Statistical interior properties of globular proteins
Jiang Zhou-Ting(姜舟婷)a)†, Zhang Lin-Xi(章林溪)b), Sun Ting-Ting(孙婷婷)c), and Wu Tai-Quan(吴太权)a)
a Department of Applied Physics, China Jiliang University, Hangzhou 310018, China; b Department of Physics, Zhejiang University, Hangzhou 310027, China; c College of Information and Electronic Engineering, Zhejiang Gongshang University, Hangzhou 310018 China
Abstract The character of forming long-range contacts affects the three-dimensional structure of globular proteins deeply. As the different ability to form long-range contacts between 20 types of amino acids and 4 categories of globular proteins, the statistical properties are thoroughly discussed in this paper. Two parameters NC and ND are defined to confine the valid residues in detail. The relationship between hydrophobicity scales and valid residue percentage of each amino acid is given in the present work and the linear functions are shown in our statistical results. It is concluded that the hydrophobicity scale defined by chemical derivatives of the amino acids and nonpolar phase of large unilamellar vesicle membranes is the most effective technique to characterise the hydrophobic behavior of amino acid residues. Meanwhile, residue percentage Pi and sequential residue length Li of a certain protein i are calculated under different conditions. The statistical results show that the average value of Pi as well as Li of all-$\alpha$ proteins has a minimum among these 4 classes of globular proteins, indicating that all-$\alpha$ proteins are hardly capable of forming long-range contacts one by one along their linear amino acid sequences. All-$\beta$ proteins have a higher tendency to construct long-range contacts along their primary sequences related to the secondary configurations, i.e. parallel and anti-parallel configurations of $\beta$ sheets. The investigation of the interior properties of globular proteins give us the connection between the three-dimensional structure and its primary sequence data or secondary configurations, and help us to understand the structure of protein and its folding process well.
Received: 31 July 2008
Revised: 08 May 2009
Accepted manuscript online:
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