell membrane. Curr Opin Chem Biol 2024; 78:102421. [PMID: 38181647 PMCID: PMC10922524 DOI: 10.1016/j.cbpa.2023.102421] [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: 10/28/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
Glycosylphosphatidylinositol (GPI) attachment to the C-terminus of proteins is a prevalent posttranslational modification in eukaryotic species, and GPIs help anchor proteins to the cell surface. GPI-anchored proteins (GPI-APs) play a key role in various biological events. However, GPI-APs are difficult to access and investigate. To tackle the problem, chemical and chemoenzymatic methods have been explored for the preparation of GPI-APs, as well as GPI probes that facilitate the study of GPIs on live cells. Substantial progress has also been made regarding GPI-AP biosynthesis, which is helpful for developing new synthetic methods for GPI-APs. This article reviews the recent advancements in the study of GPI-AP biosynthesis, GPI-AP synthesis, and GPI interaction with the cell membrane utilizing synthetic probes.
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Affiliation(s)
- Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32611, USA.
| | - Sayan Kundu
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
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2
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Li X, Fu L, Zhang S, Dong Y, Gao L. Relationship between Protein-Induced Membrane Curvature and Membrane Thermal Undulation. J Phys Chem B 2024; 128:515-525. [PMID: 38181399 DOI: 10.1021/acs.jpcb.3c06775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
This work studied the membrane curvature generated by anchored proteins lacking amphipathic helices and intrinsic morphologies, including the Epsin N-terminal homology domain, intrinsically disordered C-terminal domain, and truncated C-terminal fragments, by using coarse-grained molecular dynamics simulations. We found that anchored proteins can stabilize the thermal undulation of membranes at a wavelength five times the protein's binding size. This proportional connection is governed by the membrane bending rigidity and protein density. Extended intrinsically disordered proteins with relatively high hydrophobicity favor colliding with the membrane, leading to a much larger binding size, and show superiority in generating membrane curvature at low density over folded proteins.
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Affiliation(s)
- Xiangyuan Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lei Fu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Shan Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yi Dong
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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3
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Kav B, Weikl TR, Schneck E. Measuring pico-Newton Forces with Lipid Anchors as Force Sensors in Molecular Dynamics Simulations. J Phys Chem B 2023; 127:4081-4089. [PMID: 37127845 PMCID: PMC10184124 DOI: 10.1021/acs.jpcb.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Binding forces between biomolecules are ubiquitous in nature but sometimes as weak as a few pico-Newtons (pN). In many cases, the binding partners are attached to biomembranes with the help of a lipid anchor. One important example are glycolipids that promote membrane adhesion through weak carbohydrate-carbohydrate binding between adjacent membranes. Here, we use molecular dynamics (MD) simulations to quantify the forces generated by bonds involving membrane-anchored molecules. We introduce a method in which the protrusion of the lipid anchors from the membrane acts as the force sensor. Our results with two different glycolipids reveal binding forces of up to 20 pN and corroborate the recent notion that carbohydrate-carbohydrate interactions are generic rather than specific.
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Affiliation(s)
- Batuhan Kav
- Max Planck Institute of Colloids and Interfaces, 14467, Potsdam, Germany
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Thomas R Weikl
- Max Planck Institute of Colloids and Interfaces, 14467, Potsdam, Germany
| | - Emanuel Schneck
- Max Planck Institute of Colloids and Interfaces, 14467, Potsdam, Germany
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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Couves EC, Gardner S, Voisin TB, Bickel JK, Stansfeld PJ, Tate EW, Bubeck D. Structural basis for membrane attack complex inhibition by CD59. Nat Commun 2023; 14:890. [PMID: 36797260 PMCID: PMC9935631 DOI: 10.1038/s41467-023-36441-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
CD59 is an abundant immuno-regulatory receptor that protects human cells from damage during complement activation. Here we show how the receptor binds complement proteins C8 and C9 at the membrane to prevent insertion and polymerization of membrane attack complex (MAC) pores. We present cryo-electron microscopy structures of two inhibited MAC precursors known as C5b8 and C5b9. We discover that in both complexes, CD59 binds the pore-forming β-hairpins of C8 to form an intermolecular β-sheet that prevents membrane perforation. While bound to C8, CD59 deflects the cascading C9 β-hairpins, rerouting their trajectory into the membrane. Preventing insertion of C9 restricts structural transitions of subsequent monomers and indirectly halts MAC polymerization. We combine our structural data with cellular assays and molecular dynamics simulations to explain how the membrane environment impacts the dual roles of CD59 in controlling pore formation of MAC, and as a target of bacterial virulence factors which hijack CD59 to lyse human cells.
