AUTOBA: Automation of backbone assignment from HN(C)N suite of experiments
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Development of efficient strategies and automation represent important milestones of progress in rapid structure determination efforts in proteomics research. In this context, we present here an efficient algorithm named as AUTOBA (Automatic Backbone Assignment) designed to automate the assignment protocol based on HN(C)N suite of experiments. Depending upon the spectral dispersion, the user can record 2D or 3D versions of the experiments for assignment. The algorithm uses as inputs: (i) protein primary sequence and (ii) peak-lists from user defined HN(C)N suite of experiments. In the end, one gets HN, 15N, Cα and C′ assignments (in common BMRB format) for the individual residues along the polypeptide chain. The success of the algorithm has been demonstrated, not only with experimental spectra recorded on two small globular proteins: ubiquitin (76 aa) and M-crystallin (85 aa), but also with simulated spectra of 27 other proteins using assignment data from the BMRB.
KeywordsStructural proteomics HN(C)N Backbone assignment Start points Checkpoints Automated assignment AUTOBA
Nuclear magnetic resonance
Heteronuclear single quantum correlation
Biological magnetic resonance data bank
Computer aided resonance assigment (a software for NMR data analysis)
Automatic backbone assignment
We thank the Government of India for providing financial support to the National Facility for High Field NMR at Tata Institute of Fundamental Research, India.
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