The nmr² method to determine rapidly the structure of the binding pocket of a protein–ligand complex with high accuracy

Author(s)

Marielle Aulikki Wälti, Julien Orts

Abstract

Structural characterization of complexes is crucial for a better understanding of biological processes and structure-based drug design. However, many protein–ligand structures are not solvable by X-ray crystallography, for example those with low affinity binders or dynamic binding sites. Such complexes are usually targeted by solution-state NMR spectroscopy. Unfortunately, structure calculation by NMR is very time consuming since all atoms in the complex need to be assigned to their respective chemical shifts. To circumvent this problem, we recently developed the Nuclear Magnetic Resonance Molecular Replacement (NMR2) method. NMR2 very quickly provides the complex structure of a binding pocket as measured by solution-state NMR. NMR2 circumvents the assignment of the protein by using previously determined structures and therefore speeds up the whole process from a couple of months to a couple of days. Here, we recall the main aspects of the method, show how to apply it, discuss its advantages over other methods and outline its limitations and future directions.

Organisation(s)

External organisation(s)

Eidgenössische Technische Hochschule Zürich

Journal

Magnetochemistry

Volume

4

No. of pages

14

ISSN

2312-7481

DOI

https://doi.org/10.3390/magnetochemistry4010012

Publication date

03-2018

Peer reviewed

Yes

Austrian Fields of Science 2012

106006 Biophysics, 106002 Biochemistry

Keywords

ASJC Scopus subject areas

Electronic, Optical and Magnetic Materials, Chemistry (miscellaneous), Materials Chemistry

Portal url

https://ucris.univie.ac.at/portal/en/publications/the-nmr2-method-to-determine-rapidly-the-structure-of-the-binding-pocket-of-a-proteinligand-complex-with-high-accuracy(6b07b75c-6c57-429f-99c8-0a926711d2ec).html