The relationship between n-gram patterns and protein secondary structure

An n-gram pattern (NP{n,m}) in a protein sequence is a set of n residues and m wildcards in a window of size n+m. Each window of n+m amino acids is associated with a collection of NP{n,m} patterns based on the combinatorics of n+m objects taken m at a time. NP{n,m} patterns that are shared between sequences reflect evolutionary relationships. Recently the authors developed an alignment-independent protein classification algorithm based on shared NP{4,2} patterns that compared favorably to PSI-BLAST. Theoretically, NP{4,2} patterns should also reflect secondary structure propensity since they contain all possible n-grams for 1 < or = n < or = 4 and a window of 6 residues is wide enough to capture periodicities in the 2 < or = n < or = 5 range. This sparked interest in differentiating the information content in NP{4,2} patterns related to evolution from the content related to local propensity. The probability of alpha-, beta-, and coil components was determined for every NP{4,2} pattern over all the chains in the Protein Data Bank (PDB). An algorithm exclusively based on the Z-values of these distributions was developed, which accurately predicted 71-76% of alpha-helical segments and 62-67% of beta-sheets in rigorous jackknife tests. This provided evidence for the strong correlation between NP{4,2} patterns and secondary structure. By grouping PDB chains into subsets with increasing levels of sequence identity, it was also possible to separate the evolutionary and local propensity contributions to the classification process. The results showed that information derived from evolutionary relationships was more important for beta-sheet prediction than alpha-helix prediction.