Bioinformatický seminár

Tue 10 May. 2011, 17:20

Title: Skolnick et al. The continuity of protein structure space is an intrinsic property of proteins
Speaker: Martin Macko

The classical view of the space of protein structures is that it is
populated by a discrete set of protein folds. For proteins up to 200
residues long, by using structural alignments and building upon ideas of
the completeness and continuity of structure space, we show that nearly
any structure is significantly related to any other using a transitive set
of no more than 7 intermediate structurally related proteins. This result
holds for all structures in the Protein Data Bank, even when structural
relationships between evolutionary related proteins (as detected by
threading or functional analyses) are excluded. A similar picture holds
for an artificial library of compact, hydrogen-bonded, homopolypeptide
structures. The 3 sets share the global connectivity features of random
graphs, in which the local connectivity of each node (i.e., the number of
neighboring structures per protein) is preserved. This high connectivity
supports the continuous view of single-domain protein structure space.
More importantly, these results do not depend on evolution, rather just on
the physics of protein structures. The fact that evolutionary divergence
need not be invoked to explain the continuous nature of protein structure
space has implications for how the universe of protein structures might
have originated, and how function should be transferred between proteins
of similar structure.