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Peracha O. PS4: a next-generation dataset for protein single-sequence secondary structure prediction. Biotechniques 2024; 76:63-70. [PMID: 37997848 DOI: 10.2144/btn-2023-0024] [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: 11/25/2023] Open
Abstract
Protein secondary structure prediction is a subproblem of protein folding. A light-weight algorithm capable of accurately predicting secondary structure from only the protein residue sequence could provide useful input for tertiary structure prediction, alleviating the reliance on multiple sequence alignments typically seen in today's best-performing models. Unfortunately, existing datasets for secondary structure prediction are small, creating a bottleneck. We present PS4, a dataset of 18,731 nonredundant protein chains and their respective secondary structure labels. Each chain is identified, and the dataset is nonredundant against other secondary structure datasets commonly seen in the literature. We perform ablation studies by training secondary structure prediction algorithms on the PS4 training set and obtains state-of-the-art accuracy on the CB513 test set in zero shots.
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Affiliation(s)
- Omar Peracha
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford, OX1 2JA, United Kingdom
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2
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Mineev KS, Kryukova EV, Kasheverov IE, Egorova NS, Zhmak MN, Ivanov IA, Senko DA, Feofanov AV, Ignatova AA, Arseniev AS, Utkin YN, Tsetlin VI. Spatial Structure and Activity of Synthetic Fragments of Lynx1 and of Nicotinic Receptor Loop C Models. Biomolecules 2020; 11:biom11010001. [PMID: 33374963 PMCID: PMC7821949 DOI: 10.3390/biom11010001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/06/2020] [Accepted: 12/19/2020] [Indexed: 11/16/2022] Open
Abstract
Lynx1, membrane-bound protein co-localized with the nicotinic acetylcholine receptors (nAChRs) and regulates their function, is a three-finger protein (TFP) made of three β-structural loops, similarly to snake venom α-neurotoxin TFPs. Since the central loop II of α-neurotoxins is involved in binding to nAChRs, we have recently synthesized the fragments of Lynx1 central loop, including those with the disulfide between Cys residues introduced at N- and C-termini, some of them inhibiting muscle-type nAChR similarly to the whole-size water-soluble Lynx1 (ws-Lynx1). Literature shows that the main fragment interacting with TFPs is the C-loop of both nAChRs and acetylcholine binding proteins (AChBPs) while some ligand-binding capacity is preserved by analogs of this loop, for example, by high-affinity peptide HAP. Here we analyzed the structural organization of these peptide models of ligands and receptors and its role in binding. Thus, fragments of Lynx1 loop II, loop C from the Lymnaea stagnalis AChBP and HAP were synthesized in linear and Cys-cyclized forms and structurally (CD and NMR) and functionally (radioligand assay on Torpedo nAChR) characterized. Connecting the C- and N-termini by disulfide in the ws-Lynx1 fragment stabilized its conformation which became similar to the loop II within the 1H-NMR structure of ws-Lynx1, the activity being higher than for starting linear fragment but lower than for peptide with free cysteines. Introduced disulfides did not considerably change the structure of HAP and of loop C fragments, the former preserving high affinity for α-bungarotoxin, while, surprisingly, no binding was detected with loop C and its analogs.
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Affiliation(s)
- Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
- Department of Physico-Chemical Biology and Biotechnology, Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Russia
- Correspondence: ; Tel.: +7-(495)-330-74-83
| | - Elena V. Kryukova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
| | - Igor E. Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Biomedical Science and Technology Park, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Natalia S. Egorova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
| | - Maxim N. Zhmak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
| | - Igor A. Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
| | - Dmitry A. Senko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alexey V. Feofanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
- Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anastasia A. Ignatova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
| | - Alexander S. Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
| | - Yuri N. Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
| | - Victor I. Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.V.K.); (I.E.K.); (N.S.E.); (M.N.Z.); (I.A.I.); (D.A.S.); (A.V.F.); (A.A.I.); (A.S.A.); (Y.N.U.); (V.I.T.)
- Institute for Physics and Engineering in Biomedicine, National Research Nuclear University MEPhI, 115409 Moscow, Russia
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3
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Lynagh T, Kiontke S, Meyhoff-Madsen M, Gless BH, Johannesen J, Kattelmann S, Christiansen A, Dufva M, Laustsen AH, Devkota K, Olsen CA, Kümmel D, Pless SA, Lohse B. Peptide Inhibitors of the α-Cobratoxin-Nicotinic Acetylcholine Receptor Interaction. J Med Chem 2020; 63:13709-13718. [PMID: 33143415 PMCID: PMC7705965 DOI: 10.1021/acs.jmedchem.0c01202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
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Venomous snakebites cause >100
000 deaths every year, in many cases
via potent depression of human neuromuscular signaling by snake α-neurotoxins.
Emergency therapy still relies on antibody-based antivenom, hampered
by poor access, frequent adverse reactions, and cumbersome production/purification.
Combining high-throughput discovery and subsequent structure–function
characterization, we present simple peptides that bind α-cobratoxin
(α-Cbtx) and prevent its inhibition of nicotinic acetylcholine
receptors (nAChRs) as a lead for the development of alternative antivenoms.
Candidate peptides were identified by phage display and deep sequencing,
and hits were characterized by electrophysiological recordings, leading
to an 8-mer peptide that prevented α-Cbtx inhibition of nAChRs.
We also solved the peptide:α-Cbtx cocrystal structure, revealing
that the peptide, although of unique primary sequence, binds to α-Cbtx
by mimicking structural features of the nAChR binding pocket. This
demonstrates the potential of small peptides to neutralize lethal
snake toxins in vitro, establishing a potential route to simple, synthetic,
low-cost antivenoms.
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Affiliation(s)
- Timothy Lynagh
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway.,Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Stephan Kiontke
- Division of Structural Biology, Department of Biology/Chemistry, University of Osnabrück, Barbarastraße 13, Osnabrück 49076, Germany.,Faculty of Biology, Department of Plant Physiology and Photobiology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
| | - Maria Meyhoff-Madsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Bengt H Gless
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jónas Johannesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Sabrina Kattelmann
- Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Anders Christiansen
- Fluid Array Systems and Technology, Nano and Bio-physical Systems, Department of Health Technology, Technical University of Denmark, Building 423 Produktionstorvet, DK-2800 Kongens Lyngby, Denmark
| | - Martin Dufva
- Fluid Array Systems and Technology, Nano and Bio-physical Systems, Department of Health Technology, Technical University of Denmark, Building 423 Produktionstorvet, DK-2800 Kongens Lyngby, Denmark
| | - Andreas H Laustsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kanchan Devkota
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Daniel Kümmel
- Division of Structural Biology, Department of Biology/Chemistry, University of Osnabrück, Barbarastraße 13, Osnabrück 49076, Germany.,Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Stephan Alexander Pless
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Brian Lohse
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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4
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Nirthanan S. Snake three-finger α-neurotoxins and nicotinic acetylcholine receptors: molecules, mechanisms and medicine. Biochem Pharmacol 2020; 181:114168. [PMID: 32710970 DOI: 10.1016/j.bcp.2020.114168] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022]
Abstract
Snake venom three-finger α-neurotoxins (α-3FNTx) act on postsynaptic nicotinic acetylcholine receptors (nAChRs) at the neuromuscular junction (NMJ) to produce skeletal muscle paralysis. The discovery of the archetypal α-bungarotoxin (α-BgTx), almost six decades ago, exponentially expanded our knowledge of membrane receptors and ion channels. This included the localisation, isolation and characterization of the first receptor (nAChR); and by extension, the pathophysiology and pharmacology of neuromuscular transmission and associated pathologies such as myasthenia gravis, as well as our understanding of the role of α-3FNTxs in snakebite envenomation leading to novel concepts of targeted treatment. Subsequent studies on a variety of animal venoms have yielded a plethora of novel toxins that have revolutionized molecular biomedicine and advanced drug discovery from bench to bedside. This review provides an overview of nAChRs and their subtypes, classification of α-3FNTxs and the challenges of typifying an increasing arsenal of structurally and functionally unique toxins, and the three-finger protein (3FP) fold in the context of the uPAR/Ly6/CD59/snake toxin superfamily. The pharmacology of snake α-3FNTxs including their mechanisms of neuromuscular blockade, variations in reversibility of nAChR interactions, specificity for nAChR subtypes or for distinct ligand-binding interfaces within a subtype and the role of α-3FNTxs in neurotoxic envenomation are also detailed. Lastly, a reconciliation of structure-function relationships between α-3FNTx and nAChRs, derived from historical mutational and biochemical studies and emerging atomic level structures of nAChR models in complex with α-3FNTxs is discussed.
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Affiliation(s)
- Selvanayagam Nirthanan
- School of Medical Science, Griffith Health Group, Griffith University, Gold Coast, Queensland, Australia.
