Stability of alpha-helical and beta-structural blocks in proteins of four structural classes

Abstract

In this article we showed the characteristic structural features of the groups of interacting alpha-helices and beta-strands (blocks) in four sets of nonhomologous proteins from different structural classes. Stability of each element of secondary structure has been checked with help of the PentaFOLD algorithm that finds intrinsic alpha-helical and beta-structural sequences of amino acid residues. We proved that the most frequent blocks of “alpha + beta” and “alpha/beta” proteins are 2 interacting alpha helices, and they demonstrate the highest level of stability. In alpha-helical proteins the most frequent blocks contain 4 alpha-helices. In beta-structural proteins alpha-helices most frequently do not interact with other helices and demonstrate the lowest level of stability. The most stable type of beta-structure is a block made from three interacting beta-strands, while the less stable one is a beta-hairpin. There is a characteristic distribution of stable alpha-helices in “alpha + beta” proteins: they are usually situated in the beginning of a block while stable beta-strands are usually situated in the end of the block. This type of distribution of stable alpha-helices and beta-strands helps the protein to form its stable three-dimensional structure in case  it begins from beta-structural domain which is the most frequent case for the structural class of proteins.