An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

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An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database


Abstract Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including 1H, 13C and 15N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001â??2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

• Content Type Journal Article
• Category Article
• Pages 1-10
• DOI 10.1007/s10858-012-9641-6
• Authors
  • Naohiro Kobayashi, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871 Osaka, Japan
  • Yoko Harano, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871 Osaka, Japan
  • Naoya Tochio, RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
  • Eiichi Nakatani, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871 Osaka, Japan
  • Takanori Kigawa, RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
  • Shigeyuki Yokoyama, RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
  • Steve Mading, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
  • Eldon L. Ulrich, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
  • John L. Markley, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
  • Hideo Akutsu, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871 Osaka, Japan
  • Toshimichi Fujiwara, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871 Osaka, Japan

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738

Source: Journal of Biomolecular NMR