Coupled vibrations in peptides and proteins: Structural information using 2D-IR spectroscopy

We describe experimental evidence of how detecting the coupling between vibrations can give access to structural information of proteins and peptides at the molecular level. We focus on the investigation of the folded and unfolded states of proteins and peptides in equilibrium. We investigate two types of vibrations: those involved in salt bridges, and backbone amide I vibrations, and the size of the systems than we study ranges from a dimer formed by a few atoms to proteins formed by several hundreds of atoms. The first three chapters are introductory. In Chapter 4 we present the characterization of the 2D-IR response of salt bridges in solution formed by guanidinium and acetate. Chapter 5 is closely related, and we show how the 2D-IR response of a salt bridge between arginine and glutamic acid can be detected in peptides in solution. In Chapter 6 we study the amide I vibrations of tripeptides, and discuss the conformational changes upon variation in the charges of the side groups and C-terminus. The next two chapters contain a study of the chemical-denaturation mechanism of guanidinium, which is a powerful denaturant. In Chapter 7 we investigate the guanidinium-induced denaturation of two well-known proteins, lysozyme and α-chymotrypsin. In Chapter 8 we study how guanidinium affects the stability of a designed mini-protein, a zinc-finger mutant, which has structural properties that differ from most natural proteins. Finally, in Chapter 9 we introduce the topic of amyloid-fibril formation, and show how the appearance of fibrils in lysozyme can be induced with a ‘temperature-shock’.