Is polyproline II a major backbone conformation in unfolded proteins?

Abstract

Protein folding is a process by which a polypeptide chain acquires its native structure from an unfolded state through a transition state. Recent studies of the unfolded states of proteins are based on a modification of the random coil model, recognizing that in many cases some residual native or non-native structure persists.. Combined evidence from the theoretical study of a blocked alanine peptide in aqueous solution and a variety of spectroscopic studies, including ultraviolet circular dichroism (CD), nuclear magnetic resonance (NMR), two-dimensional vibrational spectroscopy, vibrational circular dichroism (VCD), and vibrational Raman optical activity (VROA) reveal that the polyproline II (P II ) conformation is the dominant conformation in a variety of short model peptides. This chapter discusses the evidence from short peptides. It reviews the circular dichroism of unfolded proteins and addresses the role of P II in unfolded proteins.