1
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Olinger E, Schaeffer C, Kidd K, Elhassan EAE, Cheng Y, Dufour I, Schiano G, Mabillard H, Pasqualetto E, Hofmann P, Fuster DG, Kistler AD, Wilson IJ, Kmoch S, Raymond L, Robert T, Eckardt KU, Bleyer AJ, Köttgen A, Conlon PJ, Wiesener M, Sayer JA, Rampoldi L, Devuyst O. An intermediate-effect size variant in UMOD confers risk for chronic kidney disease. Proc Natl Acad Sci U S A 2022; 119:e2114734119. [PMID: 35947615 PMCID: PMC9388113 DOI: 10.1073/pnas.2114734119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/04/2022] [Indexed: 12/12/2022] Open
Abstract
The kidney-specific gene UMOD encodes for uromodulin, the most abundant protein excreted in normal urine. Rare large-effect variants in UMOD cause autosomal dominant tubulointerstitial kidney disease (ADTKD), while common low-impact variants strongly associate with kidney function and the risk of chronic kidney disease (CKD) in the general population. It is unknown whether intermediate-effect variants in UMOD contribute to CKD. Here, candidate intermediate-effect UMOD variants were identified using large-population and ADTKD cohorts. Biological and phenotypical effects were investigated using cell models, in silico simulations, patient samples, and international databases and biobanks. Eight UMOD missense variants reported in ADTKD are present in the Genome Aggregation Database (gnomAD), with minor allele frequency (MAF) ranging from 10-5 to 10-3. Among them, the missense variant p.Thr62Pro is detected in ∼1/1,000 individuals of European ancestry, shows incomplete penetrance but a high genetic load in familial clusters of CKD, and is associated with kidney failure in the 100,000 Genomes Project (odds ratio [OR] = 3.99 [1.84 to 8.98]) and the UK Biobank (OR = 4.12 [1.32 to 12.85). Compared with canonical ADTKD mutations, the p.Thr62Pro carriers displayed reduced disease severity, with slower progression of CKD and an intermediate reduction of urinary uromodulin levels, in line with an intermediate trafficking defect in vitro and modest induction of endoplasmic reticulum (ER) stress. Identification of an intermediate-effect UMOD variant completes the spectrum of UMOD-associated kidney diseases and provides insights into the mechanisms of ADTKD and the genetic architecture of CKD.
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Affiliation(s)
- Eric Olinger
- Institute of Physiology, University of Zurich, CH-8057 Zurich, Switzerland
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Céline Schaeffer
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan, 20132 Italy
| | - Kendrah Kidd
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
| | - Elhussein A. E. Elhassan
- Division of Nephrology, Beaumont General Hospital, 1297 Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, 1297 Dublin, Ireland
| | - Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, D-79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, D-79106 Freiburg, Germany
| | - Inès Dufour
- Institute of Physiology, University of Zurich, CH-8057 Zurich, Switzerland
- Division of Nephrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Guglielmo Schiano
- Institute of Physiology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Holly Mabillard
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
- Renal Services, Newcastle Upon Tyne Hospitals National Health Service Trust, Newcastle upon Tyne NE7 7DN, United Kingdom
| | - Elena Pasqualetto
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan, 20132 Italy
| | - Patrick Hofmann
- Institute of Physiology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Daniel G. Fuster
- Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Andreas D. Kistler
- Department of Medicine, Cantonal Hospital Frauenfeld, 8501 Frauenfeld, Switzerland
| | - Ian J. Wilson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Stanislav Kmoch
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
| | - Laure Raymond
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, 69007 France
| | - Thomas Robert
- Centre de Néphrologie et Transplantation Rénale, Centre Hospitalier Universitaire (CHU) la Conception, Assistance Publique - Hôpitaux de Marseille (AP-HM), Marseille, 13005 France
- Marseille Medical Genetics, Bioinformatics & Genetics, Unité Mixte de Recherche (UMR)_S910, Aix-Marseille Université, Marseille, 13005 France
| | | | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Anthony J. Bleyer
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, D-79106 Freiburg, Germany
- Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79106 Freiburg, Germany
| | - Peter J. Conlon
- Division of Nephrology, Beaumont General Hospital, 1297 Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, 1297 Dublin, Ireland
| | - Michael Wiesener
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - John A. Sayer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
- Renal Services, Newcastle Upon Tyne Hospitals National Health Service Trust, Newcastle upon Tyne NE7 7DN, United Kingdom
- National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle upon Tyne NE4 5PL, United Kingdom
| | - Luca Rampoldi
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan, 20132 Italy
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, CH-8057 Zurich, Switzerland
- Division of Nephrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
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2
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Kini RM. Toxinology provides multidirectional and multidimensional opportunities: A personal perspective. Toxicon X 2020; 6:100039. [PMID: 32550594 PMCID: PMC7285919 DOI: 10.1016/j.toxcx.2020.100039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/28/2020] [Accepted: 05/05/2020] [Indexed: 01/16/2023] Open
Abstract
In nature, toxins have evolved as weapons to capture and subdue the prey or to counter predators or competitors. When they are inadvertently injected into humans, they cause symptoms ranging from mild discomfort to debilitation and death. Toxinology is the science of studying venoms and toxins that are produced by a wide variety of organisms. In the past, the structure, function and mechanisms of most abundant and/or most toxic components were characterized to understand and to develop strategies to neutralize their toxicity. With recent technical advances, we are able to evaluate and determine the toxin profiles using transcriptomes of venom glands and proteomes of tiny amounts of venom. Enormous amounts of data from these studies have opened tremendous opportunities in many directions of basic and applied research. The lower costs for profiling venoms will further fuel the expansion of toxin database, which in turn will provide greater exciting and bright opportunities in toxin research.
