Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools

  • Daniel Monleón
  • Kimberly Colson
  • Hunter N. B. Moseley
  • Clemens Anklin
  • Robert Oswald
  • Thomas Szyperski
  • Gaetano T. Montelione
Article

Abstract

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.Abbreviations: BPTI – bovine pancreatic trypsin inhibitor; LP – linear prediction; FT – Fourier transform; S/N – signal-to-noise ratio; FID – free induction decay

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Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Daniel Monleón
    • 1
  • Kimberly Colson
    • 2
  • Hunter N. B. Moseley
    • 1
  • Clemens Anklin
    • 2
  • Robert Oswald
    • 3
  • Thomas Szyperski
    • 4
  • Gaetano T. Montelione
    • 1
  1. 1.Center for Advanced Biotechnology, and Medicine and Department of Molecular Biology and BiochemistryRutgers UniversityPiscatawayUSA
  2. 2.Bruker Instruments Inc.BillericaUSA
  3. 3.Department of Molecular MedicineCornell UniversityIthacaUSA
  4. 4.Department of Chemistry, University of BuffaloThe State University of New YorkBuffaloUSA

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