Abstract
Structurally analogous protein pairs with low sequence identity, such as analogues and remote homologues, comprise a large part of structurally similar pairs thus complicating the relationship between sequence and structure. To obtain clues for clarifying such intricate relationships, we developed a method to analyze the coarse-grained charge distribution in an amino acid sequence and analyzed the pattern of charge distribution for the pairs of structurally similar proteins with sequence identities lower than 20%. We found two types of pairs, those with similar patterns of charge distribution and those with inverted charge distribution. This finding suggested that the charge distribution in a sequence might be a good parameter for clustering the structures as analogs and remote homologs. The possibility of automatic fold recognition is discussed by a quantitative comparison of charge distribution patterns.