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Affiliation(s)
- R. Manjunatha Kini
- Protein Science Laboratory, Department of Biological Sciences, Faculty of Science and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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3
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Fajloun Z, Andreotti N, Fathallah M, Sabatier JM, De Waard M. Analysis of the interacting surface of maurotoxin with the voltage-gated Shaker B K(+) channel. J Pept Sci 2011; 17:200-10. [PMID: 21308876 DOI: 10.1002/psc.1313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 08/13/2010] [Accepted: 09/10/2010] [Indexed: 01/12/2023]
Abstract
Maurotoxin (MTX) is a 34-residue toxin that was isolated initially from the venom of the scorpion Scorpio maurus palmatus. Unlike the other toxins of the α-KTx6 family (Pi1, Pi4, Pi7, and HsTx1), MTX exhibits a unique disulfide bridge organization of the type C(1) C(5) , C(2) C(6) , C(3) C(4) , and C(7) C(8) (instead of the conventional C(1) C(5) , C(2) C(6) , C(3) C(7) , and C(4) C(8) , herein referred to as Pi1-like) that does not prevent its folding along the classic α/β scaffold of scorpion toxins. MTX(Pi1) is an MTX variant with a conventional pattern of disulfide bridging without any primary structure alteration of the toxin. Here, using MTX and/or MTX(Pi1) as models, we investigated how the type of folding influences toxin recognition of the Shaker B potassium channel. Amino acid residues of MTX that were studied for Shaker B recognition were selected on the basis of their homologous position in charybdotoxin, a three disulfide-bridged scorpion toxin also active on this channel type. These residues favored either an MTX- or MTX(Pi1) -like folding. Our data indicate clearly that Lys(23) and Tyr(32) (two out of ten amino acid residues studied) are the most important residues for Shaker B channel blockage by MTX. For activity on SKCa channels, the same amino acid residues also affect, directly or indirectly, the recognition of SK channels. The molecular modeling technique and computed docking indicate the existence of a correlation between the half cystine pairings of the mutated analogs and their activity on the Shaker B K(+) channel. Overall, mutations in MTX could, or could not, change the reorganization of disulfide bridges of this molecule without affecting its α/β scaffold. However, changing of the peptide backbone (cross linking disulfide bridges from MTX-like type vs MTX(Pi1) -like type) appears to have less impact on the molecule activity than mutation of certain key amino acids such as Lys(23) and Tyr(32) in this toxin.
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Affiliation(s)
- Ziad Fajloun
- ERT 62, Faculté de Médecine Nord, 13916 Marseille Cedex 15, France.
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4
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Kang TS, Kini RM. Structural determinants of protein folding. Cell Mol Life Sci 2009; 66:2341-61. [PMID: 19367367 PMCID: PMC11115868 DOI: 10.1007/s00018-009-0023-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 03/07/2009] [Accepted: 03/20/2009] [Indexed: 12/11/2022]
Abstract
The last several decades have seen an explosion of knowledge in the field of structural biology. With critical advances in spectroscopic techniques in examining structures of biomacromolecules, in maturation of molecular biology techniques, as well as vast improvements in computation prowess, protein structures are now being elucidated at an unprecedented rate. In spite of all the recent advances, the protein folding puzzle remains as one of the fundamental biochemical challenges. A facet to this empiric problem is the structural determinants of protein folding. What are the driving forces that pivot a polypeptide chain to a specific conformation amongst the vast conformation space? In this review, we shall discuss some of the structural determinants to protein folding that have been identified in the recent decades.
