Amino Acids in Nine Ligand-Prefer Ramachandran Regions.
Biomed Res Int
; 2015: 757495, 2015.
Article
em En
| MEDLINE
| ID: mdl-26491686
ABSTRACT
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 Ï/ψ box residues are exposed more to solvents, whereas amino acids following ligand-prefer Ï/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.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Proteínas
/
Modelos Moleculares
/
Ligantes
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Biomed Res Int
Ano de publicação:
2015
Tipo de documento:
Article
País de afiliação:
China