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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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Kulbatskii D, Shenkarev Z, Bychkov M, Loktyushov E, Shulepko M, Koshelev S, Povarov I, Popov A, Peigneur S, Chugunov A, Kozlov S, Sharonova I, Efremov R, Skrebitsky V, Tytgat J, Kirpichnikov M, Lyukmanova E. Human Three-Finger Protein Lypd6 Is a Negative Modulator of the Cholinergic System in the Brain. Front Cell Dev Biol 2021; 9:662227. [PMID: 34631692 PMCID: PMC8494132 DOI: 10.3389/fcell.2021.662227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 08/30/2021] [Indexed: 11/19/2022] Open
Abstract
Lypd6 is a GPI-tethered protein from the Ly-6/uPAR family expressed in the brain. Lypd6 enhances the Wnt/β-catenin signaling, although its action on nicotinic acetylcholine receptors (nAChRs) have been also proposed. To investigate a cholinergic activity of Lypd6, we studied a recombinant water-soluble variant of the human protein (ws-Lypd6) containing isolated “three-finger” LU-domain. Experiments at different nAChR subtypes expressed in Xenopus oocytes revealed the negative allosteric modulatory activity of ws-Lypd6. Ws-Lypd6 inhibited ACh-evoked currents at α3β4- and α7-nAChRs with IC50 of ∼35 and 10 μM, respectively, and the maximal amplitude of inhibition of 30–50%. EC50 of ACh at α3β4-nAChRs (∼30 μM) was not changed in the presence of 35 μM ws-Lypd6, while the maximal amplitude of ACh-evoked current was reduced by ∼20%. Ws-Lypd6 did not elicit currents through nAChRs in the absence of ACh. Application of 1 μM ws-Lypd6 significantly inhibited (up to ∼28%) choline-evoked current at α7-nAChRs in rat hippocampal slices. Similar to snake neurotoxin α-bungarotoxin, ws-Lypd6 suppressed the long-term potentiation (LTP) in mouse hippocampal slices. Colocalization of endogenous GPI-tethered Lypd6 with α3β4- and α7-nAChRs was detected in primary cortical and hippocampal neurons. Ws-Lypd6 interaction with the extracellular domain of α7-nAChR was modeled using the ensemble protein-protein docking protocol. The interaction of all three Lypd6 loops (“fingers”) with the entrance to the orthosteric ligand-binding site and the loop C of the primary receptor subunit was predicted. The results obtained allow us to consider Lypd6 as the endogenous negative modulator involved in the regulation of the cholinergic system in the brain.
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Affiliation(s)
- Dmitrii Kulbatskii
- Bioengineering Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Zakhar Shenkarev
- Structural Biology Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia.,Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Maxim Bychkov
- Bioengineering Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Eugene Loktyushov
- Bioengineering Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Mikhail Shulepko
- Bioengineering Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Sergey Koshelev
- Department of Molecular Neurobiology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Igor Povarov
- Brain Research Department, Research Center of Neurology, Moscow, Russia
| | - Alexander Popov
- Department of Molecular Neurobiology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia.,Institute of Neuroscience, Nizhny Novgorod University, Nizhny Novgorod, Russia
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Anton Chugunov
- Structural Biology Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia.,Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia.,International Laboratory for Supercomputer Atomistic Modelling and Multi-Scale Analysis, National Research University Higher School of Economics, Moscow, Russia
| | - Sergey Kozlov
- Department of Molecular Neurobiology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Irina Sharonova
- Brain Research Department, Research Center of Neurology, Moscow, Russia
| | - Roman Efremov
- Structural Biology Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia.,Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia.,International Laboratory for Supercomputer Atomistic Modelling and Multi-Scale Analysis, National Research University Higher School of Economics, Moscow, Russia
| | | | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Mikhail Kirpichnikov
- Bioengineering Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia.,Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Lyukmanova