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Affiliation(s)
- Tse Siang Kang
- The Scripps Research Institute, 10550 North Torrey Pines Road GAC 1200, La Jolla, CA 92037 USA
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Block S4, Singapore, 117543 Singapore
| | - R. Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Block S3 #03-17, Singapore, 117543 Singapore
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5
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Combelles C, Gracy J, Heitz A, Craik DJ, Chiche L. Structure and folding of disulfide-rich miniproteins: insights from molecular dynamics simulations and MM-PBSA free energy calculations. Proteins 2009; 73:87-103. [PMID: 18393393 DOI: 10.1002/prot.22054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The fold of small disulfide-rich proteins largely relies on two or more disulfide bridges that are main components of the hydrophobic core. Because of the small size of these proteins and their high cystine content, the cysteine connectivity has been difficult to ascertain in some cases, leading to uncertainties and debates in the literature. Here, we use molecular dynamics simulations and MM-PBSA free energy calculations to compare similar folds with different disulfide pairings in two disulfide-rich miniprotein families, namely the knottins and the short-chain scorpion toxins, for which the connectivity has been discussed. We first show that the MM-PBSA approach is able to discriminate the correct knotted topology of knottins from the laddered one. Interestingly, a comparison of the free energy components for kalata B1 and MCoTI-II suggests that cyclotides and squash inhibitors, although sharing the same scaffold, are stabilized through different interactions. Application to short-chain scorpion toxins suggests that the conventional cysteine pairing found in many homologous toxins is significantly more stable than the unconventional pairing reported for maurotoxin and for spinoxin. This would mean that native maurotoxin and spinoxin are not at the lowest free energy minimum and might result from kinetically rather than thermodynamically driven oxidative folding processes. For both knottins and toxins, the correct or conventional disulfide connectivities provide lower flexibilities and smaller deviations from the initial conformations. Overall, our work suggests that molecular dynamics simulations and the MM-PBSA approach to estimate free energies are useful tools to analyze and compare disulfide bridge connectivities in miniproteins.
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Affiliation(s)
- Cecil Combelles
- Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale, 34090 Montpellier, France
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6
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Combes A, Choi SJ, Pimentel C, Darbon H, Waidelich D, Mestivier D, Camadro JM. Determination with matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry of the extensive disulfide bonding in tarantula venom peptide Psalmopeotoxin I. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009; 15:517-529. [PMID: 19661560 DOI: 10.1255/ejms.1000] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Psalmopeotoxin I (PcFK1) is a 33-residue peptide isolated from the venom of the tarantula Psalmopoeus cambridgei. This peptide specifically inhibits the intra-erythrocyte stage of Plasmodium falciparum in vitro. It contains six cysteine residues forming three disulfide bridges and belongs to the superfamily of natural peptides containing the inhibitor cystine knot (ICK) fold. We produced the wild-type and mutated forms of the recombinant peptide to examine the mechanism of action of PcFK1. The purified toxins were consistently produced as two isobaric peptides (r-PcFK1-1 and r-PcFK1-2) with different retention properties but identical anti-plasmodial -biological activity. Comparison of (15)N-NMR heteronuclear single quantum correlation spectra revealed that although rPcFK1-1 was highly structured, rPcFK1-2 does not have a stable three-dimensional structure. We used high-energy collision-induced fragmentation of the peptides with a matrix-assisted laser desorption/ionization tandem time-of- flight mass spectrometer to further investigate the structure of the native peptides in its natural form and produced in E. coli. The fragmentation spectra of the native peptides were very complex due to the occurrence in the spectrum of ions resulting from (1) cross-linking of fragments through a disulfide bridge and (2) asymmetric fragmentations of the disulfide bridges and (3) multiple neutral losses. The tandem mass spectrometry fragmentation pattern of r-PcFK1-1 was similar to that of the natural peptide isolated from crude venom, but r-PcFK1-2 had a clearly distinct fragmentation pattern, more closely resembling the fragmentation spectra of reduced and alkylated peptides. Observed ions could be attributed to specific fragments by comparing spectra between the wild-type and selected variants with point mutations (Y11W, R20T, Y26W, K28V). The disulfide connections in r-PcFK1-2 differed from those of the native peptide and showed a rare disulfide bridge between vicinal cysteine residues. The r-PcFK1_(R20T) variant showed a very limited fragmentation pattern when analyzed in positive mode but displayed much more fragmentation in negative mode pointing out the importance of the R20 residue in the fragmentation of PcFK1. Using the reductive matrix 1,5-diaminonaphtalene promoted strongly in source decay fragmentation of the peptides in MS mode. Our findings illustrated the critical role of the electronic environment around the central Cys(18)-Cys(19) doublet in PcFK1 in internal fragmentation of the peptide.
