Amino acid residue burial & co-evolution in proteins

Auro, Bhima (2013). Amino acid residue burial & co-evolution in proteins. University of Birmingham. Ph.D.

Preview

Auro13PhD.pdf
PDF - Accepted Version
Download (13MB)

Abstract

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.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):