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Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens
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...
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| Format: | Thesis |
| Language: | English |
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Department of Computer Science
2014
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| _version_ | 1867613267124289536 |
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| access_status_str | Open Access |
| author | Mathai, Neann Sarah |
| author2 | Kuttel, Michelle Mary |
| author_browse | Kuttel, Michelle Mary Mathai, Neann Sarah |
| author_facet | Kuttel, Michelle Mary Mathai, Neann Sarah |
| author_sort | Mathai, Neann Sarah |
| collection | Thesis |
| description | 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. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/6641 |
| institution | University of Cape Town (South Africa) |
| language | eng |
| last_indexed | 2026-06-10T12:33:25.185Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2014 |
| publishDateRange | 2014 |
| publishDateSort | 2014 |
| publisher | Department of Computer Science |
| publisherStr | Department of Computer Science |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/6641 Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens Mathai, Neann Sarah Kuttel, Michelle Mary Ravenscroft, Neil 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. 2014-08-20T19:41:53Z 2014-08-20T19:41:53Z 2013 Master Thesis Masters MSc http://hdl.handle.net/11427/6641 eng application/pdf Department of Computer Science Faculty of Science University of Cape Town |
| spellingShingle | Mathai, Neann Sarah Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens |
| thesis_degree_str | Master's |
| title | Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens |
| title_full | Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens |
| title_fullStr | Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens |
| title_full_unstemmed | Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens |
| title_short | Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens |
| title_sort | molecular modelling of the streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens |
| url | http://hdl.handle.net/11427/6641 |
| work_keys_str_mv | AT mathaineannsarah molecularmodellingofthestreptococcuspneumoniaeserogroup6capsularpolysaccharideantigens |