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Affiliation(s)
- Audrey Combes
- Protein Engineering and Metabolic Control, Molecular and Cellular Pathology Program, Jacques Monod Institute, UMR7592,-CNRS-Université Paris Diderot, 15 rue Hélène Brion, 75205, Paris Cedex 13, France
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7
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Kang TS, Radić Z, Talley TT, Jois SDS, Taylor P, Kini RM. Protein folding determinants: structural features determining alternative disulfide pairing in alpha- and chi/lambda-conotoxins. Biochemistry 2007; 46:3338-55. [PMID: 17315952 PMCID: PMC4778399 DOI: 10.1021/bi061969o] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alpha-conotoxins isolated from Conus venoms contain 11-19 residues and preferentially fold into the globular conformation that possesses a specific disulfide pairing pattern (C1-3, C2-4). We and others isolated a new family of chi-conotoxins (also called lambda conotoxins) with the conserved cysteine framework of alpha-conotoxins but with alternative disulfide pairing (C1-4, C2-3) resulting in the ribbon conformation. In both families, disulfide pairing and hence folding are important for their biological potency. By comparing the structural differences, we identified potential structural determinants responsible for the folding tendencies of these conotoxins. We examined the role of conserved proline in the first intercysteine loop and the conserved C-terminal amide on folding patterns of synthetic analogues of ImI conotoxin by comparing the isoforms with the regiospecifically synthesized conformers. Deamidation at the C-terminus and substitution of proline in the first intercysteine loop switch the folding pattern from the globular form of alpha-conotoxins to the ribbon form of chi/lambda-conotoxins. The findings are corroborated by reciprocal folding of CMrVIA chi/lambda-conotoxins. Substitution of Lys-6 from the first intercysteine loop of CMrVIA conotoxin with proline, as well as the inclusion of an amidated C-terminal shifted the folding preference of CMrVIA conotoxin from its native ribbon conformation toward the globular conformation. Binding assays of ImI conotoxin analogues with Aplysia and Bulinus acetylcholine binding protein indicate that both these substitutions and their consequent conformational change substantially impact the binding affinity of ImI conotoxin. These results strongly indicate that the first intercysteine loop proline and C-terminal amidation act as conformational switches in alpha- and chi/lambda-conotoxins.
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Affiliation(s)
- Tse Siang Kang
- Protein Science Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117 543
| | - Zoran Radić
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093
| | - Todd T. Talley
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093
| | - Seetharama D. S. Jois
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore 117 543
| | - Palmer Taylor
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093
| | - R. Manjunatha Kini
- Protein Science Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117 543
- Department of Biochemistry, Medical College of Virginia, Virginia Commonwealth University, Richmond, Virginia 13298
- To whom correspondence to should be addressed at Protein Science Laboratory, Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117 543. Tel: (65) 6516-5235. Fax: (65) 67792486.
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8
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Han YH, Wang Q, Jiang H, Liu L, Xiao C, Yuan DD, Shao XX, Dai QY, Cheng JS, Chi CW. Characterization of novel M-superfamily conotoxins with new disulfide linkage. FEBS J 2006; 273:4972-82. [PMID: 17042781 DOI: 10.1111/j.1742-4658.2006.05493.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The M-superfamily with the typical Cys framework (-CC-C-C-CC-) is one of the seven major superfamilies of conotoxins found in the venom of cone snails. Based on the number of residues in the last Cys loop (between C4 and C5), M-superfamily conotoxins can be provisionally categorized into four branches (M-1, M-2, M-3, M-4) [Corpuz GP, Jacobsen RB, Jimenez EC, Watkins M, Walker C, Colledge C, Garrett JE, McDougal O, Li W, Gray WR, et al. (2005) Biochemistry44, 8176-8186]. Here we report the purification of seven M-superfamily conotoxins from Conus marmoreus (five are novel and two are known as mr3a and mr3b) and one known M-1 toxin tx3a from Conus textile. In addition, six novel cDNA sequences of M-superfamily conotoxins have been identified from C. marmoreus, Conus leopardus and Conus quercinus. Most of the above novel conotoxins belong to M-1 and M-2 and only one to M-3. The disulfide analyses of two M-1 conotoxins, mr3e and tx3a, revealed that they possess a new disulfide bond arrangement (C1-C5, C2-C4, C3-C6) which is different from those of the M-4 branch (C1-C4, C2-C5, C3-C6) and M-2 branch (C1-C6, C2-C4, C3-C5). This newly characterized disulfide connectivity was confirmed by comparing the HPLC profiles of native mr3e and its two regioselectively folded isoforms. This is the first report of three different patterns of disulfide connectivity in conotoxins with the same cysteine framework.
