Skip Navigation



PEDS Advance Access published online on January 10, 2006
Protein Engineering Design and Selection, doi:10.1093/protein/gzj002
This Article
Right arrow FREE Full Text (PDF) Freely available
Right arrowOA All Versions of this Article:
19/2/67    most recent
gzj002v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Saito, M.
Right arrow Articles by Shirai, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Saito, M.
Right arrow Articles by Shirai, T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved.
Received July 12, 2005
Revised November 12, 2005
Accepted November 12, 2005

Article

An empirical approach for detecting nucleotide-binding sites on proteins

Mihoko Saito 1, Mitiko Go 2, and Tsuyoshi Shirai 3 *

1 Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
2 Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8601, Japan; Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama 526-0829, Japan
3 Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama 526-0829, Japan; Department of Computational Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; Japan Science and Technology Corporation-Bioinformatics Research and Development

* To whom correspondence should be addressed.
Tsuyoshi Shirai, E-mail: t_shirai{at}nagahama-i-bio.ac.jp


  Abstract

Protein structure data in the PDB (Protein Data Bank) were used to construct empirical scores of nucleotide-protein interactions. A simple strategy to evaluate the spatial distribution of protein atoms around the base moieties of nucleotides was applied to categorize adenine, guanine, nicotinamide and flavin nucleotide-binding sites. In addition to the known nucleotide-binding motifs, the empirical scores detected several other features that were shared among proteins with different folds. The empirical scores were also used to predict the binding sites on protein molecules and a comprehensive test of the prediction system was performed. As a result, adenine, guanine, nicotinamide and flavin sites were detected with efficiencies of 31, 29, 32 and 40%, respectively. The predictions were judged to be successful if the predicted base with the best score was located within a 3.0 Å r.m.s.d. from the known ligand positions.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J Exp BotHome page
W.-Q. Song, Y.-M. Qin, M. Saito, T. Shirai, F. M. Pujol, A. J. Kastaniotis, J. K. Hiltunen, and Y.-X. Zhu
Characterization of two cotton cDNAs encoding trans-2-enoyl-CoA reductase reveals a putative novel NADPH-binding motif
J. Exp. Bot., April 1, 2009; 60(6): 1839 - 1848.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.