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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Authors: | Naohiro Kobayashi Junji Iwahara Seizo Koshiba Tadashi Tomizawa Naoya Tochio Peter Güntert Takanori Kigawa Shigeyuki Yokoyama |
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Institution: | (1) RIKEN Genomic Sciences Center, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan;(2) University of Tokyo, Tokyo 113-0033, Japan;(3) Present address: Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA;(4) Tokyo Institute of Technology, Yokohama 226-8502, Japan |
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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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Keywords: | NMR Structure determination High-throughput Software KUJIRA CYANA NMRView |
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