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Affiliation(s)
- Yu-Hong Han
- Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, 320 YueYang Road, Shanghai 200031, China
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9
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M'Barek S, Chagot B, Andreotti N, Visan V, Mansuelle P, Grissmer S, Marrakchi M, El Ayeb M, Sampieri F, Darbon H, Fajloun Z, De Waard M, Sabatier JM. Increasing the molecular contacts between maurotoxin and Kv1.2 channel augments ligand affinity. Proteins 2006; 60:401-11. [PMID: 15971207 DOI: 10.1002/prot.20509] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Scorpion toxins interact with their target ion channels through multiple molecular contacts. Because a "gain of function" approach has never been described to evaluate the importance of the molecular contacts in defining toxin affinity, we experimentally examined whether increasing the molecular contacts between a toxin and an ion channel directly impacts toxin affinity. For this purpose, we focused on two scorpion peptides, the well-characterized maurotoxin with its variant Pi1-like disulfide bridging (MTX(Pi1)), used as a molecular template, and butantoxin (BuTX), used as an N-terminal domain provider. BuTX is found to be 60-fold less potent than MTX(Pi1) in blocking Kv1.2 (IC(50) values of 165 nM for BuTX versus 2.8 nM for MTX(Pi1)). Removal of its N-terminal domain (nine residues) further decreases BuTX affinity for Kv1.2 by 5.6-fold, which is in agreement with docking simulation data showing the importance of this domain in BuTX-Kv1.2 interaction. Transfer of the BuTX N-terminal domain to MTX(Pi1) results in a chimera with five disulfide bridges (BuTX-MTX(Pi1)) that exhibits 22-fold greater affinity for Kv1.2 than MTX(Pi1) itself, in spite of the lower affinity of BuTX as compared to MTX(Pi1). Docking experiments performed with the 3-D structure of BuTX-MTX(Pi1) in solution, as solved by (1)H-NMR, reveal that the N-terminal domain of BuTX participates in the increased affinity for Kv1.2 through additional molecular contacts. Altogether, the data indicate that acting on molecular contacts between a toxin and a channel is an efficient strategy to modulate toxin affinity.
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Affiliation(s)
- Sarrah M'Barek
- Laboratoire d'Ingénierie des Protéines, CNRS FRE 2738, IFR Jean Roche, Faculté de Médecine Nord, Marseille, France
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10
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Zhu S, Huys I, Dyason K, Verdonck F, Tytgat J. Evolutionary trace analysis of scorpion toxins specific for K-channels. Proteins 2003; 54:361-70. [PMID: 14696198 DOI: 10.1002/prot.10588] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Scorpion alpha-K(+) channel toxins are a large family of polypeptides with a similar structure but diverse pharmacological activities. Despite many structural and functional data available at present, little progress has been made in understanding the toxin's molecular basis responsible for the functional diversification. In this paper, we report the first complete cDNA sequences of toxins belonging to subfamily 6 and identify five new members, called alpha-KTx 6.6-6.10. By analyzing the rates of mutations that occurred in the corresponding cDNAs, we suggest that accelerated evolution in toxin-coding regions may be associated with the functional diversification of this subfamily. To pinpoint sites probably involved in the functional diversity of alpha-KTx family, we analyzed this family of sequences using the evolutionary trace method. This analysis highlighted one channel-binding surface common for all the members. This surface is composed of one conserved lysine residue at position 29 assisted by other residues at positions 10, 26, 27, 32, 34, and 36. Of them, the positions 29, 32, and 34 have been reported to be the most major determinants of channel specificity. Interestingly, another contrary surface was also observed at a higher evolutionary time cut-off value, which may be involved in the binding of ERG (ether-a-go-go-related gene) channel-specific toxins. The good match between the trace residues and the functional epitopes of the toxins suggested that the evolutionary trace results reported here can be applied to predict channel-binding sites of the toxins. Because, the side-chain variation in the trace positions is strongly linked with the functional alteration and channel-binding surface transfer of alpha-KTx family, we conclude that our findings should also be important for the rational design of new toxins targeting a given potassium channel with high selectivity.
