Occurrence of protein structure elements in conserved sequence regions

Abstract

Background. Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified. Results. Helices and turns were found to be underrepresented in conserved regions, while strands were found to be overrepresented. Similar numbers of loops were found in conserved and random regions. Conclusion. These results can be understood in light of the structural constraints on different secondary structure elements, and their role in protein structural stabilization and topology. Strands can tolerate fewer sequence changes and nonetheless keep their specific shape and function. They thus tend to be more conserved than helices, which can keep their shape and function with more changes. Loop behavior can be explained by the presence of both constrained and freely changing loops in proteins. Our detailed statistical analysis of diverse proteins links protein evolution to the biophysics of protein thermodynamic stability and folding. The basic structural features of conserved sequence regions are also important determinants of protein structure motifs and their function. © 2007 Sitbon and Pietrokovski; licensee BioMed Central Ltd.