Ab initio 3-D structure prediction of an artificially designed three-alpha-helix bundle via all-atom molecular dynamics simulations
Genet. mol. res. (Online)
; Genet. mol. res. (Online);6(4): 901-910, 2007. ilus
Article
em En
| LILACS
| ID: lil-520058
Biblioteca responsável:
BR26.1
ABSTRACT
The rate at which knowledge about genomic sequences and their protein products is produced is increasing much faster than the rate of 3-dimensional protein structure determination by experimental methods, such as X-ray diffraction and nuclear magnetic resonance. One of the major challenges in structural bioinformatics is the conversion of genomic sequences into useful information, such as characterization of protein structure and function. Using molecular dynamics (MD) simulations, we predicted the 3-dimensional structure of an artificially designed three-alpha-helix bundle, called A3, from a fully extended initial conformation, based on its amino acid sequence. The MD protocol enabled us to obtain the secondary, in 1.0 ns, as well as the supersecondary and tertiary structures, in 4.0-10.0 ns, of A3, much faster than previously described for a similar protein system. The structure obtained at the end of the 10.0-ns MD simulation was topologically a three-alpha-helix bundle.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
LILACS
Assunto principal:
Simulação por Computador
/
Proteínas
/
Modelos Moleculares
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Genet. mol. res. (Online)
Assunto da revista:
BIOLOGIA MOLECULAR
/
GENETICA
Ano de publicação:
2007
Tipo de documento:
Article
/
Congress and conference
País de afiliação:
Brasil
País de publicação:
Brasil