{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T03:36:28Z","timestamp":1792121788796,"version":"4.4.0"},"reference-count":54,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2012,12,18]],"date-time":"2012-12-18T00:00:00Z","timestamp":1355788800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Toxins"],"abstract":"<jats:p>Hanatoxin 1 (HaTx1) is a polypeptide toxin isolated from spider venoms. HaTx1 inhibits the voltage-gated potassium channel kv2.1 potently with nanomolar affinities. Its receptor site has been shown to contain the S3b-S4a paddle of the voltage sensor (VS). Here, the binding of HaTx1 to the VSs of human Kv2.1 in the open and resting states are examined using a molecular docking method and molecular dynamics. Molecular docking calculations predict two distinct binding modes for the VS in the resting state. In the two binding modes, the toxin binds the S3b-S4a from S2 and S3 helices, or from S1 and S4 helices. Both modes are found to be stable when embedded in a lipid bilayer. Only the mode in which the toxin binds the S3b-S4a paddle from S2 and S3 helices is consistent with mutagenesis experiments, and considered to be correct. The toxin is then docked to the VS in the open state, and the toxin-VS interactions are found to be less favorable. Computational mutagenesis calculations performed on F278R and E281K mutant VSs show that the mutations may reduce toxin binding affinity by weakening the non-bonded interactions between the toxin and the VS. Overall, our calculations reproduce a wide range of experimental data, and suggest that HaTx1 binds to the S3b-S4a paddle of Kv2.1 from S2 and S3 helices.<\/jats:p>","DOI":"10.3390\/toxins4121552","type":"journal-article","created":{"date-parts":[[2012,12,18]],"date-time":"2012-12-18T11:10:39Z","timestamp":1355829039000},"page":"1552-1564","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Binding of Hanatoxin to the Voltage Sensor of Kv2.1"],"prefix":"10.3390","volume":"4","author":[{"given":"Rong","family":"Chen","sequence":"first","affiliation":[{"name":"Research School of Biology, Australian National University, Canberra, ACT 0200, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Robinson","sequence":"additional","affiliation":[{"name":"Research School of Biology, Australian National University, Canberra, ACT 0200, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shin-Ho","family":"Chung","sequence":"additional","affiliation":[{"name":"Research School of Biology, Australian National University, Canberra, ACT 0200, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2012,12,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/nature02632","article-title":"A membrane-access mechanism of ion channel inhibition by voltage sensor toxins from spider venom","volume":"430","author":"Lee","year":"2004","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"6015","DOI":"10.1021\/bi0477034","article-title":"Solution structure and lipid membrane partitioning of VSTx1, an inhibitor of the KvAP potassium channel","volume":"44","author":"Jung","year":"2005","journal-title":"Biochemistry"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1085\/jgp.200709869","article-title":"Tarantula toxins interact with voltage sensors within lipid membranes","volume":"130","author":"Milescu","year":"2007","journal-title":"J. Gen. Physiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1038\/nsmb.1679","article-title":"Interactions between lipids and voltage sensor paddles detected with tarantula toxins","volume":"16","author":"Milescu","year":"2009","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.toxicon.2006.09.024","article-title":"Tarantula toxins interacting with voltage sensors in potassium channels","volume":"49","author":"Swartz","year":"2007","journal-title":"Toxicon"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1038\/nature03873","article-title":"Voltage-sensor activation with a tarantula toxin as cargo","volume":"436","author":"Phillips","year":"2005","journal-title":"Nature"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1016\/0896-6273(95)90184-1","article-title":"An inhibitor of the Kv2.1 potassium channel isolated from the venom of a Chilean tarantula","volume":"15","author":"Swartz","year":"1995","journal-title":"Neuron"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1046\/j.1432-1327.1999.00726.x","article-title":"Isolation, amino acid sequence and functional assays of SGTx1. The first toxin purified from the venom of the spider scodra griseipes","volume":"265","author":"Marvin","year":"1999","journal-title":"Eur. J. Biochem."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/nature01473","article-title":"Functional analysis of an archaebacterial voltage-dependent K+ channel","volume":"422","author":"Ruta","year":"2003","journal-title":"Nature"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/S0026-895X(24)13491-8","article-title":"Heteropodatoxins: Peptides isolated from spider venom that block Kv4.2 potassium channels","volume":"51","author":"Sanguinetti","year":"1997","journal-title":"Mol. Pharmacol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/sj.bjp.0702283","article-title":"Effects of phrixotoxins on the Kv4 family of potassium channels and implications for the role of Ito1 in cardiac electrogenesis","volume":"126","author":"Diochot","year":"1999","journal-title":"Br. J. Pharmacol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1038\/nature06266","article-title":"Portability