Identification of Latent Periodicity in Domains of Alkaline Proteases

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Xiaofeng Ji¹, Jun Sheng¹, Fang Wang¹, Suzhen Zhang², Jianhua Hao¹, Haiying Wang¹, and Mi Sun^1*

¹Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China; fax: +86(532)8583-3525; E-mail: sunmi@ysfri.ac.cn

²Department of Physics, Dezhou University, Dezhou 253023, Shandong, China

^* To whom correspondence should be addressed.

Received March 4, 2010; Revision received June 29, 2010

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Internal repeats in protein sequences have wide-ranging implications for the structure and function of proteins. A keen analysis of the repeats in protein sequences may help us to better understand the structural organization of proteins and their evolutionary relations. In this paper, a mathematical method for searching for latent periodicity in protein sequences is developed. Using this method, we identified simple sequence repeats in the alkaline proteases and found that the sequences could show the same periodicity as their tertiary structures. This result may help us to reduce difficulties in the study of the relationship between sequences and their structures.

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KEY WORDS: latent periodicity, alkaline protease, correlation, primary sequence

DOI: 10.1134/S0006297911090082

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