TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra
While NMR studies of proteins typically aim at structure, dynamics or interactions, resonance assignments represent in almost all cases the initial step of the analysis. With increasing complexity of the NMR spectra, for example due to decreasing extent of ordered structure, this task often becomes both difficult and time-consuming, and the recording of high-dimensional data with high-resolution may be essential. Random sampling of the evolution time space, combined with sparse multidimensional Fourier transform (SMFT), allows for efficient recording of very high dimensional spectra (≥4 dimensions) while maintaining high resolution. However, the nature of this data demands for automation of the assignment process. Here we present the program TSAR (Tool for SMFT-based Assignment of Resonances), which exploits all advantages of SMFT input. Moreover, its flexibility allows to process data from any type of experiments that provide sequential connectivities. The algorithm was tested on several protein samples, including a disordered 81-residue fragment of the δ subunit of RNA polymerase from Bacillus subtilis containing various repetitive sequences. For our test examples, TSAR achieves a high percentage of assigned residues without any erroneous assignments.
KeywordsAlgorithm Automated resonance assignment High-dimensional fast NMR Intrinsically disordered protein
This work has been supported by the Bio-NMR project under the 7th Framework Programme of the EC grant agreement 261863 for conducting the research. A.Z.-K. thanks the Foundation for Polish Science for supporting her with the MPD Programme that was co-financed by the EU European Regional Development Fund. The experiments were performed in the Structural Research Laboratory at the Faculty of Chemistry, University of Warsaw, Poland (calbindin, CsPin and delta), and the Swedish NMR Centre, University of Gothenburg, Sweden (azurin). We thank Jiří Nováček of the Masaryk University for providing data from 13C-detected experiments for the delta protein, which were used for testing of an early version of the TSAR program. We are grateful to Göran Karlsson of the Swedish NMR Centre for the loan of labeled azurin.
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