Building Geometric Models of Biological Molecules. Master's Thesis of Haruna Katayama.
This thesis applies Z-system theory to a large biomolecular system, namely the Light Harvesting Complex II (LH2) in the photosynthetic bacterium Rhodobacter Sphaeroides. An elementary mathematical account of Z-system theory is given and applied first to a simple molecular system of sodium bicarbonate dissolved in water. The molecular biology and the chemistry of the light harvesting complex are discussed from first principles. Also, since there is no X-ray crystal structure of LH2 in Rhodobacter Sphaeroides, the thesis discusses the process of homology modelling whereby molecular structures can be transferred between species sharing a high degree of amino acid sequence similarity. The process of building a labelled Z-system for LH2 is described in detail and the resulting structure is evaluated in terms of the presence or absence of steric conflicts.
Structure files (.imi) for amino acids, chlorophylls, carotenoids, lipids, and various subcomplexes.
Additional images: 1PC, 9PC, imimol canvas images and rasmol 3D images.
Software for averaging Z-systems and for converting PDB files to XYZ files.
Derivation of the ring closure formulae for Prolines.
Some XYZ files used to build the Light Harvesting Complex II