Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains

Intrinsically Disordered Proteins
Robert W WilliamsA Keith Dunker

Abstract

The Pfam database groups regions of proteins by how well hidden Markov models (HMMs) can be trained to recognize similarities among them. Conservation pressure is probably in play here. The Pfam seed training set includes sequence and structure information, being drawn largely from the PDB. A long standing hypothesis among intrinsically disordered protein (IDP) investigators has held that conservation pressures are also at play in the evolution of different kinds of intrinsic disorder, but we find that predicted intrinsic disorder (PID) is not always conserved across Pfam domains. Here we analyze distributions and clusters of PID regions in 193024 members of the version 23.0 Pfam seed database. To include the maximum information available for proteins that remain unfolded in solution, we employ the 10 linearly independent Kidera factors(1-3) for the amino acids, combined with PONDR(4) predictions of disorder tendency, to transform the sequences of these Pfam members into an 11 column matrix where the number of rows is the length of each Pfam region. Cluster analyses of the set of all regions, including those that are folded, show 6 groupings of domains. Cluster analyses of domains with mean VSL2b scores greater than 0.5 (half p...Continue Reading

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Methods Mentioned

BETA
X-ray
neutron diffraction
NMR
small
protein folding
PCA

Software Mentioned

PAM
RGgobi
MoRF
PONDR
VSL2b
Disprot PONDR
Disprot
Kidera
R
Rose

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