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Protein Engineering vol. 7 no. 12 pp. 1433-1440, 1994
© 1994 Oxford University Press

OTHER

A simple procedure for assigning a sequence motif with an obscure pattern: application to the basic/helix-loop-helix motif

Katsuhisa Horimoto1,1, Hisanori Yamamoto2, Kazuo Yanagi2, Kunio Ohshima3 and Jinya Otsuka4

1Research Institute for Biosciences, Faculty of Science and Technology, Science University of Tokyo Noda 278 3Departments of Mathematics, Faculty of Science and Technology, Science University of Tokyo Noda 278 4Departments of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo Noda 278 2Laboratory of Herpesviruses, Department of Virology 1, National Institute of Health Toyama, Shinjuku-ku, Tokyo 162, Japan

1To whom correspondence should be addressed

We have developed a simple method to assign a sequence motif with an obscure pattern. Given a multiple sequence alignment for a region of protein that is known or strongly believed to have the same secondary and tertiary structures, the quantification method by principal component analysis is designed to find the regions most likely to have the same structure in a protein outside of the original set The potential of this newly developed method was evaluated with reference to the known basic/helix-loop-helix (bHLH) motifs, and its characteristics were discussed with four obscure but well-defined motifs and compared with the other methods for searching sequence motifs. The method was also applied to assign the bHLH motif in Epstein-Barr virus nuclear antigen 1 (EBNA-1). This application revealed one candidate for the basic/helix 1 region and two candidates for the helix 2 region in the bHLH motif, within the region from amino acid residues 460 to 600, which is in good agreement with our previous experimental studies on the DNA binding region of EBNA-1. The basic/helix-loop-helix-loop-helix structure thus assigned suggests a function of EBNA-1 which is associated with both replication and transcription.

Keywords: basic/helix-loop-helix motif/Epstein-Barr virus nuclear antigen I/principal component analysis

Received April 13, 1994; revised September 5, 1994; accepted September 20, 1994.


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