An analysis of structural instances of low complexity sequence segments

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Abstract
Amino acid sequence databases contain many low complexity, compositionally biased sequence segments. However, only a limited number of relatively short instances of these segments occur in proteins of known structure. An analysis is presented of structural instances of these low complexity sequence segments in the Brookhaven Protein Data Bank with regard to preferences for sequence composition, secondary structural conformation and the local atomic environment. The complexity varies almost linearly with segment length, reflecting the absence of very long, low complexity segments in the structural database. The low complexity segments identified are not disordered and have temperature factors which are generally the same as the rest of the protein. It is observed that these segments are predominantly exposed and either helical or coiled, in excess of what would be expected by chance. Secondary structure prediction methods perform well in correctly predicting those low complexity segments which are helical but poorly in correctly predicting segments that are strands.

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