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2000
Volume 21, Issue 6
  • ISSN: 1570-1646
  • E-ISSN: 1875-6247

Abstract

Aims

This study aims to gain insights into the Sec1 binding mechanism and the corresponding amino acids responsible for interacting with the amoebic SNARE proteins, Syntaxin1A/1B, which would enable to create a platform for further exploration of the functions and applications of Sec1 in managing amoebiasis.

Background

Parasitic protozoa have long been responsible for increasing the burden on healthcare. However, the enteric protozoan , is dangerously neglected despite accounting for the greatest number of deaths from parasitic infection, closely after malaria and schistosomiasis. launches its attack secretion of tissue degrading arsenal through vesicular transport. Sec1/Munc18-1 -like (SM) proteins are one of the key players of the vesicle transport system and, along with their interacting partners, play crucial roles in this transport machinery. This provides the basis for exploring the uncharacterized SM protein in and its roles in vesicle transport.

Objectives

This study aims to decode the novel SM protein, Sec1, by performing detailed sequence and structure analysis and delving into the protein interaction studies with its partner SNARE proteins (Syntaxins) through molecular dynamic simulations and docking. The interactions will be compared with crystal structure exhibiting co-complexes of Sec1_Syntaxin to further highlight the role of Sec1 amino acids in interacting with amoebic SNAREs, Syntaxin 1A/1B.

Methods

The objectives were fulfilled by performing rigorous studies on Sec1, falling under the heads of comparative sequence and structure analysis, physicochemical studies, modeling, and molecular docking, and protein-protein interaction studies supported by molecular dynamic simulations.

Results

Sec1 is a thermally stable, 70kDa globular protein composed of three domains where domains 1 and 2 adopt an α-β-α fold. Domain 2 is split into 2a and 2b, separated by domain 3. This domain has two parts, 3a and 3b, at an angle of 56.7° to each other. Sec1 shows stable interaction with Syntaxin 1 isoforms (Syntaxin1A/1B) and Rab GTPase (RabX10). Molecular simulation investigating the dynamics of Sec1 with Syntaxin1A, showed that the interaction is stable due to the formation of 14 strong hydrogen bonds (bond length <2.4 Å). The pivotal residues of the interaction interface belong to domain 1 (53D, 60K, and 62E) and domain 3a (259K and 314N) of Sec1; Hc region (110R and 114N) and SNARE motif (234E, 237E, 242E) of Syntaxin 1A/1B. RabX10 binds to Sec1 its G3 region, and the key interacting residues of Sec1 (224R-225H, 490L-495F, and 518K) fall in domain 2.

Conclusion

Our study reveals that the Syntaxin 1 isoforms and RabX10 form stable complexes with Sec1, assembling the minimal template for the SNARE-based vesicle transport of . Our investigation aims to enhance comprehension of vesicle transport in and establish the potential of Sec1 as a viable drug target in future applications.

