Proteins and peptides are flexible and fluctuating molecules whose dynamics occur on a wide range of time scales, extending from seconds to femtoseconds.
Without these conformational fluctuations most biological molecules would cease to function. It is therefore important to develop methods to investigate the dynamics
of peptides and proteins in order to understand different phenomena such as protein folding, motor proteins, catalysis and allosteric regulation. Dynamical processes on millisecond and slower time scales can be efficiently studied by NMR spectroscopy. Information on picosecond time scales can be obtained by infrared spectroscopy. The extension of linear spectroscopy to multidimensional
techniques allows us to obtain also structural information. It has been demonstrated that two-dimensional infrared (2D-IR) spectroscopy makes it possible to resolve distributions and dynamics of fast (on a sub-picosecond time scale) interconverting structures in equilibrium. The high time resolution of 2D-IR spectroscopy can be put to full use in the investigation of transient structures. Transient 2D-IR (T-2D-IR) spectroscopy is a promising tool to obtain information on peptides geometry during conformational transitions. Transient 2D-IR experiments
require an external trigger to induce the structural changes at a well defined time.
The aims of this thesis are to further develop 2D-IR and transient 2D-IR spectroscopic techniques dynamics which mimic natural processes as closely as possible. To this end, 2DIR and T-2D-IR spectroscopy are first introduced. In particular a fully detailed comparison (theoretical and experimental) between two experimental implementations
of 2D-IR spectroscopy is given. One of these spectroscopic techniques is then applied to study photoinduced conformational changes in a small photoswitchable
polypeptide. The photo-switch in the polypeptide is a thioxo-peptide unit, i.e. a peptide where a sulfur atom has replaced one backbone carbonyl oxygen.
The one atom substitution does not alter significantly the structure of the thiopeptide from the original oxopeptide structure but renders the peptide selectively photo-isomerizable from the trans to the cis conformation without photodecomposition.
In order to investigate the isomerization mechanism of the thioamide bond, we have first followed the isomerization mechanism of the smallest molecule isomerizable containing a thioamide bond, N-Methylthioacetamide (NMTAA), by means of time resolved IR spectroscopy. The isomerization of
NMTAA occurs with a high quantum yield on a few hundred picoseconds time scale. After establishing the NMTAA isomerization mechanism we have inserted the thioamide bond in a model peptide constituted by two symmetric alanine units separated by a thioswitch unit and two terminal groups. The molecules can adopt a cyclic conformation stabilized by a hydrogen bond in coexistence with more
extended conformations. UV-pump IR-probe measurements show that the isomerization of the thiounit is an efficient process, and causes the opening of the loop conformation. At the end of this thesis we analyze carefully T-2D-IR spectra obtained for the thioxopeptide, and we show that this molecule is a good model to explore how the transient 2D-IR signals are related to peptide conformational dynamics.