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Dubovskii PV, Dubova KM, Bourenkov G, Starkov VG, Konshina AG, Efremov RG, Utkin YN, Samygina VR. Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling. Toxins (Basel) 2022; 14:toxins14020149. [PMID: 35202176 PMCID: PMC8880459 DOI: 10.3390/toxins14020149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/05/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
Cobra cytotoxins (CTs) belong to the three-fingered protein family and possess membrane activity. Here, we studied cytotoxin 13 from Naja naja cobra venom (CT13Nn). For the first time, a spatial model of CT13Nn with both “water” and “membrane” conformations of the central loop (loop-2) were determined by X-ray crystallography. The “water” conformation of the loop was frequently observed. It was similar to the structure of loop-2 of numerous CTs, determined by either NMR spectroscopy in aqueous solution, or the X-ray method. The “membrane” conformation is rare one and, to date has only been observed by NMR for a single cytotoxin 1 from N. oxiana (CT1No) in detergent micelle. Both CT13Nn and CT1No are S-type CTs. Membrane-binding of these CTs probably involves an additional step—the conformational transformation of the loop-2. To confirm this suggestion, we conducted molecular dynamics simulations of both CT1No and CT13Nn in the Highly Mimetic Membrane Model of palmitoiloleoylphosphatidylglycerol, starting with their “water” NMR models. We found that the both toxins transform their “water” conformation of loop-2 into the “membrane” one during the insertion process. This supports the hypothesis that the S-type CTs, unlike their P-type counterparts, require conformational adaptation of loop-2 during interaction with lipid membranes.
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Affiliation(s)
- Peter V. Dubovskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia; (V.G.S.); (A.G.K.); (R.G.E.); (Y.N.U.)
- Correspondence: or
| | - Kira M. Dubova
- FSRC “Crystallography and Photonics”, Russian Academy of Sciences, 111933 Moscow, Russia; (K.M.D.); (V.R.S.)
- NRC “Kurchatov Institute”, 123182 Moscow, Russia
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, 22607 Hamburg, Germany;
| | - Vladislav G. Starkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia; (V.G.S.); (A.G.K.); (R.G.E.); (Y.N.U.)
| | - Anastasia G. Konshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia; (V.G.S.); (A.G.K.); (R.G.E.); (Y.N.U.)
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia; (V.G.S.); (A.G.K.); (R.G.E.); (Y.N.U.)
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., 141700 Dolgoprudny, Russia
- Higher School of Economics, National Research University, 20 Myasnitskaya str., 101000 Moscow, Russia
| | - Yuri N. Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia; (V.G.S.); (A.G.K.); (R.G.E.); (Y.N.U.)
| | - Valeriya R. Samygina
- FSRC “Crystallography and Photonics”, Russian Academy of Sciences, 111933 Moscow, Russia; (K.M.D.); (V.R.S.)
- NRC “Kurchatov Institute”, 123182 Moscow, Russia
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Chen ST, Wang KT. Facile Synthesis of Biologically Active Peptides Using Phase Transfer Reagents as C-Terminal Protecting Group. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199100016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Wu CY, Chen ST, Ho CL, Wang KT. Engineering of Cardiotoxin by Chemical Synthesis: (I) Rapid Synthesis of Fully Active Cardiotoxin II and IV of Taiwan Cobra Venom. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199600011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Facile Peptide-Bond Formation Using Polystyrene-Bound o-Nitrophenol as an Active Ester. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199300075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Chen ST, Chang CH, Lin J, Wang KT. Selective Alkaline Protease Catalyzed Hydrolysis of Peptide Esters. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199000041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Chang LS, Lin J, Wu PF. cDNA sequence analysis and expression of cardiotoxin V and a new cardiotoxin VII from Naja naja atra (Taiwan cobra). BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1295:1-4. [PMID: 8679666 DOI: 10.1016/0167-4838(96)00047-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The cDNAs encoding cardiotoxin V and a new cardiotoxin VII were constructed from the cellular RNA isolated from the venom glands of Naja naja atra by reverse transcription-polymerase chain reaction. Although 95% nucleotide sequence homology was observed with the two cardiotoxins, there were nine amino-acid substitutions between cardiotoxin V and cardiotoxin VII. The cardiotoxins were subcloned into the expression vector pET 20b(+) and transformed into BL21(DE3) E. coli strain. The expressed protein was isolated from the inclusion bodies of E. coli, and purified by reverse-phase high-performance liquid chromatography. The purified recombinant cardiotoxin showed immunoreactivity with anti-cardiotoxin III antibodies as revealed by immunoblot analysis.
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Affiliation(s)
- L S Chang
- Department of Biochemistry, Kaohsiung Medical College, Taiwan, ROC.
