Journal of Biomolecular NMR

, Volume 27, Issue 1, pp 69–79 | Cite as

Fully automated sequence-specific resonance assignments of hetero- nuclear protein spectra

  • Daniel Malmodin
  • Christina H.M. Papavoine
  • Martin Billeter
Article

Abstract

Full automation of the analysis of spectra is a prerequisite for high-throughput NMR studies in structural or functional genomics. Sequence-specific assignments often form the major bottleneck. Here, we present a procedure that yields nearly complete backbone and side chain resonance assignments starting from a set of heteronuclear three-dimensional spectra. Neither manual intervention, e.g., to correct lists obtained from peak picking before feeding these to an assignment program, nor protein-specific information, e.g., structures of homologous proteins, were required. By combining two earlier published procedures, AUTOPSY [Koradi et al. (1998) J. Magn. Reson., 135, 288–297] and GARANT [Bartels et al. (1996) J. Biomol. NMR, 7, 207–213], with a new program, PICS, all necessary steps from spectra analyses to sequence-specific assignments were performed fully automatically. Characteristic features of the present approach are a flexible design allowing as input almost any combination of NMR spectra, applicability to side chains, robustness with respect to parameter choices (such as noise levels) and reproducibility. In this study, automated resonance assignments were obtained for the 14 kD blue copper protein azurin from P. aeruginosa using five spectra: HNCACB, HNHA, HCCH-TOCSY, 15N-NOESY-HSQC and 13C-NOESY-HSQC. Peaks from these three-dimensional spectra were filtered and calibrated with the help of two two-dimensional spectra: 15N-HSQC and 13C-HSQC. The rate of incorrect assignments is less than 1.5% for backbone nuclei and about 3.5% when side chain protons are also considered.

automation AUTOPSY azurin GARANT peak picking resonance assignments structure genomics 

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Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Daniel Malmodin
    • 1
  • Christina H.M. Papavoine
    • 2
  • Martin Billeter
    • 1
  1. 1.Biochemistry and BiophysicsGöteborg UniversityGöteborgSweden
  2. 2.Medicinal Chemistry, AstraZeneca R&D MölndalMölndalSweden

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