Amino Acids in Nine Ligand-Prefer Ramachandran Regions

作者：Cao Chen; Wang Lincong; Chen Xiaoyang; Zou Shuxue; Wang Guishen; Xu Shutan^*

来源：Biomed Research International, 2015, 2015: 757495.

DOI：10.1155/2015/757495

Several secondary structures, such as pi-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-prefer phi/psi box residues are exposed more to solvents, whereas amino acids following ligand-prefer phi/psi box residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand- bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function.

• 出版日期2015
• 单位吉林大学