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5
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Liu J, Kim YS, Richardson CE, Tom A, Ramakrishnan C, Birey F, Katsumata T, Chen S, Wang C, Wang X, Joubert LM, Jiang Y, Wang H, Fenno LE, Tok JBH, Pașca SP, Shen K, Bao Z, Deisseroth K. Genetically targeted chemical assembly of functional materials in living cells, tissues, and animals. Science 2020; 367:1372-1376. [PMID: 32193327 DOI: 10.1126/science.aay4866] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 01/21/2020] [Indexed: 12/30/2022]
Abstract
The structural and functional complexity of multicellular biological systems, such as the brain, are beyond the reach of human design or assembly capabilities. Cells in living organisms may be recruited to construct synthetic materials or structures if treated as anatomically defined compartments for specific chemistry, harnessing biology for the assembly of complex functional structures. By integrating engineered-enzyme targeting and polymer chemistry, we genetically instructed specific living neurons to guide chemical synthesis of electrically functional (conductive or insulating) polymers at the plasma membrane. Electrophysiological and behavioral analyses confirmed that rationally designed, genetically targeted assembly of functional polymers not only preserved neuronal viability but also achieved remodeling of membrane properties and modulated cell type-specific behaviors in freely moving animals. This approach may enable the creation of diverse, complex, and functional structures and materials within living systems.
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Affiliation(s)
- Jia Liu
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Ariane Tom
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Fikri Birey
- Department of Psychiatry, Stanford University, Stanford, CA 94305, USA
| | - Toru Katsumata
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Shucheng Chen
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Cheng Wang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Xiao Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lydia-Marie Joubert
- Cell Sciences Imaging Facility, Stanford University, Stanford, CA 94305, USA
| | - Yuanwen Jiang
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Huiliang Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lief E Fenno
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Department of Psychiatry, Stanford University, Stanford, CA 94305, USA
| | - Jeffrey B-H Tok
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Sergiu P Pașca
- Department of Psychiatry, Stanford University, Stanford, CA 94305, USA
| | - Kang Shen
- Department of Biology, Stanford University, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Zhenan Bao
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. .,Department of Psychiatry, Stanford University, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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6
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Complex approach for analysis of snake venom α-neurotoxins binding to HAP, the high-affinity peptide. Sci Rep 2020; 10:3861. [PMID: 32123252 PMCID: PMC7052197 DOI: 10.1038/s41598-020-60768-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/14/2020] [Indexed: 12/30/2022] Open
Abstract
Snake venom α-neurotoxins, invaluable pharmacological tools, bind with high affinity to distinct subtypes of nicotinic acetylcholine receptor. The combinatorial high-affinity peptide (HAP), homologous to the C-loop of α1 and α7 nAChR subunits, binds biotinylated α-bungarotoxin (αBgt) with nanomolar affinity and might be a protection against snake-bites. Since there are no data on HAP interaction with other toxins, we checked its binding of α-cobratoxin (αCtx), similar to αBgt in action on nAChRs. Using radioiodinated αBgt, we confirmed a high affinity of HAP for αBgt, the complex formation is supported by mass spectrometry and gel chromatography, but only weak binding was registered with αCtx. A combination of protein intrinsic fluorescence measurements with the principal component analysis of the spectra allowed us to measure the HAP-αBgt binding constant directly (29 nM). These methods also confirmed weak HAP interaction with αCtx (>10000 nM). We attempted to enhance it by modification of HAP structure relying on the known structures of α-neurotoxins with various targets and applying molecular dynamics. A series of HAP analogues have been synthesized, HAP[L9E] analogue being considerably more potent than HAP in αCtx binding (7000 nM). The proposed combination of experimental and computational approaches appears promising for analysis of various peptide-protein interactions.
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7
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Rajendran BK, Xavier Suresh M, Bhaskaran SP, Harshitha Y, Gaur U, Kwok HF. Pharmacoinformatic Approach to Explore the Antidote Potential of Phytochemicals on Bungarotoxin from Indian Krait, Bungarus caeruleus. Comput Struct Biotechnol J 2018; 16:450-461. [PMID: 30455855 PMCID: PMC6231056 DOI: 10.1016/j.csbj.2018.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/08/2018] [Accepted: 10/12/2018] [Indexed: 12/25/2022] Open
Abstract
Venomous reptiles especially serpents are well known for their adverse effects after accidental conflicts with humans. Upon biting humans these serpents transmit arrays of detrimental toxins with diverse physiological activities that may either lead to minor symptoms such as dermatitis and allergic response or highly severe symptoms such as blood coagulation, disseminated intravascular coagulation, tissue injury, and hemorrhage. Other complications like respiratory arrest and necrosis may also occur. Bungarotoxins are a group of closely related neurotoxic proteins derived from the venom of kraits (Bungarus caeruleus) one of the six most poisonous snakes in India whose bite causes respiratory paralysis and mortality without showing any local symptoms. In the current study, by employing various pharmacoinformatic approaches, we have explored the antidote properties of 849 bioactive phytochemicals from 82 medicinal plants which have already shown antidote properties against various venomous toxins. These herbal compounds were taken and pharmacoinformatic approaches such as ADMET, docking and molecular dynamics were employed. The three-dimensional modelling approach provides structural insights on the interaction between bungarotoxin and phytochemicals. In silico simulations proved to be an effective analytical tools to investigate the toxin-ligand interaction, correlating with the affinity of binding. By analyzing the results from the present study, we proposed nine bioactive phytochemical compounds which are, 2-dodecanol, 7-hydroxycadalene, indole-3-(4'-oxo)butyric acid, nerolidol-2, trans-nerolidol, eugenol, benzene propanoic acid, 2-methyl-1-undecanol, germacren-4-ol can be used as antidotes for bungarotoxin.
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Affiliation(s)
- Barani Kumar Rajendran
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau
| | - M. Xavier Suresh
- Department of Physics, Sathyabama Institute of Science and Technology, Deemed to be University, Chennai 600119, India
| | - Shanmuga Priya Bhaskaran
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau
| | - Yarradoddi Harshitha
- Department of Physics, Sathyabama Institute of Science and Technology, Deemed to be University, Chennai 600119, India
| | - Uma Gaur
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau
| | - Hang Fai Kwok
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau
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8
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Dutertre S, Nicke A, Tsetlin VI. Nicotinic acetylcholine receptor inhibitors derived from snake and snail venoms. Neuropharmacology 2017. [PMID: 28623170 DOI: 10.1016/j.neuropharm.2017.06.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nicotinic acetylcholine receptor (nAChR) represents the prototype of ligand-gated ion channels. It is vital for neuromuscular transmission and an important regulator of neurotransmission. A variety of toxic compounds derived from diverse species target this receptor and have been of elemental importance in basic and applied research. They enabled milestone discoveries in pharmacology and biochemistry ranging from the original formulation of the receptor concept, the first isolation and structural analysis of a receptor protein (the nAChR) to the identification, localization, and differentiation of its diverse subtypes and their validation as a target for therapeutic intervention. Among the venom-derived compounds, α-neurotoxins and α-conotoxins provide the largest families and still represent indispensable pharmacological tools. Application of modified α-neurotoxins provided substantial structural and functional details of the nAChR long before high resolution structures were available. α-bungarotoxin represents not only a standard pharmacological tool and label in nAChR research but also for unrelated proteins tagged with a minimal α-bungarotoxin binding motif. A major advantage of α-conotoxins is their smaller size, as well as superior selectivity for diverse nAChR subtypes that allows their development into ligands with optimized pharmacological and chemical properties and potentially novel drugs. In the following, these two groups of nAChR antagonists will be described focusing on their respective roles in the structural and functional characterization of nAChRs and their development into research tools. In addition, we provide a comparative overview of the diverse α-conotoxin selectivities that can serve as a practical guide for both structure activity studies and subtype classification. This article is part of the Special Issue entitled 'Venom-derived Peptides as Pharmacological Tools.'
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Affiliation(s)
- Sébastien Dutertre
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier - CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Annette Nicke
- Walther Straub Institute for Pharmacology and Toxicology, Ludwig-Maximilians-Universität, Nußbaumstr. 26, 80336 Munich, Germany.
