Infrared spectroscopic characterization of secondary structure elements of gas-phase biomolecules

Vibrational spectroscopy is a commonly used method in structural investigations of biomolecules in the condensed phase. Vibrational modes, such as C−O stretching vibrations (amide-I) in the range of 1700 cm−1 or N−H bending vibrations (amide-II) at around 1500 cm−1 , are sensitive to the three-dimensional arrangement of the atoms in the proteins. Knowledge of the band positions makes it possible to obtain a global picture of the fundamental conformation of the molecule. Investigations on gas-phase biomolecules allow for an insight into the intrinsic intra-molecular interactions, which determine the molecular structure. Many proteins possess secondary structural elements, including for instance α-helix and β-sheet, and these motifs often determine the structure of the entire protein. For this thesis biomolecules in the gas phase were investigated using infrared spectroscopy, the goal being to define band positions of significant structural characteristics in the infrared spectrum. The amide-I band position for the various secondary structural elements was an area of particular research interest. In the pursuit of these research aims mass spectrometry, infrared spectroscopy, and density functional theory methodologies were employed. The effectiveness of infrared spectroscopy in combination with theoretical calculations in determining molecular structure of molecules in the gas phase was confirmed in this thesis using the highly symmetrical systems C – 60 und C – 70. Cytochrome c, a protein with a predominantly α-helical secondary structure in the condensed phase, was investigated in the charge states 7+ to 16+. A shift of the amide-I band towards higher frequencies was observed with increasing charge state. The secondary structure of the second investigated protein, tendamistat, is characterized in the condensed phase by a β-sheet motif. As a model system for α-helical secondary structures in the gas phase, alanine based peptides were used due to their demonstrated helical structure in the gas phase. The cyclic peptide gramicidin S was used as a possible model system for a β-sheet motif in the gas phase. Interactions between charged side chains and the backbone of the peptide were suppressed through complexation with crown ether molecules. Measurements were taken on the molecule VW01, which was synthesized so that in the condensed phase the dimer possesses a coiled coil structure. The monomer, which is not observed in the condensed phase, exhibits a random coil structure. The observed shifts in the amide-I band position of the investigated molecules were as expected: With increasing hydrogen bonding strength the band shifts towards lower frequencies. The observed band positions varied for the different molecules, which could be due to their differing structures. It is difficult to differentiate between amide-I band positions for molecules with either an α-helical or random coil structure in the gas phase, which however also applies for the condensed phase. It became evident that it may be beneficial to use a system other than gramicidin S as a model for the β-sheet structure in the gas phase. These small, rigid molecules possess namely only four hydrogen bonds in this secondary structural motif. In regards to the dimer of VW01, it was shown that a non-covalently bound protein complex can be transferred intact into the gas phase. The amide-I band position observed for this complex was the lowest of all investigated molecules, leading to the conclusion that it possesses the strongest hydrogen bonding network. In general this research indicates that the definition of band position to determine molecular structure is still problematic. Nevertheless it was suggested that the