Local Hydrophobicity in Protein Secondary Structure Formation
Ming-Chya Wu1,2*, Tian Yow Tsong3
1Research Center for Adaptive Data Analysis, National Central University, Chungli, Taiwan
2Institute of Physics, Academia Sinica, Taipei, Taiwan
3College of Biological Sciences, University of Minnesota, Minneapolis, United States of America
* presenting author:吳明佳, email:mcwu@ncu.edu.tw
In this paper, the effect of local hydrophobicity (LHP) in protein secondary structure formation is investigated using time series analysis approach. The LHP around a residue in a protein is defined as the sum of hydrophobicity (HP) of the surrounding residues within an effective range in a three-dimensional structure. HP and LHP as functions of the linear amino acid sequence are considered as time series, and are decomposed into a number of intrinsic mode functions (IMFs) using the empirical mode decomposition method. Correlation analysis of IMFs of HP and LHP of the wild-type (WT) proteins shows that the relative strength among IMF pairs is associated with the length scales of secondary structures. Examining the variations of secondary structures in mutants from the WT protein as a result of LHP changes, we propose that LHP is a useful parameter to describe secondary structure formation in proteins.

Keywords: Local hydrophobicity, Empirical mode decomposition, Protein secondary structure, Wild-type, Mutant