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str.16/10, Moscow 117999, Russian Federation
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9
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Development of a novel imaging agent using peptide-coated gold nanoparticles toward brain glioma stem cell marker CD133. Acta Biomater 2017; 47:182-192. [PMID: 27721007 DOI: 10.1016/j.actbio.2016.10.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 12/13/2022]
Abstract
CD133 is known as biomarker for glioblastoma (GBM) and also serves as a marker for cancer stem cells (CSCs), which carry out tumorigenesis and resist conventional therapeutics. The presence of CD133-presenting CSC is a one of the factors in maintenance of the tumorigenic potential of GBM. Thus, CD133 is a potential target for accurate diagnosis of GBM, which could improve its poor prognosis for patients when CSCs are present. Herein we designed a small peptide-based imaging agent with stimulus-responsive properties. A novel small peptide, CBP4, was screened by a phage display technique, and demonstrated binding to the target CD133 (ECD) comparable to that of an antibody. As a quencher, we used gold nanoparticles (GNPs); the targeting peptide was conjugated to GNPs with high efficiency. By means of a quenching effect, the peptide-coated GNP showed 'signal on-off' properties depending upon the presence of the target. In addition, the particles exhibited biocompatibility when localized in the cytosol. Thus, this study demonstrated that the peptide-coated GNPs can be utilized as an imaging agent for accurate diagnosis of GBM, and further as a drug carrier for therapeutic approaches. STATEMENT OF SIGNIFICANCE The diagnosis and determination of prognosis made by cancer stem cell markers could be a key strategy to eradicate cancer stem cells and cure the cancer. The significance of this study is the characterization of quenching-based signal on-off mechanism and showed that the active targeting via peptide can contribute to the design of a stimulus-responsive cellular imaging agent. Moreover, small peptide based nano complexation showed specific recognition of the target stem cell and internalized on cellular cyotosol with stimulus responsive fluorescence. With its novel biocompatibility, the strategy might be a promising tool for drug carrier systems able to measure and visualize the delivered efficiency at intracellular sites.
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10
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Localized force application reveals mechanically sensitive domains of Piezo1. Nat Commun 2016; 7:12939. [PMID: 27694883 PMCID: PMC5063965 DOI: 10.1038/ncomms12939] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 08/16/2016] [Indexed: 01/12/2023] Open
Abstract
Piezos are mechanically activated ion channels that function as sensors of touch and pressure in various cell types. However, the precise mechanism and structures mediating mechanical activation and subsequent inactivation have not yet been identified. Here we use magnetic nanoparticles as localized transducers of mechanical force in combination with pressure-clamp electrophysiology to identify mechanically sensitive domains important for activation and inactivation.
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11
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Penas C, Mascareñas JL, Vázquez ME. Coupling the folding of a β-hairpin with chelation-enhanced luminescence of Tb(III) and Eu(III) ions for specific sensing of a viral RNA. Chem Sci 2016; 2016:2674-2678. [PMID: 27293537 PMCID: PMC4898589 DOI: 10.1039/c5sc04501k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rational modification of a natural RNA-binding peptide with a lanthanide EDTA chelator, and a phenanthroline ligand yields a highly selective luminescent sensor. The sensing mechanism relies on the RNA-triggered folding of the peptide into a β-hairpin, which promotes the coordination of the phenanthroline sensitizer, and the efficient sensitization of complexed lanthanide ions.
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12
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Zhao H, Shen A, Xiang YK, Corey DP. Three Recombinant Engineered Antibodies against Recombinant Tags with High Affinity and Specificity. PLoS One 2016; 11:e0150125. [PMID: 26943906 PMCID: PMC4778845 DOI: 10.1371/journal.pone.0150125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/09/2016] [Indexed: 12/03/2022] Open
Abstract
We describe three recombinant engineered antibodies against three recombinant epitope tags, constructed with divalent binding arms to recognize divalent epitopes and so achieve high affinity and specificity. In two versions, an epitope is inserted in tandem into a protein of interest, and a homodimeric antibody is constructed by fusing a high-affinity epitope-binding domain to a human or mouse Fc domain. In a third, a heterodimeric antibody is constructed by fusing two different epitope-binding domains which target two different binding sites in GFP, to polarized Fc fragments. These antibody/epitope pairs have affinities in the low picomolar range and are useful tools for many antibody-based applications.
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Affiliation(s)
- Hongyu Zhao
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ao Shen
- Department of Pharmacology, School of Medicine, University of California, Davis, California, United States of America
| | - Yang K. Xiang
- Department of Pharmacology, School of Medicine, University of California, Davis, California, United States of America
| | - David P. Corey
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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13
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Yu H, Zhou P, Deng M, Shang Z. Indirect Readout in Protein-Peptide Recognition: A Different Story from Classical Biomolecular Recognition. J Chem Inf Model 2014; 54:2022-32. [DOI: 10.1021/ci5000246] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Peng Zhou
- Center
of Bioinformatics (COBI), School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, Sichuan 610054, China
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14
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Brady ML, Moon CE, Jacob TC. Using an α-bungarotoxin binding site tag to study GABA A receptor membrane localization and trafficking. J Vis Exp 2014. [PMID: 24747556 DOI: 10.3791/51365] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
It is increasingly evident that neurotransmitter receptors, including ionotropic GABA A receptors (GABAAR), exhibit highly dynamic trafficking and cell surface mobility(1-7). To study receptor cell surface localization and endocytosis, the technique described here combines the use of fluorescent α-bungarotoxin with cells expressing constructs containing an α-bungarotoxin (Bgt) binding site (BBS). The BBS (WRYYESSLEPYPD) is based on the α subunit of the muscle nicotinic acetylcholine receptor, which binds Bgt with high affinity(8,9). Incorporation of the BBS site allows surface localization and measurements of receptor insertion or removal with application of exogenous fluorescent Bgt, as previously described in the tracking of GABAA and metabotropic GABAB receptors(2,10). In addition to the BBS site, we inserted a pH-sensitive GFP (pHGFP(11)) between amino acids 4 and 5 of the mature GABAAR subunit by standard molecular biology and PCR cloning strategies (see Figure 1)(12). The BBS is 3' of the pH-sensitive GFP reporter, separated by a 13-amino acid alanine/proline linker. For trafficking studies described in this publication that are based on fixed samples, the pHGFP serves as a reporter of total tagged GABAAR subunit protein levels, allowing normalization of the Bgt labeled receptor population to total receptor population. This minimizes cell to cell Bgt staining signal variability resulting from higher or lower baseline expression of the tagged GABAAR subunits. Furthermore the pHGFP tag enables easy identification of construct expressing cells for live or fixed imaging experiments.
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Affiliation(s)
- Megan L Brady
- Pharmacology & Chemical Biology Department, University of Pittsburgh School of Medicine
| | - Charles E Moon
- Pharmacology & Chemical Biology Department, University of Pittsburgh School of Medicine
| | - Tija C Jacob
- Pharmacology & Chemical Biology Department, University of Pittsburgh School of Medicine;
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15
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Modeling the binding mechanism of Alzheimer's Aβ1-42 to nicotinic acetylcholine receptors based on similarity with snake α-neurotoxins. Neurotoxicology 2012; 34:236-42. [PMID: 23022323 DOI: 10.1016/j.neuro.2012.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/14/2012] [Accepted: 09/14/2012] [Indexed: 11/21/2022]
Abstract
For over a decade, it has been known that amyloid β (Aβ) peptides of Alzheimer's disease bind to the nicotinic α7 acetylcholine receptor (AChR) with picomolar affinity, and that snake α-neurotoxins competitively inhibit this binding. Here we propose a model of the binding mechanism of Aβ peptides to α7-AChR at atomic level. The binding mechanism is based on sequence and structure similarities of Aβ residues with functional residues of snake α-neurotoxins (ATX) in complex with AChR. The binding mechanism involves residue (Aβ)K28 (similar to (ATX)R32) which forms cation/π interactions in the acetylcholine binding site, and residues (Aβ)G29-(Aβ)I32 [GAII] (similar to (ATX)G33-(ATX)I36 [GTII]) which form an intermolecular β-sheet with residues (α7)F189-(α7)E191 of AChR. Through these interactions, we propose that the AChR serves as a chaperone for Aβ conformational changes from α- to β-hairpin. The interactions which block channel opening provide fundamental insight into Aβ neurotoxicity and cognition impairment, that could contribute to pathogenic processes in Alzheimer's disease, thus paving the way for structure based therapies.
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16
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Sergeev M, Godin AG, Kao L, Abuladze N, Wiseman PW, Kurtz I. Determination of membrane protein transporter oligomerization in native tissue using spatial fluorescence intensity fluctuation analysis. PLoS One 2012; 7:e36215. [PMID: 22558387 PMCID: PMC3338697 DOI: 10.1371/journal.pone.0036215] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 04/02/2012] [Indexed: 11/18/2022] Open
Abstract
Membrane transporter proteins exist in a complex dynamic equilibrium between various oligomeric states that include monomers, dimers, dimer of dimers and higher order oligomers. Given their sub-optical microscopic resolution size, the oligomerization state of membrane transporters is difficult to quantify without requiring tissue disruption and indirect biochemical methods. Here we present the application of a fluorescence measurement technique which combines fluorescence image moment analysis and spatial intensity distribution analysis (SpIDA) to determine the oligomerization state of membrane proteins in situ. As a model system we analyzed the oligomeric state(s) of the electrogenic sodium bicarbonate cotransporter NBCe1-A in cultured cells and in rat kidney. The approaches that we describe offer for the first time the ability to investigate the oligomeric state of membrane transporter proteins in their native state.