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Fletcher JE, Jiang MS. Possible mechanisms of action of cobra snake venom cardiotoxins and bee venom melittin. Toxicon 1993; 31:669-95. [PMID: 8342168 DOI: 10.1016/0041-0101(93)90375-s] [Citation(s) in RCA: 116] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cobra snake venom cardiotoxins and bee venom melittin share a number of pharmacological properties in intact tissues including hemolysis, cytolysis, contractures of muscle, membrane depolarization and activation of tissue phospholipase C and, to a far lesser extent, an arachidonic acid-associated phospholipase A2. The toxins have also been demonstrated to open the Ca2+ release channel (ryanodine receptor) and alter the activity of the Ca(2+)+Mg(2+)-ATPase in isolated sarcoplasmic reticulum preparations derived from cardiac or skeletal muscle. However, a relationship of these actions in isolated organelles to contracture induction has not yet been established. The toxins also bind to and, in some cases, alter the function of a number of other proteins in disrupted tissues. The most difficult tasks in understanding the mechanism of action of these toxins have been dissociating the primary from secondary effects and distinguishing between effects that only occur in disrupted tissues and those that occur in intact tissue. The use of cardiotoxin and melittin fractions contaminated with trace ('undetectable') amounts of venom-derived phospholipases A2 has continued to be common practice, despite the problems associated with the synergism between the toxins and enzymes and the availability of methods to overcome this problem. With adequate precautions taken with regard to methodology and interpretation of results, the cobra venom cardiotoxins and bee venom melittin may prove to be useful probes of a number of cell processes, including lipid metabolism and Ca2+ regulation in skeletal and cardiac muscle.
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Affiliation(s)
- J E Fletcher
- Department of Anesthesiology, Hahnemann University, Philadelphia, PA 19102-1192
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Abstract
The synthetic approach to the structure-function relationship of lapemis toxin has been very useful in clarifying the important binding regions. To identify the neurotoxic binding domain(s) of lapemis toxin, several peptides were synthesized using the 9-fluorenylmethoxycarbonyl protocols. These peptides were based on the sequence of lapemis toxin, a 60-amino-acid, short-chain postsynaptic neurotoxin found in sea snake (Lapemis hardwickii) venom. The peptides were purified using high-performance liquid chromatography and sequenced to verify the correct synthesis, isolation, and purity. The synthetic peptide names and single letter sequences were Peptide A1 (15 mer) CCNQQSSQPKTTTNC Peptide B1 (18 mer) CYKKTWSDHRGTRIERGC Peptide B2 (16 mer) YKKTWSDHRGTRIERG Peptide C1 (12 mer) CPQVKPGIKLEC Peptide NS (20 mer) EACDFGHIKLMNPQRSTVWY. The peptide NS (nonsense peptide) sequence was arbitrarily determined and used as a control peptide. Biological activities of the synthetic peptides were determined by in vivo as well as by in vitro assay methods. For the in vivo assay, lethality was determined by intravenous injection in mice (Swiss Webster). For the in vitro assay, peptide binding to the Torpedo californica nicotinic acetylcholine receptor was determined. The peptides were found to be nontoxic at approximately 114 times the known LD50 of lapemis toxin. Binding studies with 125I-radiolabeled lapemis toxin and tyrosine-containing peptides indicated that lapemis toxin and peptide B1 bound the receptor, while the other peptides had no detectable binding. The central loop domain of lapemis toxin (peptide B1) plays a dominate role in the toxin's binding ability to the receptor. These results and the hydrophilicity analysis predict peptide B1 may serve as an antagonist or antigen to neutralize the neurotoxin effects in vivo.
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Affiliation(s)
- R A Miller
- Department of Biochemistry, Colorado State University, Fort Collins 80523
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Yu HM, Chen ST, Chiou SH, Wang KT. Determination of amino acids on Merrifield resin by microwave hydrolysis. J Chromatogr A 1988; 456:357-62. [PMID: 3243875 DOI: 10.1016/0021-9673(86)80032-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- H M Yu
- Institute of Biochemical Sciences, National Taiwan University, Taipei
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Wu SS, Tseng MJ, Wang KT. Separation of four cardiotoxins of Taiwan cobra (Naja Naja atra) by reversed-phase high-performance liquid chromatography. J Chromatogr A 1982. [DOI: 10.1016/s0021-9673(00)81716-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
It has been established that cardiotoxins isolated from Elapidae snakes tend to be contaminated with phospholipase. After a thorough comparison of the methods available for the separation of these two components, both hydrophobic and immunoaffinity chromatography have been found to be convenient and effective methods. With cardiotoxins isolated from Naja naja siamensis we observed that as the contaminating phospholipase was removed, the cardiotoxins were converted from relatively powerful haemolytic agents to essentially nonlytic agents. In contrast, removal of the contaminating phospholipase did not abolish the ability of the cardiotoxins to contract smooth muscle. Homologous toxins isolated from Naja melanoleuca and Haematchatus haematchates have been isolated with powerful lytic activity and weak or low cardiotoxicity. This data is interpreted in the light of the homologous group of cardiotoxins possessing two different properties (1) cardiotoxicity and (2) lytic activity; some molecules in the group possess both properties and other possess only one or the other. Structure activity relationships are presented in support of this concept.
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Narita M, Itsuno SI, Hirata M, Kusano K. Liquid-phase Peptide Synthesis by Fragment Condensation on a Soluble Polymer Support. III. The Influence of the Content and the Chain Length of a Peptide Anchored to a Soluble Polymer Support on the Reactivity of the Amino-free Terminal of the Peptide. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1980. [DOI: 10.1246/bcsj.53.1028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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