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2025-09-30

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References

  1. CarreroJ.C. Reyes-LópezM. Serrano-LunaJ. ShibayamaM. UnzuetaJ. León-SicairosN. de la GarzaM. Intestinal amoebiasis: 160 years of its first detection and still remains as a health problem in developing countries.Int. J. Med. Microbiol.2020310115135810.1016/j.ijmm.2019.15135831587966
     [Google Scholar]
  2. KantorM. AbrantesA. EstevezA. SchillerA. TorrentJ. GasconJ. HernandezR. OchnerC. Entamoeba histolytica: Updates in clinical manifestation, pathogenesis, and vaccine development.Can. J. Gastroenterol. Hepatol.201820181610.1155/2018/460142030631758
     [Google Scholar]
  3. Martínez-PalomoA. The pathogenesis of amoebiasis.Parasitol. Today19873411111810.1016/0169‑4758(87)90048‑215462926
     [Google Scholar]
  4. BercuT.E. PetriW.A. BehmB.W. Amebic colitis: New insights into pathogenesis and treatment.Curr. Gastroenterol. Rep.20079542943310.1007/s11894‑007‑0054‑817991346
     [Google Scholar]
  5. RawatA. RoyM. JyotiA. KaushikS. VermaK. SrivastavaV.K. Cysteine proteases: Battling pathogenic parasitic protozoans with omnipresent enzymes.Microbiol. Res.202124912678410.1016/j.micres.2021.12678433989978
     [Google Scholar]
  6. BurkhardtP. HattendorfD.A. WeisW.I. FasshauerD. Munc18a controls SNARE assembly through its interaction with the syntaxin N-peptide.EMBO J.200827792393310.1038/emboj.2008.3718337752
     [Google Scholar]
  7. KatagiriH. TerasakiJ. MurataT. IshiharaH. OgiharaT. InukaiK. FukushimaY. AnaiM. KikuchiM. MiyazakiJ. YazakiY. OkaY. A novel isoform of syntaxin-binding protein homologous to yeast Sec1 expressed ubiquitously in mammalian cells.J. Biol. Chem.1995270104963496610.1074/jbc.270.10.49637890599
     [Google Scholar]
  8. HalachmiN. LevZ. The Sec1 family: A novel family of proteins involved in synaptic transmission and general secretion.J. Neurochem.199666388989710.1046/j.1471‑4159.1996.66030889.x8769846
     [Google Scholar]
  9. ZuckerR.S. KullmannD.M. KaeserP.S. Release of neurotransmitters.From Molecules to Networks: An Introduction to Cellular and Molecular NeuroscienceAcademic Press201444344810.1016/B978‑0‑12‑397179‑1.00015‑4
     [Google Scholar]
  10. AraçD. DulubovaI. PeiJ. HuryevaI. GrishinN.V. RizoJ. Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5.J. Mol. Biol.2005346258960110.1016/j.jmb.2004.12.00415670607
     [Google Scholar]
  11. BakerR.W. JeffreyP.D. ZickM. PhillipsB.P. WicknerW.T. HughsonF.M. A direct role for the Sec1/Munc18-family protein Vps33 as a template for SNARE assembly.Science201534962521111111410.1126/science.aac790626339030
     [Google Scholar]
  12. RoyM. KaushikS. JyotiA. SrivastavaV.K. Probing the peculiarity of EhRabX10, a pseudoRab GTPase, from the enteric parasite Entamoeba histolytica through in silico modeling and docking studies.BioMed Res. Int.2021202111310.1155/2021/991362534660804
     [Google Scholar]
  13. GasteigerE. GattikerA. HooglandC. IvanyiI. AppelR.D. BairochA. ExPASy: The proteomics server for in-depth protein knowledge and analysis.Nucleic Acids Res.200331133784378810.1093/nar/gkg56312824418
     [Google Scholar]
  14. GasteigerE. HooglandC. GattikerA. DuvaudS. WilkinsM.R. AppelR.D. BairochA. Protein identification and analysis tools on the ExPASy server.The Proteomics Protocols Handbook.Humana Press200557160710.1385/1‑59259‑890‑0:571
     [Google Scholar]
  15. MadeiraF. MadhusoodananN. LeeJ. EusebiA. NiewielskaA. TiveyA.R.N. LopezR. ButcherS. The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024.Nucleic Acids Res.202452W1W521W52510.1093/nar/gkae24138597606
     [Google Scholar]
  16. LarkinM.A. BlackshieldsG. BrownN.P. ChennaR. McGettiganP.A. McWilliamH. ValentinF. WallaceI.M. WilmA. LopezR. ThompsonJ.D. GibsonT.J. HigginsD.G. ClustalW. Clustal W and Clustal X version 2.0.Bioinformatics200723212947294810.1093/bioinformatics/btm40417846036
     [Google Scholar]
