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’.
If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let
the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible
and/or remove it from the website. Please Ask the Library, or send a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands.
You will be contacted as soon as possible.