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Affiliation(s)
- Mikhail Sergeev
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Antoine G. Godin
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Liyo Kao
- David Geffen School Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Natalia Abuladze
- David Geffen School Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Paul W. Wiseman
- Department of Physics, McGill University, Montréal, Québec, Canada
- Department of Chemistry, McGill University, Montréal, Québec, Canada
| | - Ira Kurtz
- David Geffen School Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Brain Research Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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Lu CH, Li J, Zhang XL, Zheng AX, Yang HH, Chen X, Chen GN. General Approach for Monitoring Peptide–Protein Interactions Based on Graphene–Peptide Complex. Anal Chem 2011; 83:7276-82. [DOI: 10.1021/ac200617k] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Chun-Hua Lu
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Juan Li
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Xiao-Long Zhang
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Ai-Xian Zheng
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Huang-Hao Yang
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Xi Chen
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Guo-Nan Chen
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
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Abstract
Recent studies suggest that cholesterol binding is widespread among GPCRs (G-protein-coupled receptors). In the present study, we analysed putative cholesterol-induced changes in the OTR [OT (oxytocin) receptor], a prototype of cholesterol-interacting GPCRs. For this purpose, we have created recombinant OTRs that are able to bind two small-sized fluorescence-labelled ligands simultaneously. An OTR antagonist was chosen as one of the ligands. To create a second ligand-binding site, a small-sized α-BTB (bungarotoxin binding) site was inserted at the N-terminus or within the third extracellular loop of the OTR. All receptor constructs were functionally active and bound both ligands with high affinity in the nanomolar range. Measurements of the quenching behaviour, fluorescence anisotropy and energy transfer of both receptor-bound ligands were performed to monitor receptor states at various cholesterol concentrations. The quenching studies suggested no major changes in the molecular environment of the fluorophores in response to cholesterol. The fluorescence anisotropy data indicated that cholesterol affects the dynamics or orientation of the antagonist. The energy transfer efficiency between both ligands clearly increased with increasing cholesterol. Overall, cholesterol induced both a changed orientation and a decreased distance of the receptor-bound ligands, suggesting a more compact receptor state in association with cholesterol.
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19
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Thwin M, Samy RP, Satyanarayanajois SD, Gopalakrishnakone P. Venom neutralization by purified bioactive molecules: Synthetic peptide derivatives of the endogenous PLA2 inhibitory protein PIP (a mini-review). Toxicon 2010; 56:1275-83. [DOI: 10.1016/j.toxicon.2009.12.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 12/17/2009] [Accepted: 12/21/2009] [Indexed: 01/06/2023]
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20
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Abramian AM, Comenencia-Ortiz E, Vithlani M, Tretter EV, Sieghart W, Davies PA, Moss SJ. Protein kinase C phosphorylation regulates membrane insertion of GABAA receptor subtypes that mediate tonic inhibition. J Biol Chem 2010; 285:41795-805. [PMID: 20940303 DOI: 10.1074/jbc.m110.149229] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tonic inhibition in the brain is mediated largely by specialized populations of extrasynaptic receptors, γ-aminobutyric acid receptors (GABA(A)Rs). In the dentate gyrus region of the hippocampus, tonic inhibition is mediated primarily by GABA(A)R subtypes assembled from α4β2/3 with or without the δ subunit. Although the gating of these receptors is subject to dynamic modulation by agents such as anesthetics, barbiturates, and neurosteroids, the cellular mechanisms neurons use to regulate their accumulation on the neuronal plasma membrane remain to be determined. Using immunoprecipitation coupled with metabolic labeling, we demonstrate that the α4 subunit is phosphorylated at Ser(443) by protein kinase C (PKC) in expression systems and hippocampal slices. In addition, the β3 subunit is phosphorylated on serine residues 408/409 by PKC activity, whereas the δ subunit did not appear to be a PKC substrate. We further demonstrate that the PKC-dependent increase of the cell surface expression of α4 subunit-containing GABA(A)Rs is dependent on Ser(443). Mechanistically, phosphorylation of Ser(443) acts to increase the stability of the α4 subunit within the endoplasmic reticulum, thereby increasing the rate of receptor insertion into the plasma membrane. Finally, we show that phosphorylation of Ser(443) increases the activity of α4 subunit-containing GABA(A)Rs by preventing current run-down. These results suggest that PKC-dependent phosphorylation of the α4 subunit plays a significant role in enhancing the cell surface stability and activity of GABA(A)R subtypes that mediate tonic inhibition.
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Affiliation(s)
- Armen M Abramian
- Department of Neuroscience, Tufts University, Boston, Massachusetts 02111, USA
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21
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Silic-Benussi M, Marin O, Biasiotto R, D'Agostino DM, Ciminale V. Effects of human T-cell leukemia virus type 1 (HTLV-1) p13 on mitochondrial K+ permeability: A new member of the viroporin family? FEBS Lett 2010; 584:2070-5. [PMID: 20170654 PMCID: PMC7163934 DOI: 10.1016/j.febslet.2010.02.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 01/29/2010] [Accepted: 02/11/2010] [Indexed: 11/06/2022]
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) encodes a mitochondrial protein named p13. p13 mediates an inward K+ current in isolated mitochondria that leads to mitochondrial swelling, depolarization, increased respiratory chain activity and reactive oxygen species (ROS) production. These effects trigger the opening of the permeability transition pore and are dependent on the presence of K+ and on the amphipathic alpha helical domain of p13. In the context of cells, p13 acts as a sensitizer to selected apoptotic stimuli. Although it is not known whether p13 influences the activity of endogenous K+ channels or forms a channel itself, it shares some structural and functional analogies with viroporins, a class of small integral membrane proteins that form pores and alter membrane permeability.
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Affiliation(s)
- Micol Silic-Benussi
- Department of Oncology and Surgical Sciences, University of Padova, I-35128 Padova, Italy
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23
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24
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Dp71, utrophin and beta-dystroglycan expression and distribution in PC12/L6 cell cocultures. Neuroreport 2008; 18:1657-61. [PMID: 17921863 DOI: 10.1097/wnr.0b013e3282f0e42d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Function of dystrophin Dp71 isoforms is unknown but seems related to neurite outgrowth and synapse formation. To evaluate Dp71 role in myoneural synapses, we established a coculture model using PC12 cells and L6 myotubes and analyzed expression and localization of Dp71 and related proteins, utrophin and beta-dystroglycan, in PC12 cells. Confocal microscopy showed Dp71d isoform in PC12 nuclei, golgi-complex-like and endoplasmic reticulum-like structures, whereas Dp71ab concentrates at neurite tips and cytoplasm, colocalizing with beta-dystroglycan, utrophin, synaptophysin and acetylcholine receptors. Evidences suggest that Dp71ab isoform, unlike Dp71d, may take part in neurite-related processes. This is the first work on Dp and members of Dp-associated protein complex roles in a cell-line based coculturing system, which may be useful in determining Dp71 isoforms associations.
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25
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Activity-dependent ubiquitination of GABA(A) receptors regulates their accumulation at synaptic sites. J Neurosci 2008; 27:13341-51. [PMID: 18045928 DOI: 10.1523/jneurosci.3277-07.2007] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
GABA(A) receptors (GABA(A)Rs) are the major mediators of fast synaptic inhibition in the brain. In neurons, these receptors undergo significant rates of endocytosis and exocytosis, processes that regulate both their accumulation at synaptic sites and the efficacy of synaptic inhibition. Here we have evaluated the role that neuronal activity plays in regulating the residence time of GABA(A)Rs on the plasma membrane and their targeting to synapses. Chronic blockade of neuronal activity dramatically increases the level of the GABA(A)R ubiquitination, decreasing their cell surface stability via a mechanism dependent on the activity of the proteasome. Coincident with this loss of cell surface expression levels, TTX treatment reduced both the amplitude and frequency of miniature inhibitory synaptic currents. Conversely, increasing the level of neuronal activity decreases GABA(A)R ubiquitination enhancing their stability on the plasma membrane. Activity-dependent ubiquitination primarily acts to reduce GABA(A)R stability within the endoplasmic reticulum and, thereby, their insertion into the plasma membrane and subsequent accumulation at synaptic sites. Thus, activity-dependent ubiquitination of GABA(A)Rs and their subsequent proteasomal degradation may represent a potent mechanism to regulate the efficacy of synaptic inhibition and may also contribute to homeostatic synaptic plasticity.