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Affiliation(s)
- Emma C Couves
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Scott Gardner
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Tomas B Voisin
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jasmine K Bickel
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, United Kingdom
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, United Kingdom
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, United Kingdom
| | - Doryen Bubeck
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, United Kingdom.
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Matamoros-Recio A, Mínguez-Toral M, Martín-Santamaría S. Modeling of Transmembrane Domain and Full-Length TLRs in Membrane Models. Methods Mol Biol 2023; 2700:3-38. [PMID: 37603172 DOI: 10.1007/978-1-0716-3366-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Toll-like receptors (TLRs), classified as pattern recognition receptors, have a primordial role in the activation of the innate immunity. In particular, TLR4 binds to lipopolysaccharides (LPS), a membrane constituent of Gram-negative bacteria, and, together with Myeloid Differentiation factor 2 (MD-2) protein, forms a heterodimeric complex which leads to the activation of the innate immune system response. Identification of TLRs has sparked great interest in the therapeutic manipulation of the innate immune system. In particular, TLR4 antagonists may be useful for the treatment of septic shock, certain autoimmune diseases, noninfectious inflammatory disorders, and neuropathic pain, and TLR4 agonists are under development as vaccine adjuvants in antitumoral treatments. Therefore, TLR4 has risen as a promising therapeutic target, and its modulation constitutes a highly relevant and active research area. Deep structural understanding of TLR4 signaling may help in the design and discovery of TLR4-modulating molecules with desirable therapeutic properties.Computational studies of the different independent domains composing the TLR4 were undertaken, to understand the differential domain organization of TLR4 in aqueous and membrane environments, including Liquid-disordered (Ld) and Liquid-ordered (Lo) membrane models, to account for the TLR4 recruitment in lipid rafts over activation. We modeled, by means of all-atom Molecular Dynamics (MD) simulations, the structural assembly of plausible full-length TLR4 models embedded into a realistic plasma membrane, accounting for the active (agonist) state of the TLR4, thus providing an analysis at both atomic/molecular and thermodynamic levels of the TLR4 assembly and biological activity. Our results unveil relevant molecular aspects involved in the mechanism of receptor activation, and adaptor recruitment in the innate immune pathways, and will promote the discovery of new TLR4 modulators and probes.
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Affiliation(s)
- Alejandra Matamoros-Recio
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, Spain
| | - Marina Mínguez-Toral
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, Spain
| | - Sonsoles Martín-Santamaría
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, Spain.
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Orientational Preferences of GPI-Anchored Ly6/uPAR Proteins. Int J Mol Sci 2022; 24:ijms24010011. [PMID: 36613456 PMCID: PMC9819746 DOI: 10.3390/ijms24010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Ly6/uPAR proteins regulate many essential functions in the nervous and immune systems and epithelium. Most of these proteins contain single β-structural LU domains with three protruding loops and are glycosylphosphatidylinositol (GPI)-anchored to a membrane. The GPI-anchor role is currently poorly studied. Here, we investigated the positional and orientational preferences of six GPI-anchored proteins in the receptor-unbound state by molecular dynamics simulations. Regardless of the linker length between the LU domain and GPI-anchor, the proteins interacted with the membrane by polypeptide parts and N-/O-glycans. Lynx1, Lynx2, Lypd6B, and Ly6H contacted the membrane by the loop regions responsible for interactions with nicotinic acetylcholine receptors, while Lypd6 and CD59 demonstrated unique orientations with accessible receptor-binding sites. Thus, GPI-anchoring does not guarantee an optimal 'pre-orientation' of the LU domain for the receptor interaction.
