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
- XYZ file for alpha apoprotein for LH2
(Rps. Acidophila), converted from 1KZU.pdb
- XYZ file for beta apoprotein for LH2
(Rps. Acidophila), converted from 1KZU.pdb
- XYZ file for Bacteriochlorophyll A, no.1 for LH2
(Rps. Acidophila), converted from 1KZU.pdb
- XYZ file for Bacteriochlorophyll A, no.2 for LH2
(Rps. Acidophila), converted from 1KZU.pdb
- XYZ file for Bacteriochlorophyll A, no.7 for LH2
(Rps. Acidophila), converted from 1KZU.pdb
- XYZ file for Rhodopin Glucoside, no.10 for LH2
(Rps. Acidophila), converted from 1KZU.pdb
- XYZ file for Rhodopin Glucoside, no.13 for LH2
(Rps. Acidophila), converted from 1KZU.pdb
- XYZ file for alpha apoprotein for LH2
(Rs. Molischianum), converted from 1LGH.pdb
- XYZ file for beta apoprotein for LH2
(Rs. Molischianum), converted from 1LGH.pdb
- Windows executable for updating XYZ files
created by Babel from PDB files. Babel does a terrible job with atom
names. This program forms atom names from the original pdb file.