Backbone assignment of proteins


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Journal of Biomolecular NMR 30 25 35 2004 2004 Kluwer Academic Publishers Printed in the Netherlands 25 Backbone assignment of proteins with known structure using residual dipolar couplings Young Sang Jung Markus Zweckstetter Max Planck Institute for Biophysical Chemistry Am Fassberg 11 D 37077 G ttingen Germany Received 8 January 2004 Accepted 12 May 2004 Key words assignment maltose binding protein Mars NMR protein ligand binding RDC software structural genomics Abstract A prerequisite for NMR studies of protein ligand interactions or protein dynamics is the assignment of backbone resonances Here we demonstrate that protein assignment can significantly be enhanced when experimental dipolar couplings RDCs are matched to values back calculated from a known three dimensional structure In case of small proteins the program MARS allows assignment of more than 90 of backbone resonances without the need for sequential connectivity information For bigger proteins we show that the combination of sequential connectivity information with RDC matching enables more residues to be assigned reliably and backbone assignment to be more robust against missing data Structural or dynamic deviations from the employed 3D coordinates do not lead to an increased error rate in RDC supported assignment RDC enhanced assignment is particularly useful when chemical shifts and sequential connectivity only provide a few reliable assignments Introduction NMR spectroscopy is a powerful tool to study proteinligand binding protein nucleic acid interactions and protein dynamics A prerequisite for these studies is assignment of NMR spin resonances W thrich 2003 In recent years good progress has been made in automating the assignment process for proteins up to 20 kDa Moseley and Montelione 1999 and in the accompanying paper we have introduced the program MARS that allows robust automatic backbone assignment also for unfolded and large proteins Jung and Zweckstetter 2003 Most assignment approaches such

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