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Brzyska A, Korycki P, Woliński K. The carbohydrate glycosylphosphatidylinositol anchor chain under mechanical stress. Carbohydr Res 2022; 522:108702. [DOI: 10.1016/j.carres.2022.108702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 11/02/2022]
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Banerjee P, Silva DV, Lipowsky R, Santer M. The importance of side branches of glycosylphosphatidylinositol anchors: a molecular dynamics perspective. Glycobiology 2022; 32:933-948. [PMID: 36197124 PMCID: PMC9620968 DOI: 10.1093/glycob/cwac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 11/14/2022] Open
Abstract
Many proteins are anchored to the cell surface of eukaryotes using a unique family of glycolipids called glycosylphosphatidylinositol (GPI) anchors. These glycolipids also exist without a covalently bound protein, in particular on the cell surfaces of protozoan parasites where they are densely populated. GPIs and GPI-anchored proteins participate in multiple cellular processes such as signal transduction, cell adhesion, protein trafficking and pathogenesis of Malaria, Toxoplasmosis, Trypanosomiasis and prion diseases, among others. All GPIs share a common conserved glycan core modified in a cell-dependent manner with additional side glycans or phosphoethanolamine residues. Here, we use atomistic molecular dynamic simulations and perform a systematic study to evaluate the structural properties of GPIs with different side chains inserted in lipid bilayers. Our results show a flop-down orientation of GPIs with respect to the membrane surface and the presentation of the side chain residues to the solvent. This finding agrees well with experiments showing the role of the side residues as active epitopes for recognition of GPIs by macrophages and induction of GPI-glycan-specific immune responses. Protein-GPI interactions were investigated by attaching parasitic GPIs to Green Fluorescent Protein. GPIs are observed to recline on the membrane surface and pull down the attached protein close to the membrane facilitating mutual contacts between protein, GPI and the lipid bilayer. This model is efficient in evaluating the interaction of GPIs and GPI-anchored proteins with membranes and can be extended to study other parasitic GPIs and proteins and develop GPI-based immunoprophylaxis to treat infectious diseases.
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Affiliation(s)
- Pallavi Banerjee
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany.,Mathematisch-Naturwissenschaftlichen Fakultät, University of Potsdam, Potsdam 14476, Germany
| | - Daniel Varon Silva
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
| | - Reinhard Lipowsky
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany.,Mathematisch-Naturwissenschaftlichen Fakultät, University of Potsdam, Potsdam 14476, Germany
| | - Mark Santer
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
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Banerjee P, Lipowsky R, Santer M. Coarse-Grained Molecular Model for the Glycosylphosphatidylinositol Anchor with and without Protein. J Chem Theory Comput 2020; 16:3889-3903. [PMID: 32392421 PMCID: PMC7303967 DOI: 10.1021/acs.jctc.0c00056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Indexed: 01/17/2023]
Abstract
Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.
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Affiliation(s)
- Pallavi Banerjee
- Max
Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
- Institute
of Biochemistry and Biology, University
of Potsdam, Potsdam 14469, Germany
| | - Reinhard Lipowsky
- Max
Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
- Institute
of Biochemistry and Biology, University
of Potsdam, Potsdam 14469, Germany
| | - Mark Santer
- Max
Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
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Echeverri D, Garg M, Varón Silva D, Orozco J. Phosphoglycan-sensitized platform for specific detection of anti-glycan IgG and IgM antibodies in serum. Talanta 2020; 217:121117. [PMID: 32498834 DOI: 10.1016/j.talanta.2020.121117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 01/29/2023]
Abstract
Glycosylphosphatidylinositol anchored proteins (GPI-APs) are natural conjugates in the plasma membrane of eukaryotic cells that result from the attachment of a glycolipid to the C-terminus of many proteins. GPI-APs play a crucial role in cell signaling and adhesion and have implications in health and diseases. GPI-APs and GPIs without protein (free GPIs) are found in abundance on the surface of the protozoan parasite Toxoplasma gondii. The detection of anti-GPI IgG and IgM antibodies allows differentiation between toxoplasmosis patients and healthy individuals using serological assays. However, these methods are limited by their poor efficiency, cross-reactivity and need for sophisticated laboratory equipment and qualified personnel. Here, we established a label-free electrochemical glycobiosensor for the detection of anti-GPI IgG and IgM antibodies in serum from toxoplasmosis seropositive patients. This biosensor uses a synthetic GPI phosphoglycan bioreceptor immobilized on screen-printed gold electrodes through a linear alkane thiol phosphodiester. The antigen-antibody interaction was detected and quantified by electrochemical impedance spectroscopy (EIS). The resultant device showed a linear dynamic range of anti-GPI antibodies in serum ranging from 1.0 to 10.0 IU mL-1, with a limit of detection of 0.31 IU mL-1. This method also holds great potential for the detection of IgG antibodies related to other multiple medical conditions characterized by overexpression of antibodies.
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Affiliation(s)
- Danilo Echeverri
- Max Planck Tandem Group in Nanobioengineering, University of Antioquia, Complejo Ruta N, Calle 67 N° 52-20, Medellín, 050010, Colombia
| | - Monika Garg
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Daniel Varón Silva
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Jahir Orozco
- Max Planck Tandem Group in Nanobioengineering, University of Antioquia, Complejo Ruta N, Calle 67 N° 52-20, Medellín, 050010, Colombia.
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