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De novo protein structure generation from incomplete chemical shift assignments

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Abstract

NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

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Acknowledgments

This work was funded by the Intramural Research Program of the NIDDK, NIH, and by the Intramural AIDS-Targeted Antiviral Program of the Office of the Director, NIH; the NIGMS, NIH, and the Howard Hughes Medical Institutes (to D. B.). We also thank Rosetta@home participants and the BOINC project for contributing computing power.

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Authors and Affiliations

  1. Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA

    Yang Shen & Ad Bax

  2. Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA

    Robert Vernon & David Baker

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  1. Yang Shen
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Correspondence to Ad Bax.

Electronic supplementary material

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A brief discussion of CS23D results for proteins discussed in this study; multiple figures detailing the quality of the selected fragments and the CS-Rosetta results for various combinations of input chemical shift data.

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Shen, Y., Vernon, R., Baker, D. et al. De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR 43, 63–78 (2009). https://doi.org/10.1007/s10858-008-9288-5

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