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Complete protein assignment from sets of spectra recorded overnight

Journal article
Authors Jonas Fredriksson
Wolfgang Bermel
Martin Billeter
Published in Journal of Biomolecular NMR
Volume 73
Issue 1-2
Pages 59-70
ISSN 0925-2738
Publication year 2019
Published at Department of Chemistry and Molecular Biology
Pages 59-70
Language en
Links https://doi.org/10.1007/s10858-019-...
Keywords Flexible characterization · Fast data acquisition · Projection · Decomposition · NMR assignment
Subject categories Structural Biology

Abstract

A flexible and scalable approach for protein NMR is introduced that builds on rapid data collection via projection spectroscopy and analysis of the spectral input data via joint decomposition. Input data may originate from various types of spectra, depending on the ultimate goal: these may result from experiments based on triple-resonance pulse sequences, or on TOCSY or NOESY sequences, or mixtures thereof. Flexible refers to the free choice of spectra for the joint decompositions depending on the purpose: assignments, structure, dynamics, interactions. Scalable means that the approach is open to the addition of similar or different experiments, e.g. larger proteins may require a wider selection of triple-resonance based experiments. Central to the proposed approach is the mutual support among the different spectra during the spectral analysis: for example, sparser triple-resonance spectra may help decomposing (separating) spin systems in a TOCSY or identifying unique NOEs. In the example presented, backbone plus side chain assignments of ubiquitin were obtained from the combination of either two or three of the following projection experiments: a 4D HCCCONH, a 4D HNCACO and a 3D HNCACB. In all cases, TOCSY data (4D HCCCONH) proved crucial not only for the side chain assignments, but also for the sequential assignment. Even when total recording time was reduced to about 10 h, nearly complete assignments were obtained, with very few missing assignments and even fewer differences to a reference.

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