of paddle motif function and pharmacology in voltage sensors","volume":"450","author":"Alabi","year":"2007","journal-title":"Nature"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/j.toxicon.2004.11.015","article-title":"Heteropoda toxin 2 is a gating modifier toxin specific for voltage-gated K+ channels of the Kv4 family","volume":"45","author":"Zarayskiy","year":"2005","journal-title":"Toxicon"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1573","DOI":"10.1016\/S0041-0101(98)00149-4","article-title":"The cystine knot structure of ion channel toxins and related polypeptides","volume":"36","author":"Norton","year":"1998","journal-title":"Toxicon"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1006\/jmbi.2000.3609","article-title":"Solution structure of hanatoxin1, a gating modifier of voltage-dependent K+ channels: Common surface features of gating modifier toxins","volume":"297","author":"Takahashi","year":"2000","journal-title":"J. Mol. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1021\/bi0353373","article-title":"Solution structure and functional characterization of SGTx1, a modifier of Kv2.1 channel gating","volume":"43","author":"Lee","year":"2004","journal-title":"Biochemistry"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1085\/jgp.200309005","article-title":"Molecular surface of tarantula toxins interacting with voltage sensors in KV channels","volume":"123","author":"Wang","year":"2004","journal-title":"J. Gen. Physiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1007\/s00249-006-0044-z","article-title":"Interaction between K+ channel gate modifier hanatoxin and lipid bilayer membranes analyzed by molecular dynamics simulation","volume":"35","author":"Nishizawa","year":"2006","journal-title":"Eur. Biophys. J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"L07","DOI":"10.1529\/biophysj.106.098681","article-title":"SGTx1, a Kv channel gating-modifier toxin, binds to the interfacial region of lipid bilayers","volume":"92","author":"Wee","year":"2007","journal-title":"Biophys. J."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"11844","DOI":"10.1021\/bi061111z","article-title":"Vstx1, a modifier of Kv channel gating, localizes to the interfacial region of lipid bilayers","volume":"45","author":"Bemporad","year":"2006","journal-title":"Biochemistry"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1558","DOI":"10.1016\/j.bpj.2009.12.4321","article-title":"Interactions between a voltage sensor and a toxin via multiscale simulations","volume":"98","author":"Wee","year":"2010","journal-title":"Biophys. J."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1016\/S0896-6273(00)80306-2","article-title":"Hanatoxin modifies the gating of a voltage-dependent K+ channel through multiple binding sites","volume":"18","author":"Swartz","year":"1997","journal-title":"Neuron"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1016\/S0896-6273(00)80307-4","article-title":"Mapping the receptor site for hanatoxin, a gating modifier of voltage-dependent K+ channels","volume":"18","author":"Swartz","year":"1997","journal-title":"Neuron"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1085\/jgp.115.6.673","article-title":"Localization and molecular determinants of the hanatoxin receptors on the voltage-sensing domains of a K+ channel","volume":"115","author":"Swartz","year":"2000","journal-title":"J. Gen. Physiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1085\/jgp.117.3.205","article-title":"Helical structure of the COOH terminus of S3 and its contribution to the gating modifier toxin receptor in voltage-gated ion channels","volume":"117","author":"Swartz","year":"2001","journal-title":"J. Gen. Physiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"10071","DOI":"10.1021\/bi049463y","article-title":"Localization of the voltage-sensor toxin receptor on KvAP","volume":"43","author":"Ruta","year":"2004","journal-title":"Biochemistry"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1016\/j.str.2007.12.015","article-title":"Structural dynamics of an isolated voltage-sensor domain in a lipid bilayer","volume":"16","author":"Chakrapani","year":"2008","journal-title":"Structure"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1002\/1439-7633(20020703)3:7<604::AID-CBIC604>3.0.CO;2-X","article-title":"Close-range electrostatic interactions in proteins","volume":"3","author":"Kumar","year":"2002","journal-title":"ChemBioChem"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1021\/ar000033j","article-title":"Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models","volume":"33","author":"Kollman","year":"2000","journal-title":"Acc. Chem. Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"287","DOI":"10.2174\/157340906778226454","article-title":"Recent advances in free energy calculations with a combination of molecular mechanics and continuum models","volume":"2","author":"Wang","year":"2006","journal-title":"Curr. Comput. Aided Drug Des."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"5045","DOI":"10.1074\/jbc.M408427200","article-title":"Common features in the functional surface of scorpion \u03b2-toxins and elements that confer specificity for insect and mammalian voltage-gated sodium channels","volume":"280","author":"Cohen","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"L20","DOI":"10.1529\/biophysj.107.112375","article-title":"Is lipid bilayer binding a common property of inhibitor cysteine knot ion-channel blockers?","volume":"93","author":"Posokhov","year":"2007","journal-title":"Biophys. J."