  17. WaterhouseA. BertoniM. BienertS. StuderG. TaurielloG. GumiennyR. HeerF.T. de BeerT.A.P. RempferC. BordoliL. LeporeR. SchwedeT. SWISS-MODEL: Homology modelling of protein structures and complexes.Nucleic Acids Res.201846W1W296W30310.1093/nar/gky42729788355
     [Google Scholar]
  18. BienertS. WaterhouseA. de BeerT.A.P. TaurielloG. StuderG. BordoliL. SchwedeT. The SWISS-MODEL Repository—new features and functionality.Nucleic Acids Res.201745D1D313D31910.1093/nar/gkw113227899672
     [Google Scholar]
  19. MarianiV. BiasiniM. BarbatoA. SchwedeT. lDDT: A local superposition-free score for comparing protein structures and models using distance difference tests.Bioinformatics201329212722272810.1093/bioinformatics/btt47323986568
     [Google Scholar]
  20. BenkertP. BiasiniM. SchwedeT. Toward the estimation of the absolute quality of individual protein structure models.Bioinformatics201127334335010.1093/bioinformatics/btq66221134891
     [Google Scholar]
  21. WiedersteinM. SipplM.J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.Nucleic Acids Res.200735Web ServerW407W41010.1093/nar/gkm29017517781
     [Google Scholar]
  22. SipplM.J. Recognition of errors in three‐dimensional structures of proteins.Proteins199317435536210.1002/prot.3401704048108378
     [Google Scholar]
  23. ColovosC. YeatesT.O. Verification of protein structures: Patterns of nonbonded atomic interactions.Protein Sci.1993291511151910.1002/pro.55600209168401235
     [Google Scholar]
  24. JumperJ. EvansR. PritzelA. GreenT. FigurnovM. RonnebergerO. TunyasuvunakoolK. BatesR. ŽídekA. PotapenkoA. BridglandA. MeyerC. KohlS.A.A. BallardA.J. CowieA. Romera-ParedesB. NikolovS. JainR. AdlerJ. BackT. PetersenS. ReimanD. ClancyE. ZielinskiM. SteineggerM. PacholskaM. BerghammerT. BodensteinS. SilverD. VinyalsO. SeniorA.W. KavukcuogluK. KohliP. HassabisD. Highly accurate protein structure prediction with AlphaFold.Nature2021596787358358910.1038/s41586‑021‑03819‑2
     [Google Scholar]
  25. AbramsonJ. AdlerJ. DungerJ. EvansR. GreenT. PritzelA. RonnebergerO. WillmoreL. BallardA.J. BambrickJ. BodensteinS.W. EvansD.A. HungC.C. O’NeillM. ReimanD. TunyasuvunakoolK. WuZ. ŽemgulytėA. ArvanitiE. BeattieC. BertolliO. BridglandA. CherepanovA. CongreveM. Cowen-RiversA.I. CowieA. FigurnovM. FuchsF.B. GladmanH. JainR. KhanY.A. LowC.M.R. PerlinK. PotapenkoA. SavyP. SinghS. SteculaA. ThillaisundaramA. TongC. YakneenS. ZhongE.D. ZielinskiM. ŽídekA. BapstV. KohliP. JaderbergM. HassabisD. JumperJ.M. Accurate structure prediction of biomolecular interactions with AlphaFold 3.Nature2024630801649350010.1038/s41586‑024‑07487‑w
     [Google Scholar]
  26. VaradiM. AnyangoS. DeshpandeM. NairS. NatassiaC. YordanovaG. YuanD. StroeO. WoodG. LaydonA. ŽídekA. GreenT. TunyasuvunakoolK. PetersenS. JumperJ. ClancyE. GreenR. VoraA. LutfiM. FigurnovM. CowieA. HobbsN. KohliP. KleywegtG. BirneyE. HassabisD. VelankarS. Alphafold protein structure database: Massively expanding the structural coverage of protein-sequence space with high-accuracy models.Nucleic Acids Res.202250D1D439D44410.1093/nar/gkab106134791371
     [Google Scholar]
  27. RobertX. GouetP. Deciphering key features in protein structures with the new ENDscript server.Nucleic Acids Res.201442W1W320W32410.1093/nar/gku31624753421
     [Google Scholar]
  28. MeringC. HuynenM. JaeggiD. SchmidtS. BorkP. SnelB. STRING: A database of predicted functional associations between proteins.Nucleic Acids Res.200331125826110.1093/nar/gkg03412519996
     [Google Scholar]
  29. SnelB. LehmannG. BorkP. HuynenM.A. STRING: A web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.Nucleic Acids Res.200028183442344410.1093/nar/28.18.344210982861
     [Google Scholar]
  30. SzklarczykD. KirschR. KoutrouliM. NastouK. MehryaryF. HachilifR. GableA.L. FangT. DonchevaN.T. PyysaloS. BorkP. JensenL.J. von MeringC. The STRING database in 2023: Protein–protein association networks and functional enrichment analyses for any sequenced genome of interest.Nucleic Acids Res.202351D1D638D64610.1093/nar/gkac100036370105
     [Google Scholar]
  31. KozakovD. HallD.R. XiaB. PorterK.A. PadhornyD. YuehC. BeglovD. VajdaS. The ClusPro web server for protein–protein docking.Nat. Protoc.201712225527810.1038/nprot.2016.16928079879
