Analysis of the amino-acid co-substitution patterns has long promised the prediction of protein structure but has failed to deliver. One possible reason is that most methods presume that co-substitution is indicative of residue-residue contact, yet the extent to which this conjecture is true is unproven. Here, a method is developed to investigate the relationship between specific co-substitution types and their propensity to occur at different physical separations in a protein structure. Amino-acids are typically segregated into two types; hydrophilic residues, predominantly found on the protein surface, and the hydrophobic residues in the protein interior. Thus, the propensity of a given amino-acid substitution occurring at the surface must differ from that in the interior of the protein, the implications of this for co-substitution has never previously been considered. To allow a definition of surface and buried residues, the cross-over point demarcating the surface residues from the protein interior was calculated here, using a Half Sphere Exposure with a radius of 13 A, as 20 HSEu, above which value a residue can be considered buried, and below which it can be considered to be on the surface.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:583142 |
| Date | January 2013 |
| Creators | Auro, Bhima |
| Publisher | University of Birmingham |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://etheses.bham.ac.uk//id/eprint/4611/ |
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