{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T09:24:13Z","timestamp":1788341053214,"version":"build-2803163510"},"reference-count":64,"publisher":"American Chemical Society (ACS)","issue":"8","license":[{"start":{"date-parts":[[2020,2,19]],"date-time":"2020-02-19T00:00:00Z","timestamp":1582070400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_ccbyncnd_termsofuse.html"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology , Ministry of Science and Technology","doi-asserted-by":"publisher","award":["BT\/RLF\/Re-entry\/40\/2014"],"award-info":[{"award-number":["BT\/RLF\/Re-entry\/40\/2014"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board","doi-asserted-by":"publisher","award":["ECR\/2017\/000010"],"award-info":[{"award-number":["ECR\/2017\/000010"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011581","name":"Indian Institute of Technology Indore","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/501100011581","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cholera is caused by Vibrio cholerae and is an example of a blood-group-dependent disease. Recent studies suggest that the receptor-binding B subunit of the cholera toxin (CT) binds histo\u2013blood group antigens at a secondary binding site. Herein, we studied the conformational dynamics of Lewis Y (LeY) oligosaccharides, H-tetrasaccharides and A-pentasaccharides, in aqueous solution by conducting accelerated molecular dynamics (aMD) simulations. The flexible nature of both oligosaccharides was displayed in aMD simulations. Furthermore, aMD simulations revealed that for both oligosaccharides in the free form, 4C1 and 1C4 puckers were sampled for all but GalNAc monosaccharides, while either the 4C1 (GlcNAc, Gal, GalNAc) or 1C4 (Fuc2, Fuc3) pucker was sampled in the CT-bound forms. In aMD, the complete transition from the 4C1 to 1C4 pucker was sampled for GlcNAc and Gal in both oligosaccharides. Further, we have observed a transition from the open to closed conformer in the case of A-pentasaccharide, while H-tetrasaccharide remains in the open conformation throughout the simulation. Both oligosaccharides adopted an open conformation in the CT binding site. Moreover, we have investigated the molecular basis of recognition of LeY oligosaccharides by the B subunit of the cholera toxin of classical and El Tor biotypes using the molecular mechanics generalized Born surface area (MM\/GBSA) scheme. The O blood group determinant, H-tetrasaccharide, exhibits a stronger affinity to both biotypes compared to the A blood group determinant, A-pentasaccharide, which agrees with the experimental data. The difference in binding free energy between O and A blood group determinants mainly arises due to the increased entropic cost and desolvation energy in the case of A-pentasaccharide compared to that of H-tetrasaccharide. Our study also reveals that the terminal Fuc3 contributes most to the binding free energy compared to other carbohydrate residues as it forms multiple hydrogen bonds with CT. Overall, our study might help in designing glycomimetic drugs targeting the cholera toxin.<\/jats:p>","DOI":"10.1021\/acsomega.9b03398","type":"journal-article","created":{"date-parts":[[2020,2,19]],"date-time":"2020-02-19T06:45:30Z","timestamp":1582094730000},"page":"3932-3942","source":"Crossref","is-referenced-by-count":32,"title":["Investigating Conformational Dynamics of Lewis Y Oligosaccharides\nand Elucidating Blood Group Dependency of Cholera Using Molecular\nDynamics"],"prefix":"10.1021","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5788-9424","authenticated-orcid":true,"given":"Rajarshi","family":"Roy","sequence":"first","affiliation":[{"name":"Indian Institute of Technology Indore , , Khandwa Road , ,","place":["Indore, India, 453552"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Biplab","family":"Ghosh","sequence":"additional","affiliation":[{"name":"Bhabha Atomic Research Centre , , Trombay, ,","place":["Mumbai, India, 400085"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8451-9739","authenticated-orcid":true,"given":"Parimal","family":"Kar","sequence":"additional","affiliation":[{"name":"Indian Institute of Technology Indore , , Khandwa Road , ,","place":["Indore, India, 453552"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,2,19]]},"reference":[{"key":"2026090205104178800_cit1","doi-asserted-by":"publisher","first-page":"4635","DOI":"10.1182\/blood-2010-01-261859","article-title":"The relationship\nbetween blood groups and disease","volume":"115","author":"Anstee","year":"2010","journal-title":"Blood"},{"key":"2026090205104178800_cit2","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1016\/S0140-6736(03)15328-7","article-title":"Cholera","volume":"363","author":"Sack","year":"2004","journal-title":"Lancet"},{"key":"2026090205104178800_cit3","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1080\/03014467700002481","article-title":"ABO blood groups and\ncholera","volume":"4","author":"Barua","year":"1977","journal-title":"Ann. Hum. Biol."},{"key":"2026090205104178800_cit4","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1093\/infdis\/170.2.468","article-title":"Severe life-threatening\ncholera associated with blood\ngroup 0 in peru: implications for the latin american epidemic","volume":"170","author":"Swerdlow","year":"1994","journal-title":"J. Infect. Dis."