Automated resonance assignment of proteins using heteronuclear 3D NMR. 1. Backbone spin systems extraction and creation of polypeptides

Heteronuclear 3D NMR has been used to determine protein solution structures for many years. Scalar magnetization transfer through peptide bonds can be observed in triple resonance 3D NMR and thus makes the sequential assignment of a protein backbone more straightforward. In this paper a generic algorithm is proposed to automate protein backbone resonance assignments. The algorithm searches and merges cross peaks among all available NMR spectra. Individual spin systems can be extracted and linked to form polypeptide chains based on observed interresidue correlations. The algorithm is not restricted to a particular type of experiments and is shown to be applicable to two sets of NMR spectra. The first set of NMR data includes five experiments: 3D HNCO, HNCA, HN(CO)CA, HCACO, and ¹⁵N TOCSY-HMQC. The second set of data is a 3D CBCANH spectrum. The implemented computer program was tested on the first NMR data set of a 90 residue protein N-domain of chicken skeletal troponin-C.