     [Google Scholar]
  32. KozakovD. BeglovD. BohnuudT. MottarellaS.E. XiaB. HallD.R. VajdaS. How good is automated protein docking?Proteins201381122159216610.1002/prot.2440323996272
     [Google Scholar]
  33. DestaI.T. PorterK.A. XiaB. KozakovD. VajdaS. Performance and its limits in rigid body protein-protein docking.Structure202028910711081.e310.1016/j.str.2020.06.00632649857
     [Google Scholar]
  34. TinaK.G. BhadraR. SrinivasanN. PIC: Protein interactions calculator.Nucleic Acids Res.200735Web ServerW473W47610.1093/nar/gkm42317584791
     [Google Scholar]
  35. LaskowskiR.A. SwindellsM.B. LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery.J. Chem. Inf. Model.201151102778278610.1021/ci200227u21919503
     [Google Scholar]
  36. WallaceA.C. LaskowskiR.A. ThorntonJ.M. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions.Protein Eng. Des. Sel.19958212713410.1093/protein/8.2.1277630882
     [Google Scholar]
  37. PronkS. PállS. SchulzR. LarssonP. BjelkmarP. ApostolovR. ShirtsM.R. SmithJ.C. KassonP.M. van der SpoelD. HessB. LindahlE. GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit.Bioinformatics201329784585410.1093/bioinformatics/btt05523407358
     [Google Scholar]
  38. BrooksB.R. BruccoleriR.E. OlafsonB.D. StatesD.J. SwaminathanS. KarplusM. CHARMM : A program for macromolecular energy, minimization, and dynamics calculations.J. Comput. Chem.19834218721710.1002/jcc.540040211
     [Google Scholar]
  39. BerendsenH.J.C. PostmaJ.P.M. van GunsterenW.F. DiNolaA. HaakJ.R. Molecular dynamics with coupling to an external bath.J. Chem. Phys.19848183684369010.1063/1.448118
     [Google Scholar]
  40. ParrinelloM. RahmanA. Crystal structure and pair potentials: A molecular-dynamics study.Phys. Rev. Lett.198045141196119910.1103/PhysRevLett.45.1196
     [Google Scholar]
  41. HessB. BekkerH. BerendsenH.J.C. FraaijeJ.G.E.M. LINCS: A linear constraint solver for molecular simulations.J. Comput. Chem.199718121463147210.1002/(SICI)1096‑987X(199709)18:12<1463::AID‑JCC4>3.0.CO;2‑H
     [Google Scholar]
  42. DardenT. YorkD. PedersenL. Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems.J. Chem. Phys.19939812100891009210.1063/1.464397
     [Google Scholar]
  43. Biovia, Dassault Systèmes, Discovey Studio.San DiegoDassault Systèmes2020
     [Google Scholar]
  44. BurkhardtP. StegmannC.M. CooperB. KloepperT.H. ImigC. VaroqueauxF. WahlM.C. FasshauerD. Primordial neurosecretory apparatus identified in the choanoflagellate Monosiga brevicollis.Proc. Natl. Acad. Sci. USA201110837152641526910.1073/pnas.110618910821876177
     [Google Scholar]
  45. ColbertK.N. HattendorfD.A. WeissT.M. BurkhardtP. FasshauerD. WeisW.I. Syntaxin1a variants lacking an N-peptide or bearing the LE mutation bind to Munc18a in a closed conformation.Proc. Natl. Acad. Sci. USA201311031126371264210.1073/pnas.130375311023858467
     [Google Scholar]
  46. StefaniI. IwaszkiewiczJ. FasshauerD. Exploring the conformational changes of the Munc18‐1 /syntaxin 1a complex.Protein Sci.2024333e487010.1002/pro.487038109275
     [Google Scholar]
  47. LiW. XingY. WangY. XuT. SongE. FengW. A non-canonical target-binding site in Munc18-1 domain 3b for assembling the Mint1-Munc18-1-syntaxin-1 complex.Structure20233116877.e510.1016/j.str.2022.11.00236608665
     [Google Scholar]
  48. GrahamS.C. WartoschL. GrayS.R. ScourfieldE.J. DeaneJ.E. LuzioJ.P. OwenD.J. Structural basis of Vps33A recruitment to the human HOPS complex by Vps16.Proc. Natl. Acad. Sci. USA201311033133451335010.1073/pnas.130707411023901104
     [Google Scholar]
  49. HackmannY. GrahamS.C. EhlS. HöningS. LehmbergK. AricòM. OwenD.J. GriffithsG.M. Syntaxin binding mechanism and disease-causing mutations in Munc18-2.Proc. Natl. Acad. Sci. USA201311047E4482E449110.1073/pnas.131347411024194549
     [Google Scholar]
  50. De VriesK.J. GeijtenbeekA. BrianE.C. De GraanP.N.E. GhijsenW.E.J.M. VerhageM. Dynamics of munc18‐1 phosphorylation/dephosphorylation in rat brain nerve terminals.Eur. J. Neurosci.200012138539010.1046/j.1460‑9568.2000.00931.x10651895
