Abstract
For several of the proteins in the BioMagResBank larger than 200 residues, 60 % or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6 × 10260 possible assignments. In “EZ-ASSIGN”, the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al. in PLoS Comput Biol 5(3):e1000307, 2009) and significantly outperformed SAGA (Crippen et al. in J Biomol NMR 46:281–298, 2010), AUTOASSIGN (Zimmerman et al. in J Mol Biol 269:592–610, 1997), and IBIS (Hyberts and Wagner in J Biomol NMR 26:335–344, 2003). Next, EZ-ASSIGN was used to investigate how well NMR data of decreasing completeness can be assigned. We found that the program could confidently assign fragments in very incomplete data. Here, EZ-ASSIGN dramatically outperformed all the other assignment programs tested.
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Acknowledgments
E.R.P.Z. acknowledges support from National Institutes of Health grant NS059690 (to G.E. Gestwicki, P.I.). I.B. was supported by National Institutes of Health grant HL 102662 (to S. Ragdale, P.I.); P.R. was supported by National Institutes of Health grant AI094623 (to C. G. Kalodimos, P.I.). The authors acknowledge N.K. Khanra (Rutgers) for the type III ATPAse sample preparation and helpful discussions.
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Zuiderweg, E.R.P., Bagai, I., Rossi, P. et al. EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data. J Biomol NMR 57, 179–191 (2013). https://doi.org/10.1007/s10858-013-9778-y
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DOI: https://doi.org/10.1007/s10858-013-9778-y