The Study Of π-π Interactions In Classical Fold Type Of α/β Protein

Protein folding study is always one of the common ways to study structural stability and mechanism of proteins. Hydrogen bond, van der Waals force, hydrophobic interaction and salt bond are the mainly nonconvalent bonds which maintain the three dimensional structure of protein. Recently, more and more researchers have found that π-π, cation...π, N-H...π, C-H...O, etl which called the non-classic interaction are also very important in the structure and function of protein, especially the interaction involved π ring system.α/β protein is a widespread protein fold type in the nature, the proteins about α/β protein almost involved all sides in the life. The study of them is very important for revealing the life activities. π-π interaction has been focused on its role in the stability of protein structure and functions. It’s a ubiquitous interaction in protein.π-π interaction is formed by the stacking of aromatic amino acids’ s benzene groups. In this paper, two typical protein folds of α/β protein ware selected for the research.This research work includes the following aspects: 1. Type and distance of π-π interaction in(α/β)8-barrel fold and classical Rossmann fold analysis.The type of π-π interactions in the two folds is mainly SS interaction types, accounts for 96.81% and 96.81% respectively, S5 S accounts for only a few, both of them didn’t contain SS5 this folding type.π-π interactions are mainly composed of long-range and short-range interactions, medium-range interaction accounts low proportion in two folds. 2. Hydrophobicity and conservation of π-π interaction amino acid residue in two fold protein analysis.Based on the analyzing hydrophobic interaction and conservative of amino acid residue involved π-π interaction.we found that most of amino acid residue were buried in the protein.Only about 2% amino acid residue in exposed or half exposed state. Conservative analysis shows that π-π interacting amino acid residues are 74.85% and 68.17% respectively with high ratings in two fold protein. 3. Distribution density of π-π interaction in(α/β)8-barrel fold and classical Rossmann fold analysis.Comparative analysis the π-π interaction distribution density in protein, in the aromatic amino acids and in the local area : π-π interaction distribution density in the protein of(α/β)8-barrel fold is 2.46 times of classic Rossmann fold, π-π interaction distribution density in aromatic amino acid of(α/β)8-barrel fold is 1.86 times of classic Rossmann fold. π-π interaction distribution density in the local area of(α/β)8-barrel fold is 5.59 times of classic Rossmann fold. 4. The participation rate of three amino acids in both(α/β)8-barrel fold and classical Rossmann fold analysis.Comparing participation of three amino acids involved in π-π interaction in two fold protein, we found that the three residues of(α/β)8-barrel fold participation rates are higher than the classic Rossmann fold. 5. The distribution of defferent combination of π-π interactions in(α/β)8-barrel fold and classical Rossmann fold analysis.Three aromatic amino acids can form six π-π interaction combination:Phe-Phe, Phe-Trp, Phe-Tyr, Trp-Trp, Trp-Tyr, Tyr-Tyr. The three π-π interaction combinations corresponding to Trp appearing in(α/β)8-barrel are significantly higher than classic Rossmann. The results are consistent with Trp participation’s preferences. 6. π-network in(α/β)8-barrel fold and classical Rossmann fold analysis.π-π interactions in protein will further formation of π-network. The π-π interaction of classic Rossmann fold structure is mostly exist independently, while π-π interaction of(α/β)8-barrel fold tends to form big π-network.(α/β)8-barrel fold has greater ability to form complex π-network than classical Rossmann fold.This article comprehensively analyzed the π-π interaction in(α/β)8-barrel fold and classical Rossmann fold. It revealed the π-π interaction characteristics in the two fold and deepened our understanding of π-π interaction. This will help to solve related proteins and drug design.