     [Google Scholar]
  51. EgertonM. ZuecoJ. BoydA. Molecular characterization of the SEC1 gene of Saccharomyces cerevisiae : Subcellular distribution of a protein required for yeast protein secretion.Yeast19939770371310.1002/yea.3200907048368004
     [Google Scholar]
  52. RoyM. RawatA. KaushikS. JyotiA. SrivastavaV.K. Endogenous cysteine protease inhibitors in upmost pathogenic parasitic protozoa.Microbiol. Res.202226112706110.1016/j.micres.2022.12706135605309
     [Google Scholar]
  53. BatraS. PancholiP. RoyM. KaushikS. JyotiA. VermaK. SrivastavaV.K. Exploring insights of syntaxin superfamily proteins from Entamoeba histolytica: A prospective simulation, protein‐protein interaction, and docking study.J. Mol. Recognit.2021346e288610.1002/jmr.288633393093
     [Google Scholar]
  54. ERRAT: An empirical atom-based method for validating protein structures.Available from: https://yeateslab.mbi.ucla.edu/structure-validation/ (accessed November 2, 2023).
  55. DulubovaI. KhvotchevM. LiuS. HuryevaI. SüdhofT.C. RizoJ. Munc18-1 binds directly to the neuronal SNARE complex.Proc. Natl. Acad. Sci. USA200710482697270210.1073/pnas.061131810417301226
     [Google Scholar]
  56. AbramovD. GuibersonN.G.L. DaabA. NaY. PetskoG.A. SharmaM. BurréJ. Targeted stabilization of Munc18‐1 function via pharmacological chaperones.EMBO Mol. Med.2021131e1235410.15252/emmm.20201235433332765
     [Google Scholar]
  57. HuS.H. ChristieM.P. SaezN.J. LathamC.F. JarrottR. LuaL.H.L. CollinsB.M. MartinJ.L. Possible roles for Munc18-1 domain 3a and Syntaxin1 N-peptide and C-terminal anchor in SNARE complex formation.Proc. Natl. Acad. Sci. USA201110831040104510.1073/pnas.091490610821193638
     [Google Scholar]
  58. HanG.A. BinN.R. KangS.Y.A. HanL. SugitaS. The domain-3a of Munc18-1 plays a crucial role at the priming stage of exocytosis.J. Cell Sci.2013126Pt 11jcs.12686210.1242/jcs.12686223525015
     [Google Scholar]
  59. LathamC.F. LopezJ.A. HuS.H. GeeC.L. WestburyE. BlairD.H. ArmishawC.J. AlewoodP.F. BryantN.J. JamesD.E. MartinJ.L. Molecular dissection of the Munc18c/syntaxin4 interaction: Implications for regulation of membrane trafficking.Traffic20067101408141910.1111/j.1600‑0854.2006.00474.x16899085
     [Google Scholar]
  60. van WeeringJ.R.T. ToonenR.F. VerhageM. The role of Rab3a in secretory vesicle docking requires association/dissociation of guanidine phosphates and Munc18-1.PLoS One200727e61610.1371/journal.pone.000061617637832
     [Google Scholar]
  61. Gengyo-AndoK. KuroyanagiH. KobayashiT. MurateM. FujimotoK. OkabeS. MitaniS. The SM protein VPS‐45 is required for RAB‐5‐dependent endocytic transport in Caenorhabditis elegans.EMBO Rep.20078215215710.1038/sj.embor.740088217235359
     [Google Scholar]
  62. HuangC.C. YangD.M. LinC.C. KaoL.S. Involvement of Rab3A in vesicle priming during exocytosis: Interaction with Munc13-1 and Munc18-1.Traffic201112101356137010.1111/j.1600‑0854.2011.01237.x21689256
     [Google Scholar]
  63. SimonsenA. GaullierJ.M. D’ArrigoA. StenmarkH. The Rab5 effector EEA1 interacts directly with syntaxin-6.J. Biol. Chem.199927441288572886010.1074/jbc.274.41.2885710506127
     [Google Scholar]
  64. StroupeC. HickeyC.M. MimaJ. BurfeindA.S. WicknerW. Minimal membrane docking requirements revealed by reconstitution of Rab GTPase-dependent membrane fusion from purified components.Proc. Natl. Acad. Sci. USA200910642176261763310.1073/pnas.090380110619826089
     [Google Scholar]
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Elucidation of EhSec1 and Interaction with EhSyntaxin1A /1B of Entamoeba Histolytica via Docking and Molecular Simulations
Curr. Proteomics 21, 711 (2024); https://doi.org/10.2174/0115701646329881241217082005
/content/journals/cp/10.2174/0115701646329881241217082005
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  • Article Type:     Research Article
Keyword(s): docking; EhSec1; EhSyntaxin 1A/1B; Entamoeba Histolytica; SNARE proteins; syntaxins

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