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26
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Takano N, Umezawa K, Ikebe J, Sonobe Y, Yagisawa R, Ito JI, Hamasaki N, Mitomo D, Miyagawa H, Yamagishi A, Higo J. Solvent Site-Dipole Field Accompanying Protein-Ligand Approach Process. CHEM-BIO INFORMATICS JOURNAL 2008. [DOI: 10.1273/cbij.8.14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Norikazu Takano
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Koji Umezawa
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Jinzen Ikebe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Yuki Sonobe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Ryosuke Yagisawa
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Jun-ichi Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Nobuyuki Hamasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Daisuke Mitomo
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | | | - Akihiko Yamagishi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Junichi Higo
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
- The Center for Advanced Medical Engineering and Informatics, Osaka University
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27
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Magidovich E, Orr I, Fass D, Abdu U, Yifrach O. Intrinsic disorder in the C-terminal domain of the Shaker voltage-activated K+ channel modulates its interaction with scaffold proteins. Proc Natl Acad Sci U S A 2007; 104:13022-7. [PMID: 17666528 PMCID: PMC1941827 DOI: 10.1073/pnas.0704059104] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction of membrane-embedded voltage-activated potassium channels (Kv) with intracellular scaffold proteins, such as the postsynaptic density 95 (PSD-95) protein, is mediated by the channel C-terminal segment. This interaction underlies Kv channel clustering at unique membrane sites and is important for the proper assembly and functioning of the synapse. In the current study, we address the molecular mechanism underlying Kv/PSD-95 interaction. We provide experimental evidence, based on hydrodynamic and spectroscopic analyses, indicating that the isolated C-terminal segment of the archetypical Shaker Kv channel (ShB-C) is a random coil, suggesting that ShB-C belongs to the recently defined class of intrinsically disordered proteins. We show that isolated ShB-C is still able to bind its scaffold protein partner and support protein clustering in vivo, indicating that unfoldedness is compatible with ShB-C activity. Pulldown experiments involving C-terminal chains differing in flexibility or length further demonstrate that intrinsic disorder in the C-terminal segment of the Shaker channel modulates its interaction with the PSD-95 protein. Our results thus suggest that the C-terminal domain of the Shaker Kv channel behaves as an entropic chain and support a "fishing rod" molecular mechanism for Kv channel binding to scaffold proteins. The importance of intrinsically disordered protein segments to the complex processes of synapse assembly, maintenance, and function is discussed.
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Affiliation(s)
- Elhanan Magidovich
- *Department of Life Sciences and
- Zlotowski Center for Neurosciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; and
| | - Irit Orr
- *Department of Life Sciences and
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Uri Abdu
- *Department of Life Sciences and
| | - Ofer Yifrach
- *Department of Life Sciences and
- Zlotowski Center for Neurosciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; and
- To whom correspondence should be addressed. E-mail:
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28
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Shelukhina IV, Kryukova EV, Skok MV, Lykhmus EY, Zhmak MN, Mordvintsev DY, Kasheverov IE, Tsetlin VI. Analysis of specificity of antibodies against synthetic fragments of different neuronal nicotinic acetylcholine receptor subunits. BIOCHEMISTRY (MOSCOW) 2006; 71:749-58. [PMID: 16903829 DOI: 10.1134/s0006297906070078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have compared specificity of a panel of polyclonal antibodies against synthetic fragments of the alpha7 subunit of homooligomeric acetylcholine receptor (AChR) and some subunits of heteromeric AChRs. The antibody interaction with extracellular domain of alpha7 subunit of rat AChR (residues 7-208) produced by heterologous expression in E. coli and rat adrenal membranes was investigated by the ELISA method. For comparison, membranes from the Torpedo californica ray electric organ enriched in muscle-type AChR and polyclonal antibodies raised against the extracellular domain (residues 1-209) of the T. californica AChR alpha1 subunit were also used. Antibody specificity was also characterized by Western blot analysis using rat AChR extracellular domain alpha7 (7-208) and the membrane-bound T. californica AChR. Epitope localization was analyzed within the framework of AChR extracellular domain model based on the crystal structure of acetylcholine-binding protein available in the literature. According to this analysis, the 179-190 epitope is located on loop C, which is exposed and mobile. Use of antibodies against alpha7 (179-190) revealed the presence of alpha7 AChR in rat adrenal membranes.
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Affiliation(s)
- I V Shelukhina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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29
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Bogdanov Y, Michels G, Armstrong-Gold C, Haydon PG, Lindstrom J, Pangalos M, Moss SJ. Synaptic GABAA receptors are directly recruited from their extrasynaptic counterparts. EMBO J 2006; 25:4381-9. [PMID: 16946701 PMCID: PMC1570424 DOI: 10.1038/sj.emboj.7601309] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 08/03/2006] [Indexed: 11/08/2022] Open
Abstract
GABAA receptors mediate the majority of fast synaptic inhibition in the brain. The accumulation of these ligand-gated ion channels at synaptic sites is a prerequisite for neuronal inhibition, but the molecular mechanisms underlying this phenomenon remain obscure. To further understand these processes, we have examined the cellular origins of synaptic GABAA receptors. To do so, we have created fluorescent GABAA receptors that are capable of binding -bungarotoxin (Bgt), facilitating the visualization of receptor endocytosis, exocytosis and delivery to synaptic sites. Imaging with Bgt in hippocampal neurons revealed that GABAA receptor endocytosis occurred exclusively at extrasynaptic sites, consistent with the preferential colocalization of extrasynaptic receptors with the AP2 adaptin. Receptor insertion into the plasma membrane was also predominantly extrasynaptic, and pulse-chase analysis revealed that these newly inserted receptors were then able to access directly synaptic sites. Therefore, our results demonstrate that synaptic GABAA receptors are directly recruited from their extrasynaptic counterparts. Moreover, they illustrate a dynamic mechanism for neurons to modulate GABAA receptor number at inhibitory synapses by controlling the stability of extrasynaptic receptors.
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Affiliation(s)
- Yury Bogdanov
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pharmacology, University College, London, UK
| | - Guido Michels
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pharmacology, University College, London, UK
- Department of Internal Medicine III, University of Cologne, Cologne, Germany
| | | | - Philip G Haydon
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Jon Lindstrom
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Stephen J Moss
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pharmacology, University College, London, UK
- Department of Neuroscience, University of Pennsylvania, 145 Johnson Pavilion, Hamilton Walk, Philadelphia, PA 19104, USA. Tel.: +1 215 898 1998; Fax: +1 215 898 1347; E-mail:
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30
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McCann CM, Bareyre FM, Lichtman JW, Sanes JR. Peptide tags for labeling membrane proteins in live cells with multiple fluorophores. Biotechniques 2005; 38:945-52. [PMID: 16018556 DOI: 10.2144/05386it02] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We describe a method to label specific membrane proteins with fluorophores for live imaging. Fusion proteins are generated that incorporate into their extracellular domains short peptide sequences (13-38 amino acids) recognized with high affinity and specificity by protein ligands, alpha-bungarotoxin (BTX), or streptavidin (SA). Many fluorophore- and enzyme-conjugated derivatives of both ligands are commercially available. To demonstrate the general utility of the methods, we tagged a vesicle-associated protein (VAMP2), a receptor tyrosine kinase [muscle-specific kinase (MuSK)], and receptors for three neurotransmitters: acetylcholine (nAChR alpha3), glutamate (mGluR2), and gamma-aminobutyric acid (GABA(A) alpha3). In all cases, we could selectively label surface-exposed proteins without interference from intracellular pools. By successive pulse-labeling with different fluorophore conjugates of a single ligand, we were able to monitor endocytosis of tagged molecules. By combining the two ligands, we could assess co-localization of synaptic components in cells. This strategy for epitope tagging provides a useful adjunct to green fluorescent protein (GFP)-tagging, which fails to distinguish intracellular from extracellular pools, sometimes interferes with protein localization or function, and requires a separate construct for each color.
