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KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies

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Abstract

The recent expansion of structural genomics has increased the demands for quick and accurate protein structure determination by NMR spectroscopy. The conventional strategy without an automated protocol can no longer satisfy the needs of high-throughput application to a large number of proteins, with each data set including many NMR spectra, chemical shifts, NOE assignments, and calculated structures. We have developed the new software KUJIRA, a package of integrated modules for the systematic and interactive analysis of NMR data, which is designed to reduce the tediousness of organizing and manipulating a large number of NMR data sets. In combination with CYANA, the program for automated NOE assignment and structure determination, we have established a robust and highly optimized strategy for comprehensive protein structure analysis. An application of KUJIRA in accordance with our new strategy was carried out by a non-expert in NMR structure analysis, demonstrating that the accurate assignment of the chemical shifts and a high-quality structure of a small protein can be completed in a few weeks. The high completeness of the chemical shift assignment and the NOE assignment achieved by the systematic analysis using KUJIRA and CYANA led, in practice, to increased reliability of the determined structure.

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Abbreviations

NOESY:

Nuclear Overhauser effect spectroscopy

HSQC:

Heteronuclear single quantum coherence

SASA:

Solvent accessible surface area

TOCSY:

Total correlated spectroscopy

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Acknowledgements

We thank Drs. Toshio Yamazaki, Yutaka Muto, Fumiaki Hayashi, Takashi Nagata, Fahu He, Yufeng Wei and Prof. Milton, H. Werner for their valuable comments and discussions, and Prof. Yo Matsuo for his helpful advice regarding the algorithm for the calculation of the solvent accessible surface area. We also thank Mr. Masatomo Tanaka and Dr. Takuma Kasai for providing the information from the structural analyses of human ubiquitin. This work was supported by the RIKEN Structural Genomics/Proteomics Initiative (RSGI), the National Project on Protein Structural and Functional Analyses, Ministry of Education, Culture, Sports, Science and Technology of Japan.

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  1. Junji Iwahara

    Present address: Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA

Authors and Affiliations

  1. RIKEN Genomic Sciences Center, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan

    Naohiro Kobayashi, Seizo Koshiba, Tadashi Tomizawa, Naoya Tochio, Peter Güntert, Takanori Kigawa & Shigeyuki Yokoyama

  2. University of Tokyo, Tokyo, 113-0033, Japan

    Junji Iwahara & Shigeyuki Yokoyama

  3. Tokyo Institute of Technology, Yokohama , 226-8502, Japan

    Takanori Kigawa

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  1. Naohiro Kobayashi
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Correspondence to Shigeyuki Yokoyama.

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Kobayashi, N., Iwahara, J., Koshiba, S. et al. KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. J Biomol NMR 39, 31–52 (2007). https://doi.org/10.1007/s10858-007-9175-5

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