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Int J Biol Sci 2018; 14(8):901-906. doi:10.7150/ijbs.24327 This issue Cite

Research Paper

A Sequential Segment Based Alpha-Helical Transmembrane Protein Alignment Method

Han Wang^1,2, Jingru Wang^1,2, Li Zhang³, Pingping Sun^1,2, Ning Du⁴, Yanwen Li^1,2,✉

1. School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.
2. Institute of Computational Biology, Northeast Normal University, Changchun, 130117, China.
3. School of Computer Science and Engineering, Changchun University of Technology, Changchun, China.
4. School of Mathematics and Statistics, Northeast Normal University, Changchun, 130024, China

✉ Corresponding author: Yanwen Li: liyw085edu.cn

Abstract

Alpha-helical transmembrane protein (αTMP) is one of the two major categories of transmembrane protein (TMP). They are abundant existing in eukaryotic cells and involved in many biological processes. The special physicochemical properties, the structures of αTMP are hard to be experimentally solved, but αTMP's sequential segments are important to determine their conformations, so that TM-specific alignment is necessary to benefit their structure prediction. We used segment information extracted from topology structure and evolutionary information as features to implement a αTMP Segment Alignment method (TMSA). The method was trained using one non-redundant dataset and tested using another non-redundant dataset. Comparing the results to a general alignment method HHalign, TMSA achieved higher alignment accuracy, and easier to recognize the fold of αTMPs.

Keywords: Transmembrane Protein, Segment Alignment, Topology

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