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31
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Samson AO, Chill JH, Anglister J. Two-dimensional measurement of proton T1rho relaxation in unlabeled proteins: mobility changes in alpha-bungarotoxin upon binding of an acetylcholine receptor peptide. Biochemistry 2005; 44:10926-34. [PMID: 16086595 PMCID: PMC2597414 DOI: 10.1021/bi050645h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A method for the measurement of proton T(1)(rho) relaxation times in unlabeled proteins is described using a variable spin-lock pulse after the initial nonselective 90 degrees excitation in a HOHAHA pulse sequence. The experiment is applied to alpha-bungarotoxin (alpha-BTX) and its complex with a 25-residue peptide derived from the acetylcholine receptor (AChR) alpha-subunit. A good correlation between high T(1)(rho) values and increased local motion is revealed. In the free form, toxin residues associated with receptor binding according to the NMR structure of the alpha-BTX complex with an AChR peptide and the model for alpha-BTX with the AChR [Samson, A. O., et al. (2002) Neuron 35, 319-332] display high mobility. When the AChR peptide binds, a decrease in the relaxation times and the level of motion of residues involved in binding of the receptor alpha-subunit is exhibited, while residues implicated in binding gamma- and delta-subunits retain their mobility. In addition, the quantitative T(1)(rho) measurements enable us to corroborate the mapping of boundaries of the AChR determinant strongly interacting with the toxin [Samson, A. O., et al. (2001) Biochemistry 40, 5464-5473] and can similarly be applied to other protein complexes in which peptides represent one of the two interacting proteins. The presented method is advantageous because of its simplicity, generality, and time efficiency and paves the way for future investigation of proton relaxation rates in small unlabeled proteins.
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Affiliation(s)
| | | | - Jacob Anglister
- To whom correspondence should be addressed. J.A. is the Dr. Joseph and Ruth Owades Professor of Chemistry. Tel: +972−8−9343394, Fax: +972−8−9344136, E-mail:
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Seshasayee ASN, Raghunathan K, Sivaraman K, Pennathur G. Role of hydrophobic interactions and salt-bridges in β-hairpin folding. J Mol Model 2005; 12:197-204. [PMID: 16231193 DOI: 10.1007/s00894-005-0018-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2005] [Accepted: 06/27/2005] [Indexed: 11/30/2022]
Abstract
Beta-hairpins are the simplest form of beta-sheets which, due to the presence of long-range interactions, can be considered as tertiary structures. Molecular dynamics simulation is a powerful tool that can unravel whole pathways of protein folding/unfolding at atomic resolution. We have performed several molecular dynamics simulations, to a total of over 250 ns, of a beta-hairpin peptide in water using GROMACS. We show that hydrophobic interactions are necessary for initiating the folding of the peptide. Once formed, the peptide is stabilized by hydrogen bonds and disruption of hydrophobic interactions in the folded peptide does not denature the structure. In the absence of hydrophobic interactions, the peptide fails to fold. However, the introduction of a salt-bridge compensates for the loss of hydrophobic interactions to a certain extent.
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34
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Byeon WH, Weisblum B. Affinity adsorbent based on combinatorial phage display peptides that bind alpha-cobratoxin. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 805:361-3. [PMID: 15135114 DOI: 10.1016/j.jchromb.2004.03.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2003] [Revised: 03/10/2004] [Accepted: 03/10/2004] [Indexed: 11/28/2022]
Abstract
Combinatorial phage display was used to discover peptides that selectively bind to the alpha-cobratoxin (neurotoxin) component of the multi-component venom of the Thai cobra, Naja kaouthia. Peptide sequences determined in this way were synthesized chemically and were covalently attached to agarose through the alpha-amino terminus. Such affinity chromatography supports selectively bound the alpha-cobratoxin component from crude venom, while passage of the crude venom over the support selectively depleted the venom of this component. The selective binding of alpha-cobratoxin to peptide-based solid-phase supports suggests that a limitless variety of peptides similarly obtained by combinatorial phage display can be used to craft specific analytical and preparative tools.
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35
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Szardenings M. Phage display of random peptide libraries: applications, limits, and potential. J Recept Signal Transduct Res 2004; 23:307-49. [PMID: 14753295 DOI: 10.1081/rrs-120026973] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The identification of ligands from large biological libraries by phage display has now been used for almost 15 years. Most of the successful reports on high-affinity ligand identification originated from work with different antibody libraries. In contrast, the progress of applying phage display to random peptide libraries was relatively slow. However, in the last few years several improvements have led to an increasing number of published peptide ligands identified by phage display from such libraries and which exhibited good biological activity and high affinity. This review summarizes the current state and the technical progress of the application of random peptide libraries using filamentous phage for ligand identification.
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Affiliation(s)
- Michael Szardenings
- Institute of Biochemistry and Biotechnology, Technical University of Braunschweig, Braunschweig, Germany.
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36
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Hsieh HC, Kumar TKS, Yu C. Cloning, overexpression, and characterization of cobrotoxin. Biochem Biophys Res Commun 2004; 320:1374-81. [PMID: 15303285 DOI: 10.1016/j.bbrc.2004.06.091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cobrotoxin (CBTX) is a highly toxic short neurotoxin, isolated from the Taiwan cobra (Naja naja atra) venom. In the present study for the first time we report the cloning and expression of CBTX in high yields (12mg/L) in Escherichia coli. CBTX fused to the IgG-binding domain of protein A (IgG-CBTX) was expressed in the soluble form. The misfolded CBTX portion (of the overexpressed fusion protein) was refolded under optimal redox conditions. The fusion protein (IgG-CBTX) was observed to undergo auto-catalytic cleavage to yield CBTX with additional 5 amino acids upstream of its N-terminal end. The far UV and near UV circular dichroism spectra of the recombinant CBTX were identical to those of the toxin isolated from the crude venom source. Recombinant CBTX was isotope labeled (15N and 13C) and all the resonances ('H, 13C, and 15N) in the protein have been unambiguously assigned. ' H '5N HSQC spectrum of recombinant CBTX revealed that the protein is in a biologically active conformation. 1H-15Nchemical shift perturbation data showed that recombinant CBTX binds to a peptide derived from the alpha7 subunit of the Torpedo acetylcholine receptor (AchR) with high affinity. The AchR peptide is found to bind to residues located at the tip of Loop-2 in CBTX. The results of the present study provide an avenue to understand the structural basis for the high toxicity exhibited by CBTX. In addition, complete resonance assignments in CBTX (reported in this study) are expected to trigger intensive research towards the design of new pharmacological agents against certain neural disorders.
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Affiliation(s)
- Hui-Chu Hsieh
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, ROC
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37
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Bernini A, Ciutti A, Spiga O, Scarselli M, Klein S, Vannetti S, Bracci L, Lozzi L, Lelli B, Falciani C, Neri P, Niccolai N. NMR and MD Studies on the Interaction Between Ligand Peptides and α-Bungarotoxin. J Mol Biol 2004; 339:1169-77. [PMID: 15178256 DOI: 10.1016/j.jmb.2004.04.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2004] [Revised: 04/07/2004] [Accepted: 04/21/2004] [Indexed: 11/18/2022]
Abstract
The interaction between alpha-bungarotoxin and linear synthetic peptides, mimotope of the nicotinic acetylcholine receptor binding site, has been characterised extensively by several methods and a wealth of functional, kinetic and structural data are available. Hence, this system represents a suitable model to explore in detail the dynamics of a peptide-protein interaction. Here, the solution structure of a new complex of the protein toxin with a tridecapeptide ligand exhibiting high affinity has been determined by NMR. As observed for three other previously reported mimotope-alpha-bungarotoxin complexes, also in this case correlations between biological activity and kinetic data are not fully consistent with a static discussion of structural data. Molecular dynamics simulations of the four mimotope-toxin complexes indicate that a relevant contribution to the complex stability is given by the extent of the residual flexibility that the protein maintains upon peptide binding. This feature, limiting the entropy loss caused by protein folding and binding, ought to be generally considered in a rational design of specific protein ligands.
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Affiliation(s)
- Andrea Bernini
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, via Fiorentina 1, I-53100 Siena, Italy.
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Matsubara T, Hiura Y, Kawahito O, Yasuzawa M, Kawashiro K. Selection of novel structural zinc sites from a random peptide library. FEBS Lett 2004; 555:317-21. [PMID: 14644435 DOI: 10.1016/s0014-5793(03)01266-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Zinc ion (Zn(2+)) can be coordinated with four or three amino acid residues to stabilize a protein's structure or to form a catalytic active center. We used phage display selection of a dodecamer random peptide library with Zn(2+) to identify structural zinc sites. The binding specificity for Zn(2+) of selected sequences was confirmed using enzyme-linked immunosorbent and competitive inhibition assays. Circular dichroism spectra indicated that the interaction with Zn(2+) induced a change in conformation, which means the peptide acts as a structural zinc site. Furthermore, a search of protein databases revealed that two selected sequences corresponded to parts of natural zinc sites of copper/zinc superoxide dismutase and zinc-containing ferredoxin. We demonstrated that Zn(2+)-binding sequences selected from the random combinatorial library would be candidates for artificial structural zinc sites.
