Erik Saparbayev
Non-covalent interactions are ubiquitous in nature. The diversity and functionality of these interactions are employed by nature as a universal tool for building the molecular mechanism of life. Although weak, these interactions play a key role in both formation of 3D structures of biomolecules through intra- and intermolecular binding and highly selective coupling between biomolecules. In this thesis, we explore these interactions in two directions: (i) for solving native 3D structures of biomolecules and (ii) for analytical identifications of isomeric carbohydrates. Both studies use the technique of cold ion spectroscopy (CIS), which often enables vibrational resolution in infrared and electronic spectra of biomolecules isolated in the gas. Although the resolved spectra can be used in solving the intrinsic molecular 3D structures of biomolecules, life science research desperately needs their native structures. It is challenging however to get vibrational resolution in solution phase, where these structures originally reside. As a compromise, we do not fully dehydrate the biomolecules during their gentle electrospray ionization (ESI) and leave a few water molecules attached to the ion. The structure of such microhydrated molecule may resemble its native one in solution while working in the gas phase enables the desired vibrational spectral resolution.The second direction of the study aims to explore the sensitivity of intermolecular noncovalent interactions in biomolecular complexes to fine structural details of the partners. The work demonstrates how this sensitivity can be used for analytical identifications of the biomolecules that are highly rich in isomers.In the first part of this work, we report on the elucidation of native structures of small protonated biomolecules glycine and triglycine. We apply cold ion IR spectroscopy to the gas-phase complexes of these biomolecules, in which they are microhydrated by a controlled number of water molecules. The complexes were produced directly from an aqueous solution, using a gentle ESI source. Our studies suggest that retaining molecules in the complexes generated from the solution allows for preserving the main structural features of the native structures.In the second part of the thesis, we report on the investigation of the sensitivity of non-covalent interaction between aromatic molecules and carbohydrates to structural details of binding partners. We calculated structures of non-covalent complexes of aromatic molecules with isomeric monosaccharides and validated them by IR spectroscopy. It appears, that the change of an analyzing isomeric carbohydrate molecule significantly influences the UV absorption of the aromatic sensor molecule. The spectral difference between the complexes is explained by the interplay of different intermolecular non-covalent bonds, which may not be all identical for different isomers. Even structural changes in the groups that are not directly involved in non-covalent binding with chromophore exhibit a significant impact on UV spectra.In the last part of the thesis, we explore the use of non-covalent carbohydrate-aromatic complexes for the identification of isomeric glycans using a unique method of 2D UV-MS CIS. We demonstrated the applicability of this method for accurate identification and quantification of all types of isomeric carbohydrates and tested the performance of the technically simpler version of the method, 1D UV fragmentation spectroscopy.
EPFL2021
