Application of information theory to a three-body coarse-grained representation of proteins in the PDB: insights into the structural and evolutionary roles of residues in protein structure.
Proteins
; 82(12): 3450-65, 2014 Dec.
Article
em En
| MEDLINE
| ID: mdl-25269778
ABSTRACT
Knowledge-based methods for analyzing protein structures, such as statistical potentials, primarily consider the distances between pairs of bodies (atoms or groups of atoms). Considerations of several bodies simultaneously are generally used to characterize bonded structural elements or those in close contact with each other, but historically do not consider atoms that are not in direct contact with each other. In this report, we introduce an information-theoretic method for detecting and quantifying distance-dependent through-space multibody relationships between the sidechains of three residues. The technique introduced is capable of producing convergent and consistent results when applied to a sufficiently large database of randomly chosen, experimentally solved protein structures. The results of our study can be shown to reproduce established physico-chemical properties of residues as well as more recently discovered properties and interactions. These results offer insight into the numerous roles that residues play in protein structure, as well as relationships between residue function, protein structure, and evolution. The techniques and insights presented in this work should be useful in the future development of novel knowledge-based tools for the evaluation of protein structure.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Conformação Proteica
/
Bioquímica
/
Modelos Moleculares
/
Evolução Molecular
/
Aminoácidos
/
Teoria da Informação
Tipo de estudo:
Prognostic_studies
Limite:
Animals
/
Humans
Idioma:
En
Revista:
Proteins
Assunto da revista:
BIOQUIMICA
Ano de publicação:
2014
Tipo de documento:
Article