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Affiliation(s)
- Teruhiko Matsubara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
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Coulon S, Metais JY, Chartier M, Briand JP, Baty D. Cyclic peptides selected by phage display mimic the natural epitope recognized by a monoclonal anti-colicin A antibody. J Pept Sci 2004; 10:648-58. [PMID: 15568679 DOI: 10.1002/psc.574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A 10-mer random peptide library displayed on filamentous bacteriophage was used to determine the molecular basis of the interaction between the monoclonal anti-colicin A antibody 1C11 and its cognate epitope. Previous studies established that the putative epitope recognized by 1C11 antibody is composed of amino acid residues 19-25 (RGSGPEP) of colicin A. Using the phage display technique it was confirmed that the epitope of 1C11 antibody was indeed restricted to residues 19-25 and the consensus motif RXXXPEP was identified. Shorter consensus sequences (RXXPEP, RXXEP, KXXEP) were also selected. It was also demonstrated that the disulfide bond found in one group of the selected peptides was crucial for 1C11 antibody recognition. It was shown that cyclization of the peptides by disulfide bond formation could result in a structure that mimics the natural epitope of colicin A.
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Affiliation(s)
- Stephane Coulon
- The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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40
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Katchalski-Katzir E, Kasher R, Balass M, Scherf T, Harel M, Fridkin M, Sussman JL, Fuchs S. Design and synthesis of peptides that bind alpha-bungarotoxin with high affinity and mimic the three-dimensional structure of the binding-site of acetylcholine receptor. Biophys Chem 2003; 100:293-305. [PMID: 12646372 DOI: 10.1016/s0301-4622(02)00287-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Alpha-bungarotoxin (alpha-BTX) is a highly toxic snake neurotoxin that binds to acetylcholine receptor (AChR) at the neuromuscular junction, and is a potent inhibitor of this receptor. In the following we review multi-phase research of the design, synthesis and structure analysis of peptides that bind alpha-BTX and inhibit its binding to AChR. Structure-based design concomitant with biological information of the alpha-BTX/AChR system yielded 13-mer peptides that bind to alpha-BTX with high affinity and are potent inhibitors of alpha-BTX binding to AChR (IC(50) of 2 nM). X-Ray and NMR spectroscopy reveal that the high-affinity peptides fold into an anti-parallel beta-hairpin structure when bound to alpha-BTX. The structures of the bound peptides and the homologous loop of acetylcholine binding protein, a soluble analog of AChR, are remarkably similar. Their superposition indicates that the toxin wraps around the binding-site loop, and in addition, binds tightly at the interface of two of the receptor subunits and blocks access of acetylcholine to its binding site. The procedure described in this article may serve as a paradigm for obtaining high-affinity peptides in biochemical systems that contain a ligand and a receptor molecule.
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41
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Fuchs S, Kasher R, Balass M, Scherf T, Harel M, Fridkin M, Sussman JL, Katchalski-Katzir E. The binding site of acetylcholine receptor: from synthetic peptides to solution and crystal structure. Ann N Y Acad Sci 2003; 998:93-100. [PMID: 14592866 DOI: 10.1196/annals.1254.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Our group has been employing short synthetic peptides, encompassing sequences from the acetylcholine receptor (AChR) alpha-subunit for the analysis of the binding site of the AChR. A 13-mer peptide mimotope, with similar structural motifs to the AChR binding region, was selected by alpha-bungarotoxin (alpha-BTX) from a phage-display peptide library. The solution structure of a complex between this library-lead peptide and alpha-BTX was solved by NMR spectroscopy. On the basis of this NMR study and on structure-function analysis of the AChR binding site, and in order to obtain peptides with higher affinity to alpha-BTX, additional peptides resulting from systematic residue replacement in the lead peptide were designed and characterized. Of these, four peptides, designated high-affinity peptides (HAPs), homologous to the binding region of the AChR, inhibited the binding of alpha-BTX to the AChR with an IC(50) of 2 nM. The solution and crystal structures of complexes of alpha-BTX with HAP were solved, demonstrating that the HAP fits snugly to alpha-BTX and adopts a beta-hairpin conformation. The X-ray structures of the bound HAP and the homologous loop of the acetylcholine binding protein (AChBP) are remarkably similar. Their superposition results in a model indicating that alpha-BTX wraps around the receptor binding-site loop and, in addition, binds tightly at the interface of two of the receptor subunits, where it inserts a finger into the ligand-binding site. Our proposed model explains the strong antagonistic activity of alpha-BTX and accommodates much of the biochemical data on the mode of interaction of alpha-BTX with the AChR.
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Affiliation(s)
- Sara Fuchs
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel.
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42
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Zeev-Ben-Mordehai T, Rydberg EH, Solomon A, Toker L, Auld VJ, Silman I, Botti S, Sussman JL. The intracellular domain of theDrosophila cholinesterase-like neural adhesion protein, gliotactin, is natively unfolded. Proteins 2003; 53:758-67. [PMID: 14579366 DOI: 10.1002/prot.10471] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Drosophila gliotactin (Gli) is a 109-kDa transmembrane, cholinesterase-like adhesion molecule (CLAM), expressed in peripheral glia, that is crucial for formation of the blood-nerve barrier. The intracellular portion (Gli-cyt) was cloned and expressed in the cytosolic fraction of Escherichia coli BLR(DE3) at 45 mg/L and purified by Ni-NTA (nitrilotriacetic acid) chromatography. Although migration on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), under denaturing conditions, was unusually slow, molecular weight determination by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) confirmed that the product was consistent with its theoretical size. Gel filtration chromatography yielded an anomalously large Stokes radius, suggesting a fully unfolded conformation. Circular dichroism (CD) spectroscopy demonstrated that Gli-cyt was >50% unfolded, further suggesting a nonglobular conformation. Finally, 1D-(1)H NMR conclusively demonstrated that Gli-cyt possesses an extended unfolded structure. In addition, Gli-cyt was shown to possess charge and hydrophobic properties characteristic of natively unfolded proteins (i.e., proteins that, when purified, are intrinsically disordered under physiologic conditions in vitro).
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Han ZY, Wu KC, He FT, Han QL, Nie YZ, Han Y, Liu XN, Zheng JY, Xu MH, Lin T, Fan DM. Screening and identification of mimotope of gastric cancer associated antigen MGb1-Ag. World J Gastroenterol 2003; 9:1920-4. [PMID: 12970876 PMCID: PMC4656644 DOI: 10.3748/wjg.v9.i9.1920] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: Using a monoclonal antibody against gastric cancer antigen named MGb1 to screen a phage-displayed random peptide library fused with coat protein pIII in order to get some information on mimotopes.
METHODS: Through affinity enrichment and ELISA screening, positive clones of phages were amplified. 10 phage clones were selected after three rounds of biopanning and the ability of specific binding of the positive phage clones to MGb1-Ab were detected by ELISA assay (DNA sequencing was performed and the amino acid sequences were deduced) By blocking test, specificity of the mimic phage epitopes was identified.
RESULTS: There were approximately 200 times of enrichment about the titer of bound phages after three rounds of biopanning procedures. DNA of 10 phage clones after the third biopanning was assayed and the result showed that the positive clones had a specific binding activity to MGb1-Ab and a weak ability of binding to control mAb or to mouse IgG. DNA sequencing of 10 phage clones was performed and the amino acid sequences were deduced. According to the homology of the amino acid sequences of the displayed peptides, most of the phage clones had motifs of H(x)Q or L(x)S. And these 10 phage clones could also partly inhibit the binding of MGb1-Ab to gastric cancer cell KATO-III. The percentage of blocking was from (21.0 ± 1.6)% to (39.0 ± 2.7)%.
CONCLUSION: Motifs of H(x)Q and L(x)S selected and identified show a high homology in the mimic epitopes of gastric cancer associated antigen. There may be one or more clones which can act as candidates of tumor vaccines.
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Affiliation(s)
- Zhe-Yi Han
- Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
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Sillerud LO, Burks EJ, Wester MJ, Brown DC, Vijayan S, Larson RS. NMR-derived model of interconverting conformations of an ICAM-1 inhibitory cyclic nonapeptide. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2003; 62:97-116. [PMID: 12895272 DOI: 10.1034/j.1399-3011.2003.00070.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have produced by phage-display a disulfide-linked cyclic nonapeptide (inhibitory peptide-01, IP01), CLLRMRSIC, that binds to intracellular adhesion molecule-1 (ICAM-1) and blocks binding to its counter-structure, leukocyte functional antigen-1 (LFA-1). As a first step towards improving its pharmacologic properties, we have performed a structural and functional analysis of this peptide inhibitor to determine the features relevant to ICAM-1 binding. We report here the solution model of our initial product, IP01, as derived from two-dimensional nuclear magnetic resonance (NMR) restraints and molecular modeling. Distance and dihedral angle restraints, generated from nuclear Overhauser effect spectroscopy (NOESY) and one-dimensional-NMR experiments respectively, were used to generate an ensemble of structures using distance geometry and simulated annealing. Molecular dynamic simulations produced three interconverting conformational families consistent with the NMR-derived constraints. We describe these conformations and their mechanism of interconversion. Furthermore, we have measured the IC50 s of a series of inhibitors generated from IP01 through alanine substitution of each residue. These results show that the L2-L3-R4-M5-R6 segment is functionally active, conformationally flexible, and contains a beta-turn involving residues R4-S7, while the C1-C9-I8-S7 segment is less functionally-active but adopts a more defined solution conformation, consistent with a scaffolding function. This model will be useful for designing nonpeptide-based organic inhibitors with improved pharmacologic properties.
