Membrane proteins play important roles in photosynthesis and electron transfer processes, in ion and molecule transport phenomena and in membrane mediated catalysis. The structure investigation of this important class of proteins has, however, been successful only for beta-based proteins using high resolution NMR spectroscopy. Furthermore, standard electron- or X-ray structure determination methods can not be applied to these proteins due to difficulties with preparation of the diffractive crystals. Recently, a new NMR approach which utilizes the sensitivity of the 19F chemical shifts to the presence of oxygen, was proposed for structure determination of such membrane proteins. The usage of 19F atoms instead of 1H atoms in NMR spectroscopy allows a significantly increased accuracy of the method as the fluorine exhibits dispersion of the chemical shifts about 100 times larger than hydrogen. The fluorine is not found in natural proteins, but can be introduced at the desired residue position of the protein through cysteine mutaganesis and subsequent chemical derivatization. Unfortunately, the analysis of results obtained in this novel NMR approach is complicated and it is in some cases difficult to properly relate observed chemical shifts with protein structure. In this situation first principles calculations of the chemical shifts in the simplified protein fragments and oxygen complexes can allow to relate the electronic and geometric structure of the complexes to the observed chemical shifts and significantly aid in the structure determination of the proteins. Therefore, we propose to investigate the19F chemical shifts of simplified protein fragments and oxygen complexes using density functional theory methods using a newly developed code at our laboratory for paramagnetic NMR calculation. This code is unique of its kind. The main goal of this investigation is to obtain relations between chemical shifts and protein electronic and geometric structure and to investigate local environment effects (hydrogen bonding, van der Waals interaction) on the ability of oxygen to induce paramagnetic shifts on the atoms in the the protein fragment.
The project involves running of simulations on computers, including structure optimization and NMR shielding computations, analysis of results and discussions with group members and NMR experimentalists which are housed in the same location.
If you are interested or have any questions about the project, feel free to contact Hans Ågren (agren-at-theochem.kth.se)