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Affiliation(s)
- Shunyi Zhu
- Laboratory of Toxicology, University of Leuven, Leuven, Belgium
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11
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Guijarro JI, M'Barek S, Gómez-Lagunas F, Garnier D, Rochat H, Sabatier JM, Possani L, Delepierre M, Possani L. Solution structure of Pi4, a short four-disulfide-bridged scorpion toxin specific of potassium channels. Protein Sci 2003; 12:1844-54. [PMID: 12930984 PMCID: PMC2323982 DOI: 10.1110/ps.03186703] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Pi4 is a short toxin found at very low abundance in the venom of Pandinus imperator scorpions. It is a potent blocker of K(+) channels. Like the other members of the alpha-KTX6 subfamily to which it belongs, it is cross-linked by four disulfide bonds. The synthetic analog (sPi4) and the natural toxin (nPi4) have been obtained by solid-phase synthesis or from scorpion venom, respectively. Analysis of two-dimensional (1)H NMR spectra of nPi4 and sPi4 indicates that both peptides have the same structure. Moreover, electrophysiological recordings of the blocking of Shaker B K(+) channels by sPi4 (K(D) = 8.5 nM) indicate that sPi4 has the same blocking activity of nPi4 (K(D) = 8.0 nM), previously described. The disulfide bonds have been independently determined by NMR and structure calculations, and by Edman-degradation/mass-spectrometry identification of peptides obtained by proteolysis of nPi4. Both approaches indicate that the pairing of the half-cystines is (6)C-(27)C, (12)C-(32)C, (16)C-(34)C, and (22)C-(37)C. The structure of the toxin has been determined by using 705 constraints derived from NMR data on sPi4. The structure, which is well defined, shows the characteristic alpha/beta scaffold of scorpion toxins. It is compared to the structure of the other alpha-KTX6 subfamily members and, in particular, to the structure of maurotoxin, which shows a different pattern of disulfide bridges despite its high degree of sequence identity (76%) with Pi4. The structure of Pi4 and the high amounts of synthetic peptide available, will enable the detailed analysis of the interaction of Pi4 with K(+) channels.
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Affiliation(s)
- J Iñaki Guijarro
- Unité de RMN des Biomolécules (CNRS URA 2185), Dépt. de Biologie Structurale et Chimie, Institut Pasteur, 75724 Paris Cedex 15, France
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12
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M'Barek S, Lopez-Gonzalez I, Andreotti N, di Luccio E, Visan V, Grissmer S, Judge S, El Ayeb M, Darbon H, Rochat H, Sampieri F, Béraud E, Fajloun Z, De Waard M, Sabatier JM. A maurotoxin with constrained standard disulfide bridging: innovative strategy of chemical synthesis, pharmacology, and docking on K+ channels. J Biol Chem 2003; 278:31095-104. [PMID: 12783861 DOI: 10.1074/jbc.m304271200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Maurotoxin (MTX) is a 34-residue toxin that has been isolated initially from the venom of the scorpion Scorpio maurus palmatus. It presents a large number of pharmacological targets, including small conductance Ca2+-activated and voltage-gated K+ channels. Contrary to other toxins of the alpha-KTx6 family (Pi1, Pi4, Pi7, and HsTx1), MTX exhibits a unique disulfide bridge organization of the type C1-C5, C2-C6, C3-C4, and C7-C8 (instead of the conventional C1-C5, C2-C6, C3-C7, and C4-C8, herein referred to as Pi1-like) that does not prevent its folding along the classic alpha/beta scaffold of scorpion toxins. Here, we developed an innovative strategy of chemical peptide synthesis to produce an MTX variant (MTXPi1) with a conventional pattern of disulfide bridging without any alteration of the toxin chemical structure. This strategy was used solely to address the impact of half-cystine pairings on MTX structural properties and pharmacology. The data indicate that MTXPi1 displays some marked changes in affinities toward the target K+ channels. Computed docking analyses using molecular models of both MTXPi1 and the various voltage-gated K+ channel subtypes (Shaker B, Kv1.2, and Kv1.3) were found to correlate with MTXPi1 pharmacology. A functional map detailing the interaction between MTXPi1 and Shaker B channel was generated in line with docking experiments.
