The relationship between sequence and structure in elementary folding units

Abstract

Publisher Summary This chapter describes the relationship between sequence and structure in α-helices, β-hairpins, and β- sheets. First, there is an analysis regarding the individual conformational preferences of 20 amino acids. These tendencies could explain the conformational preferences detected in the random coil state, as well as the secondary structure propensities of the 20 amino acids. This is followed by a description of the extent of the knowledge regarding α-helices. The α-helix is the best known and most easily recognized of the polypeptide regular structures. The chapter focuses on β-hairpins and β-sheets, about which much less is known. Finally, the importance of secondary structure elements in protein folding and stability is discussed. Kinetic analysis of proteins with stabilized α-helices demonstrates that an increase in the contribution of favorable local native interactions can, in some cases, optimize folding rates. Essentially, when a secondary structure element is folded in the transition state, its stabilization will accelerate folding. As in the case of the protein stabilization the increase in folding speed will not be equivalent to the stabilization of the secondary structure element, since the denatured state will also be stabilized.