Abstract
It has been demonstrated that protein folds can be determined using appropriate computational protocols with NMR chemical shifts as the sole source of experimental restraints. While such approaches are very promising they still suffer from low convergence resulting in long computation times to achieve accurate results. Here we present a suite of time- and sensitivity optimized NMR experiments for rapid measurement of up to six RDCs per residue. Including such an RDC data set, measured in less than 24 h on a single aligned protein sample, greatly improves convergence of the Rosetta-NMR protocol, allowing for overnight fold calculation of small proteins. We demonstrate the performance of our fast fold calculation approach for ubiquitin as a test case, and for two RNA-binding domains of the plant protein HYL1. Structure calculations based on simulated RDC data highlight the importance of an accurate and precise set of several complementary RDCs as additional input restraints for high-quality de novo structure determination.
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Acknowledgments
The authors thank Martin Blackledge for stimulating discussions, Nicolas Bologna for providing clones of HYL1 domains, Isabel Ayala for help with sample preparation and the Grenoble Partnership for Structural Biology for access to the high field NMR and isotope labeling platforms. This work was supported by the French research agency (ANR JCJC05-0077 and ANR JCJC06-0034), HFSP (RG-0057/2006), the Agencia Nacional para la Promoción de la Ciencia y la Tecnología (PICT-2007-720), and the European commission (I3, Contract No. 026145).
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Rasia, R.M., Lescop, E., Palatnik, J.F. et al. Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins. J Biomol NMR 51, 369–378 (2011). https://doi.org/10.1007/s10858-011-9567-4
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DOI: https://doi.org/10.1007/s10858-011-9567-4