Abstract High-throughput functional protein NMR studies, like protein interactions or dynamics, require an automated approach for the assignment of the protein backbone. With the availability of a growing number of protein 3D structures, a new class of automated approaches, called
structure-
based assignment, has been developed quite recently. Structure-based approaches use primarily NMR input data that are not based on J-coupling and for which connections between residues are not limited by through bonds magnetization transfer efficiency. We present here a robust structure-based assignment approach using mainly
H N â??
H N NOEs networks, as well as 1
Hâ??15
N residual dipolar couplings and chemical shifts. The NOE
net complete search algorithm is robust against assignment errors, even for sparse input data. Instead of a unique and partly erroneous assignment solution, an optimal assignment ensemble with an accuracy equal or near to 100% is given by NOE
net. We show that even low precision assignment ensembles give enough information for functional studies, like modeling of protein-complexes. Finally, the combination of NOE
net with a low number of ambiguous J-coupling sequential connectivities yields a high precision assignment ensemble. NOE
net will be available under:
http://www.icsn.cnrs-gif.fr/download/nmr.
- Content Type Journal Article
- DOI 10.1007/s10858-009-9390-3
- Authors
- Dirk Stratmann, NMR, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
- Eric Guittet, Centre de Recherche de Gif, Laboratoire de Chimie et Biologie Structurales ICSN-CNRS 1, av. de la terrasse 91190 Gif-sur-Yvette France
- Carine van Heijenoort, Centre de Recherche de Gif, Laboratoire de Chimie et Biologie Structurales ICSN-CNRS 1, av. de la terrasse 91190 Gif-sur-Yvette France
Source: Journal of Biomolecular NMR