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Affiliation(s)
- L O Sillerud
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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45
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Lozzi L, Lelli B, Runci Y, Scali S, Bernini A, Falciani C, Pini A, Niccolai N, Neri P, Bracci L. Rational design and molecular diversity for the construction of anti-alpha-bungarotoxin antidotes with high affinity and in vivo efficiency. CHEMISTRY & BIOLOGY 2003; 10:411-7. [PMID: 12770823 DOI: 10.1016/s1074-5521(03)00094-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The structure of peptide p6.7, a mimotope of the nicotinic receptor ligand site that binds alpha-bungarotoxin and neutralizes its toxicity, was compared to that of the acetylcholine binding protein. The central loop of p6.7, when complexed with alpha-bungarotoxin, fits the structure of the acetylcholine binding protein (AChBP) ligand site, whereas peptide terminal residues seem to be less involved in toxin binding. The minimal binding sequence of p6.7 was confirmed experimentally by synthesis of progressively deleted peptides. Affinity maturation was then achieved by random addition of residues flanking the minimal binding sequence and by selection of new alpha-bungarotoxin binding peptides on the basis of their dissociation kinetic rate. The tetra-branched forms of the resulting high-affinity peptides were effective as antidotes in vivo at a significantly lower dose than the tetra-branched lead peptide.
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Affiliation(s)
- Luisa Lozzi
- Department of Molecular Biology, University of Siena, via Fiorentina 1, I-53100 Siena, Italy
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Abstract
Protein-protein interactions mediate essentially all biological processes. A detailed understanding of these interactions is thus a major goal of modern biological chemistry. In recent years, genome sequencing efforts have revealed tens of thousands of novel genes, but the benefits of genome sequences will only be realized if these data can be translated to the level of protein function. While genome databases offer tremendous opportunities to expand our knowledge of protein-protein interactions, they also present formidable challenges to traditional protein chemistry methods. Indeed, it has become apparent that efficient analysis of proteins on a proteome-wide scale will require the use of rapid combinatorial approaches. In this regard, phage display is an established combinatorial technology that is likely to play an even greater role in the future of biology. This article reviews recent applications of phage display to the analysis of protein-protein interactions. With combinatorial mutagenesis strategies, it is now possible to rapidly map the binding energetics at protein-protein interfaces through statistical analysis of phage-displayed protein libraries. In addition, naïve phage-displayed peptide libraries can be used to obtain small peptide ligands to essentially any protein of interest, and in many cases, these binding peptides act as antagonists or even agonists of natural protein functions. These methods are accelerating the pace of research by enabling the study of complex protein-protein interactions with simple molecular biology methods. With further optimization and automation, it may soon be possible to study hundreds of different proteins in parallel with efforts comparable to those currently expended on the analysis of individual proteins.
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Affiliation(s)
- Sachdev S Sidhu
- Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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47
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Moise L, Zeng H, Caffery P, Rogowski RS, Hawrot E. STRUCTURE AND FUNCTION OF α-BUNGAROTOXIN. ACTA ACUST UNITED AC 2002. [DOI: 10.1081/txr-120014407] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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48
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Zeng H, Hawrot E. NMR-based binding screen and structural analysis of the complex formed between alpha-cobratoxin and an 18-mer cognate peptide derived from the alpha 1 subunit of the nicotinic acetylcholine receptor from Torpedo californica. J Biol Chem 2002; 277:37439-45. [PMID: 12133834 DOI: 10.1074/jbc.m205483200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The alpha18-mer peptide, spanning residues 181-198 of the Torpedo nicotinic acetylcholine receptor alpha1 subunit, contains key binding determinants for agonists and competitive antagonists. To investigate whether the alpha18-mer can bind other alpha-neurotoxins besides alpha-bungarotoxin, we designed a two-dimensional (1)H-(15)N heteronuclear single quantum correlation experiment to screen four related neurotoxins for their binding ability to the peptide. Of the four toxins tested (erabutoxin a, erabutoxin b, LSIII, and alpha-cobratoxin), only alpha-cobratoxin binds the alpha18-mer to form a 1:1 complex. The NMR solution structure of the alpha-cobratoxin.alpha18-mer complex was determined with a backbone root mean square deviation of 1.46 A. In the structure, alpha-cobratoxin contacts the alpha18-mer at the tips of loop I and II and through C-terminal cationic residues. The contact zone derived from the intermolecular nuclear Overhauser effects is in agreement with recent biochemical data. Furthermore, the structural models support the involvement of cation-pi interactions in stabilizing the complex. In addition, the binding screen results suggest that C-terminal cationic residues of alpha-bungarotoxin and alpha-cobratoxin contribute significantly to binding of the alpha18-mer. Finally, we present a structural model for nicotinic acetylcholine receptor-alpha-cobratoxin interaction by superimposing the alpha-cobratoxin.alpha18-mer complex onto the crystal structure of the acetylcholine-binding protein (Protein Data Bank code ).
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Affiliation(s)
- Haoyu Zeng
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown Medical School, Providence, Rhode Island 02912, USA
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Samson A, Scherf T, Eisenstein M, Chill J, Anglister J. The mechanism for acetylcholine receptor inhibition by alpha-neurotoxins and species-specific resistance to alpha-bungarotoxin revealed by NMR. Neuron 2002; 35:319-32. [PMID: 12160749 DOI: 10.1016/s0896-6273(02)00773-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The structure of a peptide corresponding to residues 182-202 of the acetylcholine receptor alpha1 subunit in complex with alpha-bungarotoxin was solved using NMR spectroscopy. The peptide contains the complete sequence of the major determinant of AChR involved in alpha-bungarotoxin binding. One face of the long beta hairpin formed by the AChR peptide consists of exposed nonconserved residues, which interact extensively with the toxin. Mutations of these receptor residues confer resistance to the toxin. Conserved AChR residues form the opposite face of the beta hairpin, which creates the inner and partially hidden pocket for acetylcholine. An NMR-derived model for the receptor complex with two alpha-bungarotoxin molecules shows that this pocket is occupied by the conserved alpha-neurotoxin residue R36, which forms cation-pi interactions with both alphaW149 and gammaW55/deltaW57 of the receptor and mimics acetylcholine.
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Affiliation(s)
- Abraham Samson
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
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Moise L, Piserchio A, Basus VJ, Hawrot E. NMR structural analysis of alpha-bungarotoxin and its complex with the principal alpha-neurotoxin-binding sequence on the alpha 7 subunit of a neuronal nicotinic acetylcholine receptor. J Biol Chem 2002; 277:12406-17. [PMID: 11790782 DOI: 10.1074/jbc.m110320200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report a new, higher resolution NMR structure of alpha-bungarotoxin that defines the structure-determining disulfide core and beta-sheet regions. We further report the NMR structure of the stoichiometric complex formed between alpha-bungarotoxin and a recombinantly expressed 19-mer peptide ((178)IPGKRTESFYECCKEPYPD(196)) derived from the alpha7 subunit of the chick neuronal nicotinic acetylcholine receptor. A comparison of these two structures reveals binding-induced stabilization of the flexible tip of finger II in alpha-bungarotoxin. The conformational rearrangements in the toxin create an extensive binding surface involving both sides of the alpha7 19-mer hairpin-like structure. At the contact zone, Ala(7), Ser(9), and Ile(11) in finger I and Arg(36), Lys(38), Val(39), and Val(40) in finger II of alpha-bungarotoxin interface with Phe(186), Tyr(187), Glu(188), and Tyr(194) in the alpha7 19-mer underscoring the importance of receptor aromatic residues as critical neurotoxin-binding determinants. Superimposing the structure of the complex onto that of the acetylcholine-binding protein (1I9B), a soluble homologue of the extracellular domain of the alpha7 receptor, places alpha-bungarotoxin at the peripheral surface of the inter-subunit interface occluding the agonist-binding site. The disulfide-rich core of alpha-bungarotoxin is suggested to be tilted in the direction of the membrane surface with finger II extending into the proposed ligand-binding cavity.
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Affiliation(s)
- Leonard Moise
- Department of Molecular Pharmacology, Brown University, Providence, Rhode Island 02912, USA
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