- Bioengineering Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia.,Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia.,Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
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Paramonov AS, Shulepko MA, Kocharovskaya MV, Alenkin AE, Evdokimova AO, Akentiev PI, Shenkarev ZO, Kirpichnikov MP, Lyukmanova EN. Bacterial Production and Structural Study of Human Neuromodulator Lynx2. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020060230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Paramonov AS, Kocharovskaya MV, Tsarev AV, Kulbatskii DS, Loktyushov EV, Shulepko MA, Kirpichnikov MP, Lyukmanova EN, Shenkarev ZO. Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors. Int J Mol Sci 2020; 21:E7280. [PMID: 33019770 PMCID: PMC7582953 DOI: 10.3390/ijms21197280] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022] Open
Abstract
Ly-6/uPAR or three-finger proteins (TFPs) contain a disulfide-stabilized β-structural core and three protruding loops (fingers). In mammals, TFPs have been found in epithelium and the nervous, endocrine, reproductive, and immune systems. Here, using heteronuclear NMR, we determined the three-dimensional (3D) structure and backbone dynamics of the epithelial secreted protein SLURP-1 and soluble domains of GPI-anchored TFPs from the brain (Lynx2, Lypd6, Lypd6b) acting on nicotinic acetylcholine receptors (nAChRs). Results were compared with the data about human TFPs Lynx1 and SLURP-2 and snake α-neurotoxins WTX and NTII. Two different topologies of the β-structure were revealed: one large antiparallel β-sheet in Lypd6 and Lypd6b, and two β-sheets in other proteins. α-Helical segments were found in the loops I/III of Lynx2, Lypd6, and Lypd6b. Differences in the surface distribution of charged and hydrophobic groups indicated significant differences in a mode of TFPs/nAChR interactions. TFPs showed significant conformational plasticity: the loops were highly mobile at picosecond-nanosecond timescale, while the β-structural regions demonstrated microsecond-millisecond motions. SLURP-1 had the largest plasticity and characterized by the unordered loops II/III and cis-trans isomerization of the Tyr39-Pro40 bond. In conclusion, plasticity could be an important feature of TFPs adapting their structures for optimal interaction with the different conformational states of nAChRs.
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MESH Headings
- Adaptor Proteins, Signal Transducing/chemistry
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Antigens, Ly/chemistry
- Antigens, Ly/genetics
- Antigens, Ly/metabolism
- Binding Sites
- Cloning, Molecular
- Elapid Venoms/chemistry
- Elapid Venoms/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- GPI-Linked Proteins/chemistry
- GPI-Linked Proteins/genetics
- GPI-Linked Proteins/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Humans
- Hydrophobic and Hydrophilic Interactions
- Models, Molecular
- Neuropeptides/chemistry
- Neuropeptides/genetics
- Neuropeptides/metabolism
- Nuclear Magnetic Resonance, Biomolecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Receptors, Nicotinic/chemistry
- Receptors, Nicotinic/genetics
- Receptors, Nicotinic/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Urokinase-Type Plasminogen Activator/chemistry
- Urokinase-Type Plasminogen Activator/genetics
- Urokinase-Type Plasminogen Activator/metabolism
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Affiliation(s)
- Alexander S. Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia; (A.S.P.); (M.V.K.); (A.V.T.); (D.S.K.); (E.V.L.); (M.A.S.); (M.P.K.)
| | - Milita V. Kocharovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia; (A.S.P.); (M.V.K.); (A.V.T.); (D.S.K.); (E.V.L.); (M.A.S.); (M.P.K.)
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia
| | - Andrey V. Tsarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia; (A.S.P.); (M.V.K.); (A.V.T.); (D.S.K.); (E.V.L.); (M.A.S.); (M.P.K.)
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia
| | - Dmitrii S. Kulbatskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia; (A.S.P.); (M.V.K.); (A.V.T.); (D.S.K.); (E.V.L.); (M.A.S.); (M.P.K.)
| | - Eugene V. Loktyushov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia; (A.S.P.); (M.V.K.); (A.V.T.); (D.S.K.); (E.V.L.); (M.A.S.); (M.P.K.)
| | - Mikhail A. Shulepko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia; (A.S.P.); (M.V.K.); (A.V.T.); (D.S.K.); (E.V.L.); (M.A.S.); (M.P.K.)