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Affiliation(s)
- Sarrah M'Barek
- Laboratoire International Associé d'Ingénierie Biomoléculaire, CNRS Unité Mixte de Recherche 6560 Bd Pierre Dramard, 13916 Marseille Cedex 20, France
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13
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Carneiro AMD, Kushmerick C, Koenen J, Arndt MHL, Cordeiro MN, Chavez-Olortegui C, Diniz CR, Gomez MV, Kalapothakis E, Prado MAM, Prado VF. Expression of a functional recombinant Phoneutria nigriventer toxin active on K+ channels. Toxicon 2003; 41:305-13. [PMID: 12565753 DOI: 10.1016/s0041-0101(02)00292-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
PnTx3-1 is a peptide isolated from the venom of the spider Phoneutria nigriventer that specifically inhibits A-type K(+) currents (I(A)) in GH(3) cells. Here we used a bacterial expression system to produce an NH(2)-extended mutant of PnTx3-1 (ISEF-PnTx3-1) and tested whether the toxin is functional. The recombinant toxin was purified from bacterial extracts by a combination of affinity and ion-exchange chromatography. The recombinant toxin blocked A-type K(+) currents in GH(3) cells in a fashion similar to that observed with the wild-type toxin purified from the spider venom. These results suggest that recombinant cDNA methods provide a novel source for the production of functional Phoneutria toxins. The recombinant ISEF-PnTx3-1 should be useful for further understanding of the role of A-type K(+) currents in biological processes.
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Affiliation(s)
- A M D Carneiro
- Departamento de Bioquímica-Imunologia, ICB, Universidade Federal de Minas Gerais, Av Antonio Carlos, 6627, Belo Horizonte, 31270-901, Minas Gerais, Brazil
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14
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Fu W, Cui M, Briggs JM, Huang X, Xiong B, Zhang Y, Luo X, Shen J, Ji R, Jiang H, Chen K. Brownian dynamics simulations of the recognition of the scorpion toxin maurotoxin with the voltage-gated potassium ion channels. Biophys J 2002; 83:2370-85. [PMID: 12414674 PMCID: PMC1302326 DOI: 10.1016/s0006-3495(02)75251-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The recognition of the scorpion toxin maurotoxin (MTX) by the voltage-gated potassium (Kv1) channels, Kv1.1, Kv1.2, and Kv1.3, has been studied by means of Brownian dynamics (BD) simulations. All of the 35 available structures of MTX in the Protein Data Bank (http://www.rcsb.org/pdb) determined by nuclear magnetic resonance were considered during the simulations, which indicated that the conformation of MTX significantly affected both the recognition and the binding between MTX and the Kv1 channels. Comparing the top five highest-frequency structures of MTX binding to the Kv1 channels, we found that the Kv1.2 channel, with the highest docking frequencies and the lowest electrostatic interaction energies, was the most favorable for MTX binding, whereas Kv1.1 was intermediate, and Kv1.3 was the least favorable one. Among the 35 structures of MTX, the 10th structure docked into the binding site of the Kv1.2 channel with the highest probability and the most favorable electrostatic interactions. From the MTX-Kv1.2 binding model, we identified the critical residues for the recognition of these two proteins through triplet contact analyses. MTX locates around the extracellular mouth of the Kv1 channels, making contacts with its beta-sheets. Lys23, a conserved amino acid in the scorpion toxins, protrudes into the pore of the Kv1.2 channel and forms two hydrogen bonds with the conserved residues Gly401(D) and Tyr400(C) and one hydrophobic contact with Gly401(C) of the Kv1.2 channel. The critical triplet contacts for recognition between MTX and the Kv1.2 channel are Lys23(MTX)-Asp402(C)(Kv1), Lys27(MTX)-Asp378(D)(Kv1), and Lys30(MTX)-Asp402(A)(Kv1). In addition, six hydrogen-bonding interactions are formed between residues Lys23, Lys27, Lys30, and Tyr32 of MTX and residues Gly401, Tyr400, Asp402, Asp378, and Thr406 of Kv1.2. Many of them are formed by side chains of residues of MTX and backbone atoms of the Kv1.2 channel. Five hydrophobic contacts exist between residues Pro20, Lys23, Lys30 and Tyr32 of MTX and residues Asp402, Val404, Gly401, and Arg377 of the Kv1.2 channel. The simulation results are in agreement with the previous molecular biology experiments and explain the binding phenomena between MTX and Kv1 channels at the molecular level. The consistency between the results of the BD simulations and the experimental data indicated that our three-dimensional model of the MTX-Kv1.2 channel complex is reasonable and can be used in additional biological studies, such as rational design of novel therapeutic agents blocking the voltage-gated channels and in mutagenesis studies in both the toxins and the Kv1 channels. In particular, both the BD simulations and the molecular mechanics refinements indicate that residue Asp378 of the Kv1.2 channel is critical for its recognition and binding functionality toward MTX. This phenomenon has not been appreciated in the previous mutagenesis experiments, indicating this might be a new clue for additional functional study of Kv1 channels.
