Positional preferences by 20 amino acids in beta sheets

Abstract

Many studies revealed that different amino acids have different preferences for taking part in alpha helices and beta sheets conformations. Different substitution matrices have been prepared to compare the proteins' secondary and tertiary structures. Unfortunately, in many cases these matrices are unable to produce reliable results, due to the complexity of these conformations. In this work, following dissection of beta sheets with different size, the amino acids compositions of each position in each class of beta sheets were extracted and compared. The amino acid contents of the same position in different beta sheets were also compared. Our results indicate great differences in amino acid contents between beta sheets with different size. Individual substitution matrices might be required in order to do alignment and comparison studies for different types of beta sheets. These results might also imply alternative evolutionary route for beta sheets with different size; longer beta sheets could be a result of merging the smaller one together in different combinations, rather than simple expansion of the smaller sheets. Based on these findings hopefully we would be able to propose an improved substitution matrix (possibly more than one) that could be used for all secondary structures, regardless of their size.