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia; (A.S.P.); (M.V.K.); (A.V.T.); (D.S.K.); (E.V.L.); (M.A.S.); (M.P.K.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ekaterina N. Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia; (A.S.P.); (M.V.K.); (A.V.T.); (D.S.K.); (E.V.L.); (M.A.S.); (M.P.K.)
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia
| | - Zakhar O. Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia; (A.S.P.); (M.V.K.); (A.V.T.); (D.S.K.); (E.V.L.); (M.A.S.); (M.P.K.)
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia
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Miwa JM, Anderson KR, Hoffman KM. Lynx Prototoxins: Roles of Endogenous Mammalian Neurotoxin-Like Proteins in Modulating Nicotinic Acetylcholine Receptor Function to Influence Complex Biological Processes. Front Pharmacol 2019; 10:343. [PMID: 31114495 PMCID: PMC6502960 DOI: 10.3389/fphar.2019.00343] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/19/2019] [Indexed: 12/19/2022] Open
Abstract
The cholinergic system modulates many biological functions, due to the widespread distribution of cholinergic neuronal terminals, and the diffuse release of its neurotransmitter, acetylcholine. Several layers of regulation help to refine and control the scope of this excitatory neurotransmitter system. One such regulatory mechanism is imparted through endogenous toxin-like proteins, prototoxins, which largely control the function of nicotinic receptors of the cholinergic system. Prototoxins and neurotoxins share the distinct three finger toxin fold, highly effective as a receptor binding protein, and the former are expressed in the mammalian brain, immune system, epithelium, etc. Prototoxins and elapid snake neurotoxins appear to be related through gene duplication and divergence from a common ancestral gene. Protein modulators can provide a graded response of the cholinergic system, and within the brain, stabilize neural circuitry through direct interaction with nicotinic receptors. Understanding the roles of each prototoxin (e.g., lynx1, lynx2/lypd1, PSCA, SLURP1, SLURP2, Lypd6, lypd6b, lypdg6e, PATE-M, PATE-B, etc.), their binding specificity and unique expression profile, has the potential to uncover many fascinating cholinergic-dependent mechanisms in the brain. Each family member can provide a spatially restricted level of control over nAChR function based on its expression in the brain. Due to the difficulty in the pharmacological targeting of nicotinic receptors in the brain as a result of widespread expression patterns and similarities in receptor sequences, unique interfaces between prototoxin and nicotinic receptor could provide more specific targeting than nicotinic receptors alone. As such, this family is intriguing from a long-term therapeutic perspective.
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Affiliation(s)
- Julie M Miwa
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, United States
| | - Kristin R Anderson
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, United States
| | - Katie M Hoffman
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, United States
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Vasilyeva NA, Loktyushov EV, Bychkov ML, Shenkarev ZO, Lyukmanova EN. Three-Finger Proteins from the Ly6/uPAR Family: Functional Diversity within One Structural Motif. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523067 DOI: 10.1134/s0006297917130090] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The discovery in higher animals of proteins from the Ly6/uPAR family, which have structural homology with snake "three-finger" neurotoxins, has generated great interest in these molecules and their role in the functioning of the organism. These proteins have been found in the nervous, immune, endocrine, and reproductive systems of mammals. There are two types of the Ly6/uPAR proteins: those associated with the cell membrane by GPI-anchor and secreted ones. For some of them (Lynx1, SLURP-1, SLURP-2, Lypd6), as well as for snake α-neurotoxins, the target of action is nicotinic acetylcholine receptors, which are widely represented in the central and peripheral nervous systems, and in many other tissues, including epithelial cells and the immune system. However, the targets of most proteins from the Ly6/uPAR family and the mechanism of their action remain unknown. This review presents data on the structural and functional properties of the Ly6/uPAR proteins, which reveal a variety of functions within a single structural motif.
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Affiliation(s)
- N A Vasilyeva
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
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