Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectroscopy of microhydrated biomolecules to develop an approach for revealing the native-like structures of biomolecules. Unlike spectroscopy in solution, gas-phase IR and UV cold-ion spectroscopy may provide vibrationally resolved spectra that can be used for stringent validation of 3D structures calculated in silico, while microhydration of biomolecules allows bridging the gap between the gas-phase and the native structures, of which only the latter remains truly biologically relevant.
The first part of this thesis describes an ion source that was developed and used for stable generation of large quantities of protonated microhydrated complexes. This source allows generating microsolvated complexes by two different methods. One of them is based on an incomplete desolvation of water droplets with the embedded biomolecule during electrospray ionization. An alternative approach relies on the cryogenic condensation of solvent molecules onto the electrosprayed bare ions.
In the second part, we study two microhydrated amino acids â protonated arginine and tryptophan. Microhydrated ArgH+ is an example of the complexes with kinetically trapped structures. The native-like structure of ArgH+ complexed with water molecules appears to be kinetically trapped due to evaporative cooling that significantly lowers the temperature of the complexes and slows down the conformational rearrangements. Microhydrated TrpH+, on the other hand, is an example of a system that, under our experimental conditions, undergoes the solution to the gas phase transition adiabatically, without kinetic trapping. All the studied complex sizes of TrpH+(H2O)n (n = 0-6) reside in their lowest energy structures, which is experimentally verified by the fact that the spectra of these complexes with retained and condensed water molecules are identical. We also performed theoretical calculations to find the structure of both of these complexes. While the standard approach of searching for the lowest energy structures provides a good match with experimental spectra for the water complexes of TrpH+, it does not work well with the complexes of ArgH+. For this case, we proposed another computational workflow, which closely mimics the conditions of generation of the complexes and finally led to a better consistency with the experiment.
The last part of this thesis demonstrates the application of cold ion spectroscopy for large biomolecules, such as proteins. We showed that both IR and UV spectroscopy can provide valuable information about the protein ubiquitin. IR spectroscopy allows tracing the global conformational rearrangements of the protein, such as unfolding, while UV spectroscopy provides information about noncovalent interactions and local molecular structures around chromophores. We also showed that evaporative cooling plays a crucial role in retaining the folded native-like structure of the protein. Even a few water molecules retained on the protein ensure its low temperature and protect the native-like structure during the electrospray ionization. However, if the water molecules are condensed on the already unfolded protein, its stricture does not refold into the native one.