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Affiliation(s)
- Wei Fu
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Meteria Medica, Chinese Academy of Sciences, 194 Taiyuan Road, Shanghai 200031, P. R. China
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15
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Fajloun Z, Ferrat G, Carlier E, M'Barek S, Regaya I, Fathallah M, Rochat H, Darbon H, de Waard M, Sabatier JM. Synthesis, 3-D structure, and pharmacology of a reticulated chimeric peptide derived from maurotoxin and Tsk scorpion toxins. Biochem Biophys Res Commun 2002; 291:640-8. [PMID: 11855838 DOI: 10.1006/bbrc.2002.6496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Maurotoxin (MTX) is a 34-mer scorpion toxin cross-linked by four disulfide bridges that acts on both Ca(2+)-activated (SK) and voltage-gated (Kv) K(+) channels. A 38-mer chimera of MTX, Tsk-MTX, has been synthesized by the solid-phase method. It encompasses residues from 1 to 6 of Tsk at N-terminal, and residues from 3 to 34 of MTX at C-terminal. As established by enzyme cleavage, Tsk-MTX displays half-cystine pairings of the type C1-C5, C2-C6, C3-C7 and C4-C8 which, contrary to MTX, correspond to a disulfide bridge pattern common to known scorpion toxins. The 3-D structure of Tsk-MTX, solved by (1)H NMR, demonstrates that it adopts the alpha/beta scaffold of scorpion toxins. In vivo, Tsk-MTX is lethal by intracerebroventricular injection in mice (LD(50) value of 0.2 microg/mouse). In vitro, Tsk-MTX is as potent as MTX, or Tsk, to interact with apamin-sensitive SK channels of rat brain synaptosomes (IC(50) value of 2.5 nM). It also blocks voltage-gated K(+) channels expressed in Xenopus oocytes, but is inactive on rat Kv1.3 contrary to MTX.
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Affiliation(s)
- Ziad Fajloun
- Boulevard Pierre Dramard, CNRS UMR 6560, 13916 Marseille Cedex 20, France
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16
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di Luccio E, Azulay DO, Regaya I, Fajloun Z, Sandoz G, Mansuelle P, Kharrat R, Fathallah M, Carrega L, Estève E, Rochat H, De Waard M, Sabatier JM. Parameters affecting in vitro oxidation/folding of maurotoxin, a four-disulphide-bridged scorpion toxin. Biochem J 2001; 358:681-92. [PMID: 11535129 PMCID: PMC1222102 DOI: 10.1042/0264-6021:3580681] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Maurotoxin (MTX) is a 34-mer scorpion toxin cross-linked by four disulphide bridges that acts on various K(+) channel subtypes. MTX adopts a disulphide bridge organization of the type C1-C5, C2-C6, C3-C4 and C7-C8, and folds according to the common alpha/beta scaffold reported for other known scorpion toxins. Here we have investigated the process and kinetics of the in vitro oxidation/folding of reduced synthetic L-MTX (L-sMTX, where L-MTX contains only L-amino acid residues). During the oxidation/folding of reduced L-sMTX, the oxidation intermediates were blocked by iodoacetamide alkylation of free cysteine residues, and analysed by MS. The L-sMTX intermediates appeared sequentially over time from the least (intermediates with one disulphide bridge) to the most oxidized species (native-like, four-disulphide-bridged L-sMTX). The mathematical formulation of the diffusion-collision model being inadequate to accurately describe the kinetics of oxidation/folding of L-sMTX, we have formulated a derived mathematical description that better fits the experimental data. Using this mathematical description, we have compared for the first time the oxidation/folding of L-sMTX with that of D-sMTX, its stereoisomer that contains only D-amino acid residues. Several experimental parameters, likely to affect the oxidation/folding process, were studied further; these included temperature, pH, ionic strength, redox potential and concentration of reduced toxin. We also assessed the effects of some cellular enzymes, peptidylprolyl cis-trans isomerase (PPIase) and protein disulphide isomerase (PDI), on the folding pathways of reduced L-sMTX and D-sMTX. All the parameters tested affect the oxidative folding of sMTX, and the kinetics of this process were indistinguishable for L-sMTX and D-sMTX, except when stereospecific enzymes were used. The most efficient conditions were found to be: 50 mM Tris/HCl/1.4 mM EDTA, pH 7.5, supplemented by 0.5 mM PPIase and 50 units/ml PDI for 0.1 mM reduced compound. These data represent the first report of potent stereoselective effects of cellular enzymes on the oxidation/folding of a scorpion toxin.
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Affiliation(s)
- E di Luccio
- CNRS UMR 6560, Bd Pierre Dramard, 13916 Marseille Cedex 20, France
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