Amino Acids in Nine Ligand-Prefer Ramachandran Regions.
Several secondary structures, such as π-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 ϕ/ψ box residues are exposed more to solvents, whereas amino acids following ligand-prefer ϕ/ψ 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.
College of Computer Science and Technology, Jilin University, Changchun, Jilin, China ; Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin, China.
Chen
C
Cao
College of Computer Science and Technology, Jilin University, Changchun, Jilin, China ; Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin, China.
Lincong
L
Wang
College of Computer Science and Technology, Jilin University, Changchun, Jilin, China ; Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin, China.
Xiaoyang
X
Chen
College of Computer Science and Technology, Jilin University, Changchun, Jilin, China ; Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin, China.
Shuxue
S
Zou
College of Computer Science and Technology, Jilin University, Changchun, Jilin, China ; Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin, China.
Guishen
G
Wang
College of Computer Science and Technology, Jilin University, Changchun, Jilin, China ; Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin, China.
Shutan
S
Xu
D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D008024:Ligands; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D008024:Ligands; D011506:Proteins