Calculation of NMR spin-spin couplings for intrinsically disordered proteins: a prospective tool to facilitate experimental NMR studies

GAFFOUR, Amina, Jana PAVLIKOVA PRECECHTELOVA, Michael BAKKER and Krishnendu BERA. Calculation of NMR spin-spin couplings for intrinsically disordered proteins: a prospective tool to facilitate experimental NMR studies. In PAVLIKOVA PRECECHTELOVA, Jana and Michael BAKKER. 5th Users’ Conference of IT4Innovations. 2021.

Basic information

Original name

Calculation of NMR spin-spin couplings for intrinsically disordered proteins: a prospective tool to facilitate experimental NMR studies

Authors

GAFFOUR, Amina, Jana PAVLIKOVA PRECECHTELOVA, Michael BAKKER and Krishnendu BERA

Edition

5th Users’ Conference of IT4Innovations, 2021

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Other information

Type of outcome

Konferenční abstrakt

Confidentiality degree

není předmětem státního či obchodního tajemství

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Abstract

V originále

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.