Correlated and Further Dynamics in Proteins by NMR Spectroscopy

Abstract

In the first part of this thesis the use of three NMR parameter for the detection of protein dynamics are investigated. The knowledge about the dynamics of proteins is essential for the understanding of many protein functions. NMR spectroscopy is a very powerful tool for the detection of protein dynamics due to its atomic resolution and its variety of experiments. Residual dipolar couplings (RDCs) are used since a few years to measure motions in the time window between nanoseconds and microseconds, which was undetectable for earlier methods. The self-consistent RDC based model free (SCRM) method can be used to extract from RDC data sets in several different alignment media the dynamical behavior of the atom pair. In this thesis the structural noise elevating ability of the SCRM approach was examined. In a second project, possibilities for the detection of correlated motions in proteins were investigated. For this purpose cross-correlated relaxation (CCR) rates between two atom pairs were measured, which are directly depending on the angle between the two internuclear vectors and therefore can deliver information about correlated motions of the two atom pairs. Several experiments for the measurement of CCR rates in the protein backbone, in the hydrophobic core and between ß-strands were developed. In addition to RDCs and CCR rates also the Nuclear Overhauser Effect (NOE) rates can reflect protein dynamics. NOESY spectra of a fully protonated protein at three field strengths were measured and assigned for a later determination and use of the NOE rates. In a second part of the thesis it was investigated if bicelles could be a valuable hydrophobic environment of membrane proteins for the process of structure determination. Bicelles are a medium between small micelles, which differ strongly from physiological membranes, and liposomes, which are to large for the use with solution NMR spectroscopy. The composition of the bicelles were determined and the bicelle protein interface was investigated. Furthermore indications of structural differences of the protein in micelles and bicelles were found.