{"id":{"repo_id":"cape-town","oai_identifier":"oai:open.uct.ac.za:11427/6641"},"canonical_url":"https://search.dev.ndltd.org/etd/cape-town/oai:open.uct.ac.za:11427/6641","repository":{"repo_id":"cape-town","name":"University of Cape Town","base_url":"https://open.uct.ac.za/oai/request"},"display":{"title":"Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens","abstract":"In this thesis, a systematic study of the structural characterization of the capsular polysaccharides of Streptococcus pneumoniae is conducted using Molecular Modelling methods. S.pneumoniae causes invasive pneumococcal disease (IPD), a leading cause of death in children under five. The serotypes in group 6 are amongst the most common of IPD causing serotypes. We performed structural characterization of serogroup 6 to understand the structural relationships between serotypes 6A, 6B, 6C and 6D in an attempt to understand the cross protection seen within the group. The 6B saccharide has been included in the early conjugate vaccine (PCV-7), and has shown to elicit protection against the 6B as well as some cross-protection against 6A. 6A has since been included in the latter conjugate vaccines in the hopes of eliciting stronger protection against 6A and 6C. Molecular Dynamics simulations were used to investigate the conformations of oligosaccharides with the aim of elucidating a conformational rationale for why small changes in the carbohydrate primary structure result in variable efficacy. We began by examining the Potential of Mean Force (PMF) plots of the disaccharide subunits which make up the Serogroup 6 oligosaccharides. The PMFs showed the free energy profiles along the torsional angles space of the disaccharides. This conformational information was then used to build the four oligosaccharides on which simulations were conducted. These simulations showed that serotype pairs 6A/6C and 6B/6D have similar structures.","abstract_html":"In this thesis, a systematic study of the structural characterization of the capsular polysaccharides of Streptococcus pneumoniae is conducted using Molecular Modelling methods. S.pneumoniae causes invasive pneumococcal disease (IPD), a leading cause of death in children under five. The serotypes in group 6 are amongst the most common of IPD causing serotypes. We performed structural characterization of serogroup 6 to understand the structural relationships between serotypes 6A, 6B, 6C and 6D in an attempt to understand the cross protection seen within the group. The 6B saccharide has been included in the early conjugate vaccine (PCV-7), and has shown to elicit protection against the 6B as well as some cross-protection against 6A. 6A has since been included in the latter conjugate vaccines in the hopes of eliciting stronger protection against 6A and 6C. Molecular Dynamics simulations were used to investigate the conformations of oligosaccharides with the aim of elucidating a conformational rationale for why small changes in the carbohydrate primary structure result in variable efficacy. We began by examining the Potential of Mean Force (PMF) plots of the disaccharide subunits which make up the Serogroup 6 oligosaccharides. The PMFs showed the free energy profiles along the torsional angles space of the disaccharides. This conformational information was then used to build the four oligosaccharides on which simulations were conducted. These simulations showed that serotype pairs 6A/6C and 6B/6D have similar structures.","abstract_has_math":false,"creators":["Mathai, Neann Sarah"],"institution":"Department of Computer Science","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Kuttel, Michelle Mary","Ravenscroft, Neil"],"committee_chairs":[],"committee_members":[],"year":2013,"date_issued":"2013","date_published":"2013","updated_at":"2026-07-22T22:23:12Z","subjects":[],"languages":["eng"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/11427/6641","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Kuttel, Michelle Mary","Ravenscroft, Neil"]},{"key":"dc:creator","label":"Author","values":["Mathai, Neann Sarah"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2014-08-20T19:41:53Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2014-08-20T19:41:53Z"]},{"key":"dc:date.issued","label":"Date","values":["2013"]},{"key":"dc:publisher.department","label":"Dc Publisher Department","values":["Department of Computer Science"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cape Town"]},{"key":"dc:type","label":"Dc Type","values":["Master Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Masters"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["MSc"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["eng"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/11427/6641"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["In this thesis, a systematic study of the structural characterization of the capsular polysaccharides of Streptococcus pneumoniae is conducted using Molecular Modelling methods. S.pneumoniae causes invasive pneumococcal disease (IPD), a leading cause of death in children under five. The serotypes in group 6 are amongst the most common of IPD causing serotypes. We performed structural characterization of serogroup 6 to understand the structural relationships between serotypes 6A, 6B, 6C and 6D in an attempt to understand the cross protection seen within the group. The 6B saccharide has been included in the early conjugate vaccine (PCV-7), and has shown to elicit protection against the 6B as well as some cross-protection against 6A. 6A has since been included in the latter conjugate vaccines in the hopes of eliciting stronger protection against 6A and 6C. Molecular Dynamics simulations were used to investigate the conformations of oligosaccharides with the aim of elucidating a conformational rationale for why small changes in the carbohydrate primary structure result in variable efficacy. We began by examining the Potential of Mean Force (PMF) plots of the disaccharide subunits which make up the Serogroup 6 oligosaccharides. The PMFs showed the free energy profiles along the torsional angles space of the disaccharides. This conformational information was then used to build the four oligosaccharides on which simulations were conducted. These simulations showed that serotype pairs 6A/6C and 6B/6D have similar structures."]},{"key":"dc:title","label":"Title","values":["Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens"]}]}],"canonical_facts":{"dc:contributor.advisor":["Kuttel, Michelle Mary","Ravenscroft, Neil"],"dc:creator":["Mathai, Neann Sarah"],"dc:date.accessioned":["2014-08-20T19:41:53Z"],"dc:date.available":["2014-08-20T19:41:53Z"],"dc:date.issued":["2013"],"dc:description.abstract":["In this thesis, a systematic study of the structural characterization of the capsular polysaccharides of Streptococcus pneumoniae is conducted using Molecular Modelling methods. S.pneumoniae causes invasive pneumococcal disease (IPD), a leading cause of death in children under five. The serotypes in group 6 are amongst the most common of IPD causing serotypes. We performed structural characterization of serogroup 6 to understand the structural relationships between serotypes 6A, 6B, 6C and 6D in an attempt to understand the cross protection seen within the group. The 6B saccharide has been included in the early conjugate vaccine (PCV-7), and has shown to elicit protection against the 6B as well as some cross-protection against 6A. 6A has since been included in the latter conjugate vaccines in the hopes of eliciting stronger protection against 6A and 6C. Molecular Dynamics simulations were used to investigate the conformations of oligosaccharides with the aim of elucidating a conformational rationale for why small changes in the carbohydrate primary structure result in variable efficacy. We began by examining the Potential of Mean Force (PMF) plots of the disaccharide subunits which make up the Serogroup 6 oligosaccharides. The PMFs showed the free energy profiles along the torsional angles space of the disaccharides. This conformational information was then used to build the four oligosaccharides on which simulations were conducted. These simulations showed that serotype pairs 6A/6C and 6B/6D have similar structures."],"dc:identifier.uri":["http://hdl.handle.net/11427/6641"],"dc:language.iso":["eng"],"dc:publisher.department":["Department of Computer Science"],"dc:publisher.institution":["University of Cape Town"],"dc:title":["Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens"],"dc:type":["Master Thesis"],"dc:type.qualificationlevel":["Masters"],"dc:type.qualificationname":["MSc"]},"updated_at":"2026-07-22T22:23:12Z"}