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"4796","DOI":"10.1021\/jp300127j","article-title":"Conserved functional surface of anti-mammalian scorpion \u03b2-toxins","volume":"116","author":"Chen","year":"2012","journal-title":"J. Phys. Chem. B"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"7775","DOI":"10.1021\/bi300776g","article-title":"Binding modes and functional surface of anti-mammalian scorpion \u03b1-toxins to sodium channels","volume":"51","author":"Chen","year":"2012","journal-title":"Biochemistry"},{"key":"ref_35","first-page":"919","article-title":"Voltage sensor-trapping: Enhanced activation of sodium channels by \u03b2-scorpion toxin bound to the S3-S4 loop in domain II","volume":"21","author":"Qu","year":"1998","journal-title":"Neuron"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1126\/science.1216533","article-title":"Mechanism of voltage gating in potassium channels","volume":"336","author":"Jensen","year":"2012","journal-title":"Science"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Amaral, C., Carnevale, V., Klein, M.L., and Treptow, W. (2012). Exploring conformational states of the bacterial voltage-gated sodium channel NavAb via molecular dynamics simulations. Proc. Natl. Acad. Sci. USA.","DOI":"10.1073\/pnas.1218087109"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1002\/elps.1150181505","article-title":"SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling","volume":"18","author":"Guex","year":"1997","journal-title":"Electrophoresis"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3381","DOI":"10.1093\/nar\/gkg520","article-title":"SWISS-MODEL: An automated protein homology-modeling server","volume":"31","author":"Schwede","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1093\/bioinformatics\/bti770","article-title":"The SWISS-MODEL Workspace: A web-based environment for protein structure homology modeling","volume":"22","author":"Arnold","year":"2006","journal-title":"Bioinformatics"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.neuron.2007.09.023","article-title":"Closing in on the resting state of the Shaker K+ channel","volume":"56","author":"Pathak","year":"2007","journal-title":"Neuron"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1126\/science.1116269","article-title":"Crystal structure of a mammalian voltage-dependent Shaker family K+ channel","volume":"309","author":"Long","year":"2005","journal-title":"Science"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"11352","DOI":"10.1073\/pnas.1000142107","article-title":"Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement","volume":"107","author":"Chen","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1016\/S1359-6446(04)03196-4","article-title":"Utility of homology models in the drug discovery process","volume":"9","author":"Hillisch","year":"2004","journal-title":"Drug Discov. Today"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1002\/prot.21502","article-title":"Integrating statistical pair potentials into protein complex prediction","volume":"69","author":"Mintseris","year":"2007","journal-title":"Proteins"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","article-title":"Scalable molecular dynamics with NAMD","volume":"26","author":"Phillips","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1021\/jp973084f","article-title":"All-atom empirical potential for molecular modeling and dynamics studies of proteins","volume":"102","author":"MacKerell","year":"1998","journal-title":"J. Phys. Chem. B"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1002\/jcc.20065","article-title":"Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations","volume":"25","author":"MacKerell","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"7830","DOI":"10.1021\/jp101759q","article-title":"Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types","volume":"114","author":"Klauda","year":"2010","journal-title":"J. Phys. Chem. B"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1982","journal-title":"J. Chem. Phys."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","article-title":"Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes","volume":"23","author":"Ryckaert","year":"1977","journal-title":"J. Comput. Phys."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1002\/jcc.540130805","article-title":"SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models","volume":"13","author":"Miyamoto","year":"1992","journal-title":"J. Comput. Chem."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"4177","DOI":"10.1063\/1.467468","article-title":"Constant pressure molecular dynamics algorithms","volume":"101","author":"Martyna","year":"1994","journal-title":"J. Chem. Phys."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."}],"container-title":["Toxins"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-6651\/4\/12\/1552\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T21:54:21Z","timestamp":1760219661000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-6651\/4\/12\/1552"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,12,18]]},"references-count":54,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2012,12]]}},"alternative-id":["toxins4121552"],"URL":"https:\/\/doi.org\/10.3390\/toxins4121552","relation":{},"ISSN":["2072-6651"],"issn-type":[{"value":"2072-6651","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12,18]]}}}