},{"key":"2026090205104178800_cit5","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/0035-9203(95)90667-3","article-title":"Extension\nof the\nvolunteer challenge model to study South American cholera in a population\nof volunteers predominantly with blood group antigen O","volume":"89","author":"Tacket","year":"1995","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"2026090205104178800_cit6","doi-asserted-by":"publisher","first-page":"7422","DOI":"10.1128\/IAI.73.11.7422-7427.2005","article-title":"Blood group, immunity, and risk of\ninfection with Vibrio cholerae in an\narea of endemicity","volume":"73","author":"Harris","year":"2005","journal-title":"Infect. Immun."},{"key":"2026090205104178800_cit7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0000221","article-title":"Susceptibility\nto Vibrio cholerae infection in a cohort\nof household contacts of patients with cholera in Bangladesh","volume":"2","author":"Harris","year":"2008","journal-title":"PLoS Neglected Trop. Dis."},{"key":"2026090205104178800_cit8","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1093\/oxfordjournals.aje.a114050","article-title":"Predisposition for cholera of individuals with O blood group possible\nevolutionary significance","volume":"121","author":"Glass","year":"1985","journal-title":"Am. J. Epidemiol."},{"key":"2026090205104178800_cit9","doi-asserted-by":"publisher","first-page":"263","DOI":"10.4269\/ajtmh.16-0440","article-title":"Cholera and ABO\nBlood Group: Understanding an Ancient\nAssociation","volume":"95","author":"Harris","year":"2016","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"2026090205104178800_cit10","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/306551a0","article-title":"Cholera toxin genes: nucleotide sequence, deletion\nanalysis and vaccine development","volume":"306","author":"Mekalanos","year":"1983","journal-title":"Nature"},{"key":"2026090205104178800_cit11","doi-asserted-by":"publisher","first-page":"1347","DOI":"10.1007\/s00018-008-7496-5","article-title":"Cholera toxin structure, gene regulation and pathophysiological\nand immunological aspects","volume":"65","author":"Sa\u0301nchez","year":"2008","journal-title":"Cell. Mol. 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Dyn."},{"key":"2026090205104178800_cit18","doi-asserted-by":"publisher","first-page":"1126","DOI":"10.1080\/07391102.2014.931825","article-title":"Molecular simulation\nof N-acetylneuraminic acid analogs\nand molecular dynamics studies of cholera toxin-Neu5Gc complex","volume":"33","author":"Blessy","year":"2015","journal-title":"J. Biomol. Struct. Dyn."},{"key":"2026090205104178800_cit19","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1080\/07391102.2015.1136689","article-title":"Molecular dynamics of sialic acid analogues complex\nwith cholera toxin and DFT optimization of ethylene glycol-mediated\nzinc nanocluster conjugation","volume":"35","author":"Sharmila","year":"2017","journal-title":"J. Biomol. Struct.\nDyn."},{"key":"2026090205104178800_cit20","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1006862","article-title":"GM1 ganglioside-independent intoxication by\nCholera toxin","volume":"14","author":"Cervin","year":"2018","journal-title":"PLoS Pathog."},{"key":"2026090205104178800_cit21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00894-010-0947-6","article-title":"Binding\nefficiencies of carbohydrate ligands with different genotypes of cholera\ntoxin B: molecular modeling, dynamics and docking simulation studies","volume":"18","author":"Fazil","year":"2012","journal-title":"J. Mol. 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Res."},{"key":"2026090205104178800_cit26","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1007\/s12551-012-0090-y","article-title":"Conformational flexibility\nof N-glycans in solution studied by REMD simulations","volume":"4","author":"Re","year":"2012","journal-title":"Biophys. Rev."},{"key":"2026090205104178800_cit27","doi-asserted-by":"publisher","first-page":"8504","DOI":"10.1021\/jp212550z","article-title":"Effect of\nbisecting GlcNAc and core fucosylation on conformational properties\nof biantennary complex-type N-glycans in solution","volume":"116","author":"Nishima","year":"2012","journal-title":"J. Phys. Chem. B"},{"key":"2026090205104178800_cit28","doi-asserted-by":"publisher","first-page":"2011","DOI":"10.1021\/acschembio.6b00333","article-title":"The hidden conformation of Lewis\nx, a human histo-blood group antigen, is a determinant for recognition\nby pathogen lectins","volume":"11","author":"Topin","year":"2016","journal-title":"ACS Chem. Biol."},{"key":"2026090205104178800_cit29","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/jcc.21253","article-title":"Using the\nlocal elevation method\nto construct optimized umbrella sampling potentials: calculation of\nthe relative free energies and interconversion barriers of glucopyranose\nring conformers in water","volume":"31","author":"Hansen","year":"2010","journal-title":"J. Comput. Chem."},{"key":"2026090205104178800_cit30","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1139\/v80-098","article-title":"The conformations\nof oligosaccharides related to the ABH and Lewis human blood group\ndeterminants","volume":"58","author":"Lemieux","year":"1980","journal-title":"Can. J. Chem."},{"key":"2026090205104178800_cit31","doi-asserted-by":"publisher","first-page":"11919","DOI":"10.1063\/1.1755656","article-title":"Accelerated molecular dynamics: a\npromising and efficient simulation method for biomolecules","volume":"120","author":"Hamelberg","year":"2004","journal-title":"J. Chem. Phys."},{"key":"2026090205104178800_cit32","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1002\/minf.201100135","article-title":"Free energy calculations\nby the molecular mechanics\nPoisson\u2013 Boltzmann surface area method","volume":"31","author":"Homeyer","year":"2012","journal-title":"Mol. Inf."},{"key":"2026090205104178800_cit33","doi-asserted-by":"publisher","first-page":"310","DOI":"10.3390\/toxins2030310","article-title":"Cholera Toxin: An\nIntracellular Journey into the Cytosol by Way of the Endoplasmic Reticulum","volume":"2","author":"Wernick","year":"2010","journal-title":"Toxins"},{"key":"2026090205104178800_cit34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0071149","article-title":"Deciphering the glycan\npreference of bacterial lectins\nby glycan array and molecular docking with validation by microcalorimetry\nand crystallography","volume":"8","author":"Topin","year":"2013","journal-title":"PLoS One"},{"key":"2026090205104178800_cit35","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1107\/S1399004714026595","article-title":"Structural insights into Aspergillus\nfumigatus lectin\nspecificity: AFL binding sites are functionally non-equivalent","volume":"71","author":"Houser","year":"2015","journal-title":"Acta Crystallogr., Sect. 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Dyn."},{"key":"2026090205104178800_cit41","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/07391102.2019.1602079","article-title":"Investigating specificity\nof the anti-hypertensive inhibitor WNK463\nagainst With-No-Lysine kinase family isoforms via multiscale simulations","author":"Jonniya","year":"2019","journal-title":"J. Biomol. Struct. Dyn."},{"key":"2026090205104178800_cit42","doi-asserted-by":"publisher","first-page":"17404","DOI":"10.1021\/acsomega.9b02187","article-title":"Investigating\nPhosphorylation-Induced\nConformational Changes in WNK1 Kinase by Molecular Dynamics Simulations","author":"Jonniya","year":"2019","journal-title":"ACS Omega"},{"key":"2026090205104178800_cit43","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1021\/acsinfecdis.7b00085","article-title":"Fucosylated\nmolecules\ncompetitively interfere with cholera toxin binding to host cells","volume":"4","author":"Wands","year":"2018","journal-title":"ACS Infect. Dis."},{"key":"2026090205104178800_cit44","doi-asserted-by":"publisher","DOI":"10.1063\/1.5024389","article-title":"Efficient sampling\nof puckering states of monosaccharides through\nreplica exchange with solute tempering and bond softening","volume":"149","author":"Wang","year":"2018","journal-title":"J. Chem. Phys."},{"key":"2026090205104178800_cit45","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2500a\nvisualization\nsystem for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"2026090205104178800_cit46","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","article-title":"ff14SB: improving\nthe accuracy of\nprotein side chain and backbone parameters from ff99SB","volume":"11","author":"Maier","year":"2015","journal-title":"J. Chem. Theory Comput."},{"key":"2026090205104178800_cit47","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1002\/jcc.20820","article-title":"GLYCAM06: a generalizable\nbiomolecular force field. Carbohydrates","volume":"29","author":"Kirschner","year":"2008","journal-title":"J.\nComput. Chem."},{"key":"2026090205104178800_cit48","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison\nof simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J. Chem. Phys."},{"key":"2026090205104178800_cit49","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","article-title":"Numerical\nintegration of the cartesian\nequations of motion of a system with constraints: molecular dynamics\nof n-alkanes","volume":"23","author":"Ryckaert","year":"1977","journal-title":"J. Comput. 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Generalized born","volume":"8","author":"Go\u0308tz","year":"2012","journal-title":"J.\nChem. Theory Comput."},{"key":"2026090205104178800_cit54","doi-asserted-by":"publisher","first-page":"3878","DOI":"10.1021\/ct400314y","article-title":"Routine\nmicrosecond molecular dynamics simulations with AMBER on GPUs. 2.\nExplicit solvent particle mesh Ewald","volume":"9","author":"Salomon-Ferrer","year":"2013","journal-title":"J. Chem.\nTheory Comput."},{"key":"2026090205104178800_cit55","doi-asserted-by":"publisher","first-page":"3084","DOI":"10.1021\/ct400341p","article-title":"PTRAJ and CPPTRAJ: software for processing\nand analysis of molecular dynamics trajectory data","volume":"9","author":"Roe","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"2026090205104178800_cit56","doi-asserted-by":"publisher","first-page":"2677","DOI":"10.1021\/ct500090q","article-title":"Improved reweighting\nof accelerated molecular dynamics\nsimulations for free energy calculation","volume":"10","author":"Miao","year":"2014","journal-title":"J.\nChem. Theory Comput."},{"key":"2026090205104178800_cit57","doi-asserted-by":"publisher","first-page":"1889","DOI":"10.1021\/acs.jcim.8b00120","article-title":"Defining the Specificity\nof Carbohydrate\u2013Protein\nInteractions by Quantifying Functional Group Contributions","volume":"58","author":"Sood","year":"2018","journal-title":"J. Chem. Inf. 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