Structural and dynamical properties in protein ligand interactions [thesis]

Mona Sarter, Jörg Fitter, Andreas Stadler
2020
In this work structural and dynamical properties of protein ligand interactions were analysed. This was done predominately by the use of scattering techniques. In addition to scattering techniques complimentary techniques were used to supplement the information obtained. The main scattering technique used was incoherent neutron scattering, as it allows for a separation of the analysed protein and its surrounding hydration layer. Two protein ligand systems were analysed. The first was the
more » ... irst was the protein streptavidin(STV) and its ligand biotin (B). In addition to this, a genetically engineered Försterresonance energy transfer (FRET) based glucose sensor was analysed with and withoutadded glucose. For the selected systems, the specific challenge was to separate the influences of the hydration layer and the protein. Similarly, it is also challenging to create models that incorporate all the separate observations to form a cohesive interpretation. In order to regard the STV protein independently from the surrounding hydration layer neutronscattering was chosen as the appropriate technique. Whereas, for the glucose sensor thestructural changes were deemed to be the most important information to obtain and therefore X-ray scattering was employed. For the STV+B interaction it was considered that molecular dynamics play a vitalrole for the biological function of proteins. Changes in the proteins conformational entropy and of the hydration layer influence the binding process for many protein ligand interactions. Here this was investigated for STV, as well as the change in the internal dynamics of STV upon biotin binding. Quasi elastic neutron scattering (QENS) was used to investigate the change of conformational entropy of the protein and its dynamics. QENS results show that the conformational entropy of STV is reduced upon biotinbinding. Thermal diffusion forced Rayleigh scattering (TDFRS) results also indicatean increased entropy of the hydration layer. This indicates that the hydration layerplays an important role in stabilising th [...]
doi:10.18154/rwth-2021-01984 fatcat:2srcj4uohvhcrigambrd7l2ehy