Speakers
Description
Intrinsically disordered proteins (IDPs) are identified by polypeptide chains that do not have a stable single well-defined structure. They are responsible for the development of neurogenetic diseases such as Alzheimer and Parkinson. Structural characterization of IDPs has to be facilitated by both NMR experiment and computational techniques. The functionality of standard techniques such as X-ray crystallography is limited due to the high flexibility of IDPs. Thus the application of quantum mechanics (QM) calculations combined with molecular dynamics (MD) simulations is highly recommended.
In this contribution, we focus on the calculation of spin-spin couplings. The prediction of J-couplings typically builds on empirically parameterized Karplus equations. Alternatively, quantum mechanics (QM) can be applied if the empirical parametrization is prevented by the lack of training experimental data. We design a computational protocol that combines the molecular dynamics (MD) calculations with density functional (DFT) calculations along with fragmentation techniques.
The poster contribution builds on the application of the adjustable density matrix assembler (ADMA) for the protein fragmentation. We will discuss the effect of the DFT method and basis set as well as the effect of the size of surroundings on the computed spin-spin couplings. In addition, the impact of statistical averaging and ensemble size will be demonstrated for an example of Tau protein fragment.
