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Journal of Biomolecular NMR

, Volume 50, Issue 3, pp 285–297 | Cite as

AUTOBA: Automation of backbone assignment from HN(C)N suite of experiments

  • Aditi Borkar
  • Dinesh Kumar
  • Ramakrishna V. HosurEmail author
Article

Abstract

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.

Keywords

Structural proteomics HN(C)N Backbone assignment Start points Checkpoints Automated assignment AUTOBA 

Abbreviations

NMR

Nuclear magnetic resonance

HSQC

Heteronuclear single quantum correlation

BMRB

Biological magnetic resonance data bank

CARA

Computer aided resonance assigment (a software for NMR data analysis)

AUTOBA

Automatic backbone assignment

Notes

Acknowledgments

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.

Supplementary material

10858_2011_9518_MOESM1_ESM.pdf (1.1 mb)
Supplementary material 1 (PDF 1104 kb)

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Aditi Borkar
    • 1
  • Dinesh Kumar
    • 1
  • Ramakrishna V. Hosur
    • 1
    • 2
    Email author
  1. 1.Department of Chemical SciencesTata Institute of Fundamental Research (TIFR)MumbaiIndia
  2. 2.UM-DAE Centre for Excellence in Basic SciencesMumbai University CampusMumbaiIndia

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