Structural Studies on Proteincarbohydrate Interactions and Inhibitor Design Using Molecular Modeling Techniques
IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata
View Archive Info| Field | Value | |
| Title |
Structural Studies on Proteincarbohydrate Interactions and
Inhibitor Design Using Molecular Modeling Techniques
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| Creator |
Patra, Madhumita
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| Subject |
Structural Biology & Bioinformatics
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| Description |
Carbohydrates are the most abundant of the four major classes of biomolecules, which also include proteins, lipids and nucleic acids. They have numerous roles in living things, such as the storage and transport of energy (starch, glycogen) and structural components (cellulose in plants, chitin in animals). Additionally, carbohydrates and their derivatives play major roles in the working process of the immune system, fertilization,
pathogenesis, blood clotting, and development. The protein-carbohydrate interactions have been investigated in recent years through the analysis of the 3-D structures of a
number of proteins and their complexes with carbohydrates, by X-ray crystallographic and NMR spectroscopic methods as well as by molecular modeling studies. In the
present work the nature of interactions between proteins and carbohydrates has been explored at the molecular level using advanced molecular modeling techniques.
The first chapter provides a general introduction to the field of study highlighting the lectins from different sources, drug design and molecular modeling approaches for 3-D structure prediction. The second chapter presents the general description of methods used in the present study. The third chapter presents the results and discussions on the prediction of 3-D structures of mannose-binding and glucose/galactose-binding lectins from different source, namely, animal, bacteria and fungi using homology modeling
techniques based on the crystal structures of mannose-binding and glucose/galactosebinding lectins available in the database. A few newly published protein sequences have
been selected for structure prediction and analysis in order to understand their functional roles. Influence of calcium ions on carbohydrate binding has also been explored
wherever relevant. The fourth chapter presents the results and discussions on the prediction of 3-D structures of all known human Siglecs based on the crystal structure of
human Siglec-7. Related specific sugars have been docked on to the carbohydratebinding sites to get the structures of the complexes. The natures of chemical forces
involved in sugar-protein interactions were analyzed to examine the strength of such binding. The knowledge of these modeled structures and particularly of their
carbohydrate recognition domains may provide valuable information in developing potent therapeutics. The fifth chapter is focused on inhibitor design of a modeled
cysteine protease of Leishmania donovani using target based drug design method.
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| Date |
2008
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| Type |
Thesis
NonPeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://www.eprints.iicb.res.in/897/1/Thesis_Madhumita.pdf
Patra, Madhumita (2008) Structural Studies on Proteincarbohydrate Interactions and Inhibitor Design Using Molecular Modeling Techniques. PhD thesis, Jadavpur University. |
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| Relation |